diff --git a/polytop_examples/README.md b/polytop_examples/README.md new file mode 100644 index 0000000..4b37f61 --- /dev/null +++ b/polytop_examples/README.md @@ -0,0 +1,69 @@ +# PolyTop example scripts + +This folder contains a handful of example scripts demonstrating the use of +*PolyTop*. All the files you need to run these examples are contained within +this folder. + +For detailed documentation of all *PolyTop* methods, please refer to the +[PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html). + +These tutorials are not intended as a primer on polymer design or +stereochemistry. It is assumed that the reader is familiar with polymer +chemistry and common types of copolymers. + +## Tutorial 01: Building a linear polyethyleneimine polymer topology using PolyTop + +The first tutorial is an example of how to make a linear 20 unit +polyethyleneimine chain using *PolyTop*. It is contained in the file +`linear_PEI.py`. + +This tutorial showcases several approaches, including: +* loading in itp files to create Topology objects +* defining appropriate Junctions for polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. + +## Tutorial 02: Building an ethlyamine dendrimer polymer topology using PolyTop + +The second tutorial shows strategies for making a more complex polymer with +levels of branching building outwards from a central monomer. It is contained +in the file `dendrimer_ethylamine.py`. + +This tutorial showcases several approaches, including: +* breaking down a polymer structure into the monomers required to build it +* loading in itp files to create Topology objects +* defining appropriate, distinct Junctions for precise polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. + +## Tutorial 03: Building a 4-arm PEG star polymer topology using PolyTop + +The third tutorial shows strategies for making another complex polymer with +long linear arms branching out from a central monomer. It is contained +in the file `star_PEG.py`. + +This tutorial showcases several approaches, including: +* breaking down a polymer structure into the monomers required to build it +* discussing different approaches to create the same polymer structure +* loading in itp files to create Topology objects +* defining appropriate, distinct Junctions for precise polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. diff --git a/polytop_examples/data/four_arm_star_overlapped_monomers.itp b/polytop_examples/data/four_arm_star.itp similarity index 99% rename from polytop_examples/data/four_arm_star_overlapped_monomers.itp rename to polytop_examples/data/four_arm_star.itp index 0ed2e6e..4fa0280 100644 --- a/polytop_examples/data/four_arm_star_overlapped_monomers.itp +++ b/polytop_examples/data/four_arm_star.itp @@ -1,5 +1,5 @@ ;----------------------------TITLE ----------------------------------------------------------------------------------------- -; four arm star polymer - overlapped monomers +; four arm star polymer ; ;----------------------------TITLE ----------------------------------------------------------------------------------------- ; Pentaerythritol @@ -182,46 +182,46 @@ [ bonds ] 1 3 2 0.1090 1.2300e+07 - 1 2 2 0.1090 1.2300e+07 1 41 2 0.1430 8.1800e+06 1 4 2 0.1540 4.0057e+06 - 4 11 2 0.1540 4.0057e+06 + 1 2 2 0.1090 1.2300e+07 4 5 2 0.1540 4.0057e+06 4 8 2 0.1540 4.0057e+06 - 5 6 2 0.1090 1.2300e+07 + 4 11 2 0.1540 4.0057e+06 5 20 2 0.1430 8.1800e+06 5 7 2 0.1090 1.2300e+07 - 8 27 2 0.1430 8.1800e+06 + 5 6 2 0.1090 1.2300e+07 8 10 2 0.1090 1.2300e+07 + 8 27 2 0.1430 8.1800e+06 8 9 2 0.1090 1.2300e+07 - 11 34 2 0.1430 8.1800e+06 - 11 13 2 0.1090 1.2300e+07 11 12 2 0.1090 1.2300e+07 + 11 13 2 0.1090 1.2300e+07 + 11 34 2 0.1430 8.1800e+06 + 14 15 2 0.1090 1.2300e+07 14 16 2 0.1090 1.2300e+07 14 17 2 0.1530 7.1500e+06 14 48 2 0.1430 8.1800e+06 - 14 15 2 0.1090 1.2300e+07 + 17 20 2 0.1430 8.1800e+06 17 18 2 0.1090 1.2300e+07 17 19 2 0.1090 1.2300e+07 - 17 20 2 0.1430 8.1800e+06 - 21 55 2 0.1430 8.1800e+06 21 23 2 0.1090 1.2300e+07 21 24 2 0.1530 7.1500e+06 + 21 55 2 0.1430 8.1800e+06 21 22 2 0.1090 1.2300e+07 + 24 26 2 0.1090 1.2300e+07 24 27 2 0.1430 8.1800e+06 24 25 2 0.1090 1.2300e+07 - 24 26 2 0.1090 1.2300e+07 - 28 30 2 0.1090 1.2300e+07 - 28 29 2 0.1090 1.2300e+07 28 31 2 0.1530 7.1500e+06 + 28 29 2 0.1090 1.2300e+07 + 28 30 2 0.1090 1.2300e+07 28 62 2 0.1430 8.1800e+06 31 34 2 0.1430 8.1800e+06 31 33 2 0.1090 1.2300e+07 31 32 2 0.1090 1.2300e+07 - 35 69 2 0.1430 8.1800e+06 - 35 38 2 0.1530 7.1500e+06 35 37 2 0.1090 1.2300e+07 35 36 2 0.1090 1.2300e+07 + 35 69 2 0.1430 8.1800e+06 + 35 38 2 0.1530 7.1500e+06 38 40 2 0.1090 1.2300e+07 38 41 2 0.1430 8.1800e+06 38 39 2 0.1090 1.2300e+07 @@ -229,30 +229,30 @@ 42 44 2 0.1090 1.2300e+07 42 45 2 0.1530 7.1500e+06 42 76 2 0.1430 8.1800e+06 + 45 48 2 0.1430 8.1800e+06 45 46 2 0.1090 1.2300e+07 45 47 2 0.1090 1.2300e+07 - 45 48 2 0.1430 8.1800e+06 49 52 2 0.1530 7.1500e+06 + 49 51 2 0.1090 1.2300e+07 49 50 2 0.1090 1.2300e+07 49 83 2 0.1430 8.1800e+06 - 49 51 2 0.1090 1.2300e+07 52 53 2 0.1090 1.2300e+07 52 55 2 0.1430 8.1800e+06 52 54 2 0.1090 1.2300e+07 + 56 90 2 0.1430 8.1800e+06 56 58 2 0.1090 1.2300e+07 56 59 2 0.1530 7.1500e+06 56 57 2 0.1090 1.2300e+07 - 56 90 2 0.1430 8.1800e+06 + 59 60 2 0.1090 1.2300e+07 59 61 2 0.1090 1.2300e+07 59 62 2 0.1430 8.1800e+06 - 59 60 2 0.1090 1.2300e+07 + 63 97 2 0.1430 8.1800e+06 63 65 2 0.1090 1.2300e+07 63 66 2 0.1530 7.1500e+06 63 64 2 0.1090 1.2300e+07 - 63 97 2 0.1430 8.1800e+06 - 66 67 2 0.1090 1.2300e+07 66 68 2 0.1090 1.2300e+07 66 69 2 0.1430 8.1800e+06 + 66 67 2 0.1090 1.2300e+07 70 71 2 0.1090 1.2300e+07 70 72 2 0.1090 1.2300e+07 70 98 2 0.1430 8.1800e+06 @@ -260,356 +260,356 @@ 73 76 2 0.1430 8.1800e+06 73 74 2 0.1090 1.2300e+07 73 75 2 0.1090 1.2300e+07 + 77 102 2 0.1430 8.1800e+06 77 79 2 0.1090 1.2300e+07 77 80 2 0.1530 7.1500e+06 77 78 2 0.1090 1.2300e+07 - 77 102 2 0.1430 8.1800e+06 - 80 81 2 0.1090 1.2300e+07 80 82 2 0.1090 1.2300e+07 80 83 2 0.1430 8.1800e+06 + 80 81 2 0.1090 1.2300e+07 + 84 106 2 0.1430 8.1800e+06 + 84 85 2 0.1090 1.2300e+07 84 86 2 0.1090 1.2300e+07 84 87 2 0.1530 7.1500e+06 - 84 85 2 0.1090 1.2300e+07 - 84 106 2 0.1430 8.1800e+06 + 87 89 2 0.1090 1.2300e+07 87 90 2 0.1430 8.1800e+06 87 88 2 0.1090 1.2300e+07 - 87 89 2 0.1090 1.2300e+07 91 94 2 0.1530 7.1500e+06 - 91 93 2 0.1090 1.2300e+07 91 110 2 0.1430 8.1800e+06 91 92 2 0.1090 1.2300e+07 - 94 97 2 0.1430 8.1800e+06 + 91 93 2 0.1090 1.2300e+07 94 96 2 0.1090 1.2300e+07 94 95 2 0.1090 1.2300e+07 + 94 97 2 0.1430 8.1800e+06 98 99 2 0.1090 1.2300e+07 98 101 2 0.1090 1.2300e+07 98 100 2 0.1090 1.2300e+07 102 104 2 0.1090 1.2300e+07 102 103 2 0.1090 1.2300e+07 102 105 2 0.1090 1.2300e+07 - 106 109 2 0.1090 1.2300e+07 106 107 2 0.1090 1.2300e+07 + 106 109 2 0.1090 1.2300e+07 106 108 2 0.1090 1.2300e+07 + 110 113 2 0.1090 1.2300e+07 110 111 2 0.1090 1.2300e+07 110 112 2 0.1090 1.2300e+07 - 110 113 2 0.1090 1.2300e+07 [ pairs ] - 1 13 1 - 1 9 1 1 12 1 - 1 7 1 - 1 10 1 + 1 13 1 1 6 1 + 1 10 1 + 1 7 1 + 1 9 1 + 2 8 1 2 5 1 2 11 1 - 2 8 1 - 3 8 1 - 3 5 1 3 11 1 - 5 10 1 + 3 5 1 + 3 8 1 5 9 1 5 12 1 + 5 10 1 5 13 1 - 6 11 1 6 8 1 - 7 11 1 + 6 11 1 7 8 1 - 8 13 1 + 7 11 1 8 12 1 + 8 13 1 9 11 1 10 11 1 15 18 1 - 15 19 1 15 20 1 + 15 19 1 16 18 1 16 20 1 16 19 1 22 26 1 - 22 25 1 22 27 1 - 23 25 1 + 22 25 1 23 26 1 23 27 1 - 29 33 1 - 29 32 1 + 23 25 1 29 34 1 - 30 34 1 - 30 32 1 + 29 32 1 + 29 33 1 30 33 1 - 36 41 1 + 30 32 1 + 30 34 1 36 40 1 + 36 41 1 36 39 1 37 40 1 - 37 41 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[";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H10", "charge_group_num": 4, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H11", "charge_group_num": 5, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "C", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C2", "charge_group_num": 6, "partial_charge": -0.014500000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H2", "charge_group_num": 8, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H3", "charge_group_num": 9, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H4", "charge_group_num": 13, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H5", "charge_group_num": 14, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H7", "charge_group_num": 18, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H8", "charge_group_num": 19, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CPos", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, 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{"atom_a": 108, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 109, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 114, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 113, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 114, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 113, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 113, "atom_b": 112, "atom_c": 114, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}], "dihedrals": [{"atom_a": 36, "atom_b": 37, "atom_c": 3, "atom_d": 16, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 16, "atom_b": 3, "atom_c": 23, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 23, "atom_b": 3, "atom_c": 16, "atom_d": 15, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 16, "atom_b": 3, "atom_c": 30, "atom_d": 29, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 44, "atom_b": 12, "atom_c": 15, "atom_d": 16, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 43, "atom_b": 44, "atom_c": 12, "atom_d": 15, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 50, "atom_b": 51, "atom_c": 19, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 51, "atom_b": 19, "atom_c": 22, "atom_d": 23, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 58, "atom_b": 26, "atom_c": 29, "atom_d": 30, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 26, "atom_d": 29, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 33, "atom_c": 36, "atom_d": 37, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 64, "atom_b": 65, "atom_c": 33, "atom_d": 36, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 72, "atom_b": 40, "atom_c": 43, "atom_d": 44, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 71, "atom_b": 72, "atom_c": 40, "atom_d": 43, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 47, "atom_c": 50, "atom_d": 51, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 78, "atom_b": 79, "atom_c": 47, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 85, "atom_b": 86, "atom_c": 54, "atom_d": 57, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 54, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 94, "atom_b": 95, "atom_c": 61, "atom_d": 64, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 95, "atom_b": 61, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 68, "atom_c": 71, "atom_d": 72, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 97, "atom_b": 96, "atom_c": 68, "atom_d": 71, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 101, "atom_b": 75, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 102, "atom_b": 101, "atom_c": 75, "atom_d": 78, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 107, "atom_b": 106, "atom_c": 82, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 106, "atom_b": 82, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 112, "atom_b": 88, "atom_c": 91, "atom_d": 94, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 88, "atom_b": 91, "atom_c": 94, "atom_d": 95, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 23, "pair_type": 1}, {"atom_a": 1, "atom_b": 16, "pair_type": 1}, {"atom_a": 1, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 16, "pair_type": 1}, {"atom_a": 2, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 4, "pair_type": 1}, {"atom_a": 5, "atom_b": 23, "pair_type": 1}, {"atom_a": 5, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 5, "pair_type": 1}, {"atom_a": 37, "atom_b": 6, "pair_type": 1}, {"atom_a": 16, "atom_b": 6, "pair_type": 1}, {"atom_a": 6, "atom_b": 30, "pair_type": 1}, {"atom_a": 16, "atom_b": 7, "pair_type": 1}, {"atom_a": 37, "atom_b": 7, "pair_type": 1}, {"atom_a": 7, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 8, "pair_type": 1}, {"atom_a": 23, "atom_b": 8, "pair_type": 1}, {"atom_a": 16, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 9, "pair_type": 1}, {"atom_a": 23, "atom_b": 9, "pair_type": 1}, {"atom_a": 16, "atom_b": 9, "pair_type": 1}, {"atom_a": 10, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 10, "atom_b": 14, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 11, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 14, "pair_type": 1}, {"atom_a": 17, "atom_b": 21, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 17, "atom_b": 20, "pair_type": 1}, {"atom_a": 18, "atom_b": 21, "pair_type": 1}, {"atom_a": 18, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/polytop_examples/data/four_arm_star.png b/polytop_examples/data/four_arm_star.png new file mode 100644 index 0000000..f5beba2 Binary files /dev/null and b/polytop_examples/data/four_arm_star.png differ diff --git a/polytop_examples/data/four_arm_star_overlapped_monomers.png b/polytop_examples/data/four_arm_star_overlapped_monomers.png deleted file mode 100644 index 18c3cec..0000000 Binary files a/polytop_examples/data/four_arm_star_overlapped_monomers.png and /dev/null differ diff --git a/polytop_examples/data/pei_linear_polymer.itp b/polytop_examples/data/pei_linear_polymer.itp index 09f46bf..9e6bc1d 100644 --- a/polytop_examples/data/pei_linear_polymer.itp +++ b/polytop_examples/data/pei_linear_polymer.itp @@ -66,639 +66,354 @@ [ moleculetype ] LHCU 3 [ atoms ] - 1 CH3 1 LHCU C62 1 0.013438 15.0350 - 2 CH2 1 LHCU C51 2 0.213438 14.0270 - 3 NOpt 1 LHCU N71 3 -0.685562 14.0067 - 4 HS14 1 LHCU H72 4 0.304437 1.0080 - 5 CH2 1 LHCU C61 5 0.210437 14.0270 - 6 CH2 1 LHCU C5 6 0.225438 14.0270 - 7 NOpt 1 LHCU N7 7 -0.698562 14.0067 - 8 HS14 1 LHCU H21 8 0.318437 1.0080 - 9 CH2 2 LHCU C51 9 0.227533 14.0270 - 10 NOpt 2 LHCU N71 10 -0.671467 14.0067 - 11 HS14 2 LHCU H72 11 0.318533 1.0080 - 12 CH2 2 LHCU C61 12 0.224533 14.0270 - 13 CH2 2 LHCU C5 13 0.239533 14.0270 - 14 NOpt 2 LHCU N7 14 -0.684467 14.0067 - 15 HS14 2 LHCU H21 15 0.332533 1.0080 - 16 CH2 3 LHCU C51 16 0.229302 14.0270 - 17 NOpt 3 LHCU N71 17 -0.669698 14.0067 - 18 HS14 3 LHCU H72 18 0.320302 1.0080 - 19 CH2 3 LHCU C61 19 0.226302 14.0270 - 20 CH2 3 LHCU C5 20 0.241302 14.0270 - 21 NOpt 3 LHCU N7 21 -0.682698 14.0067 - 22 HS14 3 LHCU H21 22 0.334302 1.0080 - 23 CH2 4 LHCU C51 23 0.229420 14.0270 - 24 NOpt 4 LHCU N71 24 -0.669580 14.0067 - 25 HS14 4 LHCU H72 25 0.320420 1.0080 - 26 CH2 4 LHCU C61 26 0.226420 14.0270 - 27 CH2 4 LHCU C5 27 0.241420 14.0270 - 28 NOpt 4 LHCU N7 28 -0.682580 14.0067 - 29 HS14 4 LHCU H21 29 0.334420 1.0080 - 30 CH2 5 LHCU C51 30 0.229428 14.0270 - 31 NOpt 5 LHCU N71 31 -0.669572 14.0067 - 32 HS14 5 LHCU H72 32 0.320428 1.0080 - 33 CH2 5 LHCU C61 33 0.226428 14.0270 - 34 CH2 5 LHCU C5 34 0.241428 14.0270 - 35 NOpt 5 LHCU N7 35 -0.682572 14.0067 - 36 HS14 5 LHCU H21 36 0.334428 1.0080 - 37 CH2 6 LHCU C51 37 0.229429 14.0270 - 38 NOpt 6 LHCU N71 38 -0.669571 14.0067 - 39 HS14 6 LHCU H72 39 0.320429 1.0080 - 40 CH2 6 LHCU C61 40 0.226429 14.0270 - 41 CH2 6 LHCU C5 41 0.241429 14.0270 - 42 NOpt 6 LHCU N7 42 -0.682571 14.0067 - 43 HS14 6 LHCU H21 43 0.334429 1.0080 - 44 CH2 7 LHCU C51 44 0.229429 14.0270 - 45 NOpt 7 LHCU N71 45 -0.669571 14.0067 - 46 HS14 7 LHCU H72 46 0.320429 1.0080 - 47 CH2 7 LHCU C61 47 0.226429 14.0270 - 48 CH2 7 LHCU C5 48 0.241429 14.0270 - 49 NOpt 7 LHCU N7 49 -0.682571 14.0067 - 50 HS14 7 LHCU H21 50 0.334429 1.0080 - 51 CH2 8 LHCU C51 51 0.229429 14.0270 - 52 NOpt 8 LHCU N71 52 -0.669571 14.0067 - 53 HS14 8 LHCU H72 53 0.320429 1.0080 - 54 CH2 8 LHCU C61 54 0.226429 14.0270 - 55 CH2 8 LHCU C5 55 0.241429 14.0270 - 56 NOpt 8 LHCU N7 56 -0.682571 14.0067 - 57 HS14 8 LHCU H21 57 0.334429 1.0080 - 58 CH2 9 LHCU C51 58 0.229429 14.0270 - 59 NOpt 9 LHCU N71 59 -0.669571 14.0067 - 60 HS14 9 LHCU H72 60 0.320429 1.0080 - 61 CH2 9 LHCU C61 61 0.226429 14.0270 - 62 CH2 9 LHCU C5 62 0.241429 14.0270 - 63 NOpt 9 LHCU N7 63 -0.682571 14.0067 - 64 HS14 9 LHCU H21 64 0.334429 1.0080 - 65 CH2 10 LHCU C51 65 0.229429 14.0270 - 66 NOpt 10 LHCU N71 66 -0.669571 14.0067 - 67 HS14 10 LHCU H72 67 0.320429 1.0080 - 68 CH2 10 LHCU C61 68 0.226429 14.0270 - 69 CH2 10 LHCU C5 69 0.241429 14.0270 - 70 NOpt 10 LHCU N7 70 -0.682571 14.0067 - 71 HS14 10 LHCU H21 71 0.334429 1.0080 - 72 CH2 11 LHCU C51 72 0.229429 14.0270 - 73 NOpt 11 LHCU N71 73 -0.669571 14.0067 - 74 HS14 11 LHCU H72 74 0.320429 1.0080 - 75 CH2 11 LHCU C61 75 0.226429 14.0270 - 76 CH2 11 LHCU C5 76 0.241429 14.0270 - 77 NOpt 11 LHCU N7 77 -0.682571 14.0067 - 78 HS14 11 LHCU H21 78 0.334429 1.0080 - 79 CH2 12 LHCU C51 79 0.229429 14.0270 - 80 NOpt 12 LHCU N71 80 -0.669571 14.0067 - 81 HS14 12 LHCU H72 81 0.320429 1.0080 - 82 CH2 12 LHCU C61 82 0.226429 14.0270 - 83 CH2 12 LHCU C5 83 0.241429 14.0270 - 84 NOpt 12 LHCU N7 84 -0.682571 14.0067 - 85 HS14 12 LHCU H21 85 0.334429 1.0080 - 86 CH2 13 LHCU C51 86 0.229429 14.0270 - 87 NOpt 13 LHCU N71 87 -0.669571 14.0067 - 88 HS14 13 LHCU H72 88 0.320429 1.0080 - 89 CH2 13 LHCU C61 89 0.226429 14.0270 - 90 CH2 13 LHCU C5 90 0.241429 14.0270 - 91 NOpt 13 LHCU N7 91 -0.682571 14.0067 - 92 HS14 13 LHCU H21 92 0.334429 1.0080 - 93 CH2 14 LHCU C51 93 0.229429 14.0270 - 94 NOpt 14 LHCU N71 94 -0.669571 14.0067 - 95 HS14 14 LHCU H72 95 0.320429 1.0080 - 96 CH2 14 LHCU C61 96 0.226429 14.0270 - 97 CH2 14 LHCU C5 97 0.241429 14.0270 - 98 NOpt 14 LHCU N7 98 -0.682571 14.0067 - 99 HS14 14 LHCU H21 99 0.334429 1.0080 - 100 CH2 15 LHCU C51 100 0.229429 14.0270 - 101 NOpt 15 LHCU N71 101 -0.669571 14.0067 - 102 HS14 15 LHCU H72 102 0.320429 1.0080 - 103 CH2 15 LHCU C61 103 0.226429 14.0270 - 104 CH2 15 LHCU C5 104 0.241429 14.0270 - 105 NOpt 15 LHCU N7 105 -0.682571 14.0067 - 106 HS14 15 LHCU H21 106 0.334429 1.0080 - 107 CH2 16 LHCU C51 107 0.229429 14.0270 - 108 NOpt 16 LHCU N71 108 -0.669571 14.0067 - 109 HS14 16 LHCU H72 109 0.320429 1.0080 - 110 CH2 16 LHCU C61 110 0.226429 14.0270 - 111 CH2 16 LHCU C5 111 0.241429 14.0270 - 112 NOpt 16 LHCU N7 112 -0.682571 14.0067 - 113 HS14 16 LHCU H21 113 0.334429 1.0080 - 114 CH2 17 LHCU C51 114 0.229429 14.0270 - 115 NOpt 17 LHCU N71 115 -0.669571 14.0067 - 116 HS14 17 LHCU H72 116 0.320429 1.0080 - 117 CH2 17 LHCU C61 117 0.226429 14.0270 - 118 CH2 17 LHCU C5 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"constants": []}, {"atom_a": 108, "atom_b": 110, "atom_c": 111, "atom_d": 113, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 110, "atom_b": 111, "atom_c": 113, "atom_d": 114, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 113, "atom_b": 114, "atom_c": 115, "atom_d": 117, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 114, "atom_b": 115, "atom_c": 117, "atom_d": 118, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 115, "atom_b": 117, "atom_c": 118, "atom_d": 120, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 117, "atom_b": 118, "atom_c": 120, "atom_d": 121, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 120, "atom_b": 121, "atom_c": 122, "atom_d": 124, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 121, "atom_b": 122, "atom_c": 124, "atom_d": 125, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 122, "atom_b": 124, "atom_c": 125, "atom_d": 127, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 124, "atom_b": 125, "atom_c": 127, "atom_d": 128, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 127, "atom_b": 128, "atom_c": 129, "atom_d": 131, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 128, "atom_b": 129, "atom_c": 131, "atom_d": 132, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 129, 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"pair_type": 1}, {"atom_a": 1, "atom_b": 5, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 3, "atom_b": 8, "pair_type": 1}, {"atom_a": 4, "atom_b": 6, "pair_type": 1}, {"atom_a": 5, "atom_b": 7, "pair_type": 1}, {"atom_a": 9, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 26, "atom_b": 28, "pair_type": 1}, {"atom_a": 30, "atom_b": 34, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 33, "atom_b": 35, "pair_type": 1}, {"atom_a": 37, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2916153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19761538461538464, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, 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2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 76, "atom_b": 86, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}], "dihedrals": [{"atom_a": 10, "atom_b": 2, "atom_c": 3, "atom_d": 4, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 2, "atom_b": 3, "atom_c": 4, "atom_d": 6, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 9, "atom_b": 10, "atom_c": 2, "atom_d": 3, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 13, "atom_b": 14, "atom_c": 8, "atom_d": 9, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 14, "atom_b": 8, "atom_c": 9, "atom_d": 10, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 17, "atom_b": 18, "atom_c": 12, "atom_d": 13, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 18, "atom_b": 12, "atom_c": 13, "atom_d": 14, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 22, "atom_b": 16, "atom_c": 17, "atom_d": 18, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 21, "atom_b": 22, "atom_c": 16, "atom_d": 17, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 26, "atom_b": 20, "atom_c": 21, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 25, "atom_b": 26, "atom_c": 20, "atom_d": 21, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 30, "atom_b": 24, "atom_c": 25, "atom_d": 26, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 29, "atom_b": 30, "atom_c": 24, "atom_d": 25, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 33, "atom_b": 34, "atom_c": 28, "atom_d": 29, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 34, "atom_b": 28, "atom_c": 29, "atom_d": 30, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 38, "atom_b": 32, "atom_c": 33, "atom_d": 34, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 37, "atom_b": 38, "atom_c": 32, "atom_d": 33, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 42, "atom_b": 36, "atom_c": 37, "atom_d": 38, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 41, "atom_b": 42, "atom_c": 36, "atom_d": 37, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 46, "atom_b": 40, "atom_c": 41, "atom_d": 42, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 45, "atom_b": 46, "atom_c": 40, "atom_d": 41, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 50, "atom_b": 44, "atom_c": 45, "atom_d": 46, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 49, "atom_b": 50, "atom_c": 44, "atom_d": 45, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 53, "atom_b": 54, "atom_c": 48, "atom_d": 49, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 54, "atom_b": 48, "atom_c": 49, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 52, "atom_d": 53, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 58, "atom_b": 52, "atom_c": 53, "atom_d": 54, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 61, "atom_b": 62, "atom_c": 56, "atom_d": 57, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 62, "atom_b": 56, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 66, "atom_b": 60, "atom_c": 61, "atom_d": 62, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 66, "atom_c": 60, "atom_d": 61, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 70, "atom_b": 64, "atom_c": 65, "atom_d": 66, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 69, "atom_b": 70, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 73, "atom_b": 74, "atom_c": 68, "atom_d": 69, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 74, "atom_b": 68, "atom_c": 69, "atom_d": 70, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 80, "atom_c": 72, "atom_d": 73, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 80, "atom_b": 72, "atom_c": 73, "atom_d": 74, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 76, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 76, "atom_b": 78, "atom_c": 79, "atom_d": 80, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 81, "atom_b": 82, "atom_c": 83, "atom_d": 85, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 82, "atom_b": 83, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 83, "atom_b": 85, "atom_c": 86, "atom_d": 76, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 3, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 2, "atom_b": 5, "pair_type": 1}, {"atom_a": 10, "atom_b": 4, "pair_type": 1}, {"atom_a": 7, "atom_b": 9, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 15, "atom_b": 17, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 25, "pair_type": 1}, {"atom_a": 27, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 33, "pair_type": 1}, {"atom_a": 35, "atom_b": 37, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 43, "atom_b": 45, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 53, "pair_type": 1}, {"atom_a": 55, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 61, "pair_type": 1}, {"atom_a": 63, "atom_b": 65, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 71, "atom_b": 73, "pair_type": 1}, {"atom_a": 77, "atom_b": 79, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 82, "atom_b": 86, "pair_type": 1}, {"atom_a": 84, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C5", "residue_atom": "N7"}, {"name": "from", "monomer_atom": "N71", "residue_atom": "C51"}]} \ No newline at end of file diff --git a/polytop_examples/data/pei_linear_polymer.png b/polytop_examples/data/pei_linear_polymer.png index c6948dd..6fff54d 100644 Binary files a/polytop_examples/data/pei_linear_polymer.png and b/polytop_examples/data/pei_linear_polymer.png differ diff --git a/polytop_examples/dendrimer_ethylamine.py b/polytop_examples/dendrimer_ethylamine.py index 247f465..4a0d200 100644 --- a/polytop_examples/dendrimer_ethylamine.py +++ b/polytop_examples/dendrimer_ethylamine.py @@ -1,56 +1,120 @@ # Construction of an ethylamine dendrimer -# import required classes from PolyTop +# Import required Classes from PolyTop from polytop.Junction import Junction from polytop.Monomer import Monomer from polytop.Visualize import Visualize from polytop.Polymer import Polymer from polytop.Topology import Topology -# load in monomer topologies from ITP files -core_mono = Topology.from_ITP("data/dendrimer_core.itp") -bifurcating_mono = Topology.from_ITP("data/dendrimer_bifurcating.itp") -terminal_mono = Topology.from_ITP("data/dendrimer_terminal.itp") -# create junctions for different 'levels' of monomers, depending on what level of branching they exist at in the dendrimer -# junctions are created with the bonding atom and then the leaving atom specified, in that order, and should be given a unique name +# ----- Load in monomer Topologies from the extended monomer ITP files ----- + +# Topology format is 'gromos' by default, but it is recommended to specify the +# format for clarity and readability. +core_mono = Topology.from_ITP("data/dendrimer_core.itp", format="gromos") +bifurcating_mono = Topology.from_ITP("data/dendrimer_bifurcating.itp", format="gromos") +terminal_mono = Topology.from_ITP("data/dendrimer_terminal.itp", format="gromos") + + +# ----- Create Junctions for the different Monomers to join to and from ----- + +# Provide the bonding atom and the leaving atom, in that order, for the Junction +# The two atoms used to create a Junction MUST have a bond between them. + +# Note that junctions are specified for extend() by their name attribute and +# NOT by the variable name they are assigned to (which are instead used to pass +# them into a Monomer object). + +# You will see that all of the Junctions created below have a unique name to +# prevent randomisation or uncertainty in the extension, and thus ensure repeatability. + +# Create junctions for different 'levels' of monomers, depending on what level +# of branching they exist at in the dendrimer (e.g. central, first branching +# level, second branching level or terminal) + +# Junctions for the 'central' Monomer that will initiate the Polymer +# One junction for each of the branches radiating out central1 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C9"), name="C1") central2 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C7"), name="C2") central3 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C2"), name="C3") central4 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C3"), name="C4") +# Junctions for the first level of branching with a 'bifurcating' Monomer +# The 'to' Junction will join to one of the 'central' Monomer Junctions, while +# the 'from1' and 'from2' Junctions will join to incoming second level of branching Monomers b1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to") b2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from1") b2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from2") +# Junctions for the second level of branching with a 'bifurcating' Monomer +# The 'to2' Junction will join to one of the first level branching 'bifurcating' +# Monomer Junctions (i.e. from1 or from2), while the 'from12' and 'from22' +# Junctions will join to incoming terminal Monomers c1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to2") c2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from12") c2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from22") +# Junctions for the 'terminal' Monomer that will terminate the Polymer +# Note how only 1 Junction is created for the terminal Monomer, as this will +# act to cap the Polymer and prevent further extension as there will be no +# remaining Junctions. +# The 'term' Junction will join to one of the second level branching 'bifurcating' +# Monomer Junctions (i.e. from12 or from22) t = Junction(terminal_mono.get_atom("C1"), terminal_mono.get_atom("N1"), name = "term") -# create monomers from their topologies and any specified junctions -# note that different 'levels' of monomers have different names for their junctions. + +# ----- Create Monomers from their Topologies and any specified Junctions ----- + +# Note that different 'levels' of monomers have different names for their junctions. # This ensures that layers are added on sequentially. -# If all monomers have the same junction names the polymerisation will be random and often defaults to a linear shape! +# If all monomers have the same junction names the polymerisation will be random +# and often defaults to a linear shape! central = Monomer(core_mono, [central1, central2, central3, central4]) bifur1 = Monomer(bifurcating_mono, [b1, b2a, b2b]) bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b]) cap = Monomer(terminal_mono, [t]) -# start the polymer with the central monomer + +# ----- Start the Polymer with one Monomer ----- + +# Only a Polymer object has access to the 'extend()' and 'extra_bond()' +# functions needed to join monomers together, so the first Monomer object must +# be converted to a Polymer object to build from. +# Since the polymer will be built starting from the 'central' Monomer and +# radiating outwards, the 'central' Monomer will be used to start the Polymer. polymer = Polymer(central) -# extend first layer of dendrimer + +# ----- Extending the Polymer to reach the desired structure ----- + +# The extend() function joins an incoming Monomer object to the Polymer object +# that is invoking the method (in this case 'polymer'). +# The argument 'from_junction_name' specifies which Junction (by its name) in +# the Polymer will form a new bond to the incoming Monomer, while the argument +# 'to_junction_name' is the Junction in the incoming Monomer that will form a +# bond to the Polymer. Such that the Polymer Junction's 'monomer atom' will +# join to the Monomer Junction's 'monomer atom' and both of their 'leaving atoms' +# will be discarded. +# To ensure that you generate a valid topology, the two Junctions you join +# should have corresponding atoms and the same bond, angle and dihedral +# parameters, which will be ensured by using an appropriately extended topology +# and defining Junctions correctly. + +# Extend first layer of dendrimer polymer.extend(bifur1, from_junction_name="C1", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C2", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C3", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C4", to_junction_name="to") -# extend second layer of dendrimer -# note how the first and second 'layers' have different monomers with different -# Junction names to ensure the correct structure is always formed. Junction and -# Monomer name ambiguity WILL cause formation of random, unreplicatable polymer topologies +# Extend second layer of dendrimer +# Note how the first and second levels of branching have different Monomers +# with different Junction names to ensure the correct structure is always +# formed. Junction and Monomer name ambiguity or redundancy *WILL* cause +# formation of random, unreplicatable polymer topologies. +# These extends could be completed within a for loop to reduce the amount of +# code, but have been expanded for this example to make sure that all commands +# are clear and explicit. polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") @@ -60,7 +124,9 @@ polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") -# finish polymer by extending on the capping monomer +# Finish polymer by extending on the capping monomer +# Note how each level of extension radiating outward from the central Monomer +# has double the number of extend() calls as the branching doubles each layer. polymer.extend(cap, from_junction_name="from12", to_junction_name="term") polymer.extend(cap, from_junction_name="from22", to_junction_name="term") polymer.extend(cap, from_junction_name="from12", to_junction_name="term") @@ -78,10 +144,15 @@ polymer.extend(cap, from_junction_name="from12", to_junction_name="term") polymer.extend(cap, from_junction_name="from22", to_junction_name="term") -# check netcharge of the monomers is preserved (in this case, close to 0) +# Optionally (but recommended), check the netcharge of the monomers is +# preserved (in this case, close to 0) print(polymer.topology.netcharge) -# save the dendrimer to a file and visualise the structure with RDKit for an easy visual structure check -polymer.save_to_file('data/ethylamine_dendrimer.json') # text dump -polymer.topology.to_ITP('data/ethylamine_dendrimer.itp') -Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/ethylamine_dendrimer.png',(400,300)) \ No newline at end of file + +# ----- Save the polymer dendrimer to an itp file ----- + +# Optionally, use Visualize to generate an image of the structure with RDKit +# for an easy visual structure check +polymer.save_to_file('data/ethylamine_dendrimer.json') # optional, text dump in a dictionary format +polymer.topology.to_ITP('data/ethylamine_dendrimer.itp') # write the itp to be used for simulation +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/ethylamine_dendrimer.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file diff --git a/polytop_examples/linear_PEI.py b/polytop_examples/linear_PEI.py index 1943729..0a24f28 100644 --- a/polytop_examples/linear_PEI.py +++ b/polytop_examples/linear_PEI.py @@ -1,33 +1,74 @@ # Construction of a simple linear homopolymer of PEI -# Import required classes from PolyTop +# This polymer will be 20 monomers long and constructed by joining Atom N71 to +# C5, and discarding the atoms C51 and N7 (and any other atoms, such as +# hydrogens, connected to them but not the rest of the polymer). + +# Import required Classes from PolyTop from polytop.Junction import Junction from polytop.Monomer import Monomer from polytop.Visualize import Visualize from polytop.Polymer import Polymer from polytop.Topology import Topology -# Load in monomer Topology from ITP file -top = Topology.from_ITP("data/pei.itp") -# Create a Junction to join 'to' and another to join 'from'. -# Provide the bonding atom and the leaving atom, in that order, for the -# Junction - they must have a bond between them. -to_j = Junction(top.get_atom("C51"), top.get_atom("C62"), name = "to") -from_j = Junction(top.get_atom("N7"), top.get_atom("C6"), name = "from") +# ----- Load in the monomer Topology from the extended PEI monomer ITP file ----- + +# Topology format is 'gromos' by default, but it is recommended to specify the +# format for clarity and readability. +top = Topology.from_ITP("data/pei.itp", format="gromos") + + +# ----- Create a Junction to join 'to' and another to join 'from' ----- + +# Provide the bonding atom and the leaving atom, in that order, for the Junction +# The two atoms used to create a Junction MUST have a bond between them. +# Note that junctions are specified for extend() by their name attribute (in +# this example 'to' and 'from', and NOT by the variable name they are assigned +# to 'to_j' and 'from_j', which are used to pass them into a Monomer object) +to_j = Junction(top.get_atom("N71"), top.get_atom("C51"), name = "from") +from_j = Junction(top.get_atom("C5"), top.get_atom("N7"), name = "to") -# Create a Monomer from the Topology and a list of the Junctions +# ----- Create a Monomer from the Topology and a list of the Junctions ----- + +# Note that you could also create an 'initial' Monomer with the 'from_j' +# Junction only and a 'terminal' Monomer with the 'to_j' only, but this is not +# necessary, as any Junctions which are not extended to or from with extend() +# will not lose their leaving atoms. However, this is a beneficial approach for +# more complex polymers, such as with branching, to prevent ambiguity during +# extension. For examples of this, see tutorial scripts in +# `dendrimer_ethlyamine.py` or `star_PEG.py` monomer = Monomer(top, [to_j, from_j]) -# Start the Polymer with one Monomer +# ----- Start the Polymer with one Monomer ----- + +# Only a Polymer object has access to the 'extend()' and 'extra_bond()' +# functions needed to join monomers together, so the first Monomer object must +# be converted to a Polymer object to build from. polymer = Polymer(monomer) -# Extend the Polymer to the desired length (in this case 20) + +# ----- Extend the Polymer to the desired length (in this case 20) ----- + +# The extend() function joins an incoming Monomer object (in this case 'monomer') +# to the Polymer object that is invoking the method (in this case 'polymer'). +# The argument 'from_junction_name' specifies which Junction (by its name) in +# the Polymer will form a new bond to the incoming Monomer, while the argument +# 'to_junction_name' is the Junction in the incoming Monomer that will form a +# bond to the Polymer. Such that the Polymer Junction's 'monomer atom' will +# join to the Monomer Junction's 'monomer atom' and both of their 'leaving atoms' +# will be discarded. +# To ensure that you generate a valid topology, the two Junctions you join +# should have corresponding atoms and the same bond, angle and dihedral +# parameters, which will be ensured by using an appropriately extended topology +# and defining Junctions correctly. for i in range(19): polymer.extend(monomer, from_junction_name="from", to_junction_name="to") -# Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check -polymer.topology.title = "pei polymer" # renames the ITP header and image -polymer.save_to_file('data/pei_linear_polymer.json') # text dump -polymer.topology.to_ITP('data/pei_linear_polymer.itp') -Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) \ No newline at end of file +# ----- Save the polymer to an itp file ----- +# Optionally, use Visualize to generate an image of the structure with RDKit +# for an easy visual structure check +polymer.topology.title = "pei polymer" # optional but good for identifying files, renames the ITP header and image +polymer.save_to_file('data/pei_linear_polymer.json') # optional, text dump in a dictionary format +polymer.topology.to_ITP('data/pei_linear_polymer.itp') # write the itp to be used for simulation +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file diff --git a/polytop_examples/star_PEG.py b/polytop_examples/star_PEG.py index f93df60..86ed8d7 100644 --- a/polytop_examples/star_PEG.py +++ b/polytop_examples/star_PEG.py @@ -1,18 +1,50 @@ # Construction of a 4-arm PEG star polymer from single monomeric units -# import required classes from PolyTop +# Import required Classes from PolyTop from polytop.Junction import Junction from polytop.Monomer import Monomer from polytop.Visualize import Visualize from polytop.Polymer import Polymer from polytop.Topology import Topology -# load in monomer topologies from ITP files -ethanol = Topology.from_ITP("data/extended_ethanol.itp") # main arm monomer -methane = Topology.from_ITP("data/extended_methane.itp") # terminal monomer -neopentane = Topology.from_ITP("data/extended_neopentane.itp") # central monomer -# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name +# ----- Load in monomer Topologies from the extended monomer ITP files ----- + +# Topology format is 'gromos' by default, but it is recommended to specify the +# format for clarity and readability. +ethanol = Topology.from_ITP("data/extended_ethanol.itp", format="gromos") # main arm monomer +methane = Topology.from_ITP("data/extended_methane.itp", format="gromos") # terminal monomer +neopentane = Topology.from_ITP("data/extended_neopentane.itp", format="gromos") # central monomer + + +# ----- Create Junctions for the different Monomers to join to and from ----- + +# Provide the bonding atom and the leaving atom, in that order, for the Junction +# The two atoms used to create a Junction MUST have a bond between them. + +# Note that junctions are specified for extend() by their name attribute and +# NOT by the variable name they are assigned to (which are instead used to pass +# them into a Monomer object). + +# You will see that all of the Junctions created below have a unique name to +# prevent randomisation or uncertainty in the extension, and thus ensure repeatability. + +# Create unique Junctions for the Monomers that make up each of the 4 arms of +# the star, as well as the central Monomer and the terminal Monomers. + +# Junctions for the central 'neopentane' Monomer that will initiate the Polymer +# One junction for each of the arms of the star +j1 = Junction(neopentane.get_atom("C1"), neopentane.get_atom("O1"), name = "branch1") +j2 = Junction(neopentane.get_atom("C3"), neopentane.get_atom("O2"), name = "branch2") +j3 = Junction(neopentane.get_atom("C4"), neopentane.get_atom("O3"), name = "branch3") +j4 = Junction(neopentane.get_atom("C5"), neopentane.get_atom("O4"), name = "branch4") + +# Junctions for each of the ethanol 'arm' Monomers +# The 'oxy*' Junctions will join to one of the central 'neopentane' Monomer +# Junctions (branch*), while the 'carb*'Junctions will join to an incoming +# ethanol Monomer to extend that arm further. Such that branch1 Junction joins +# to oxy1 Junction, and the carb1 Junction of the same Monomer will join to +# another incoming Monomer's oxy1 Junction. oxy_j1 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy1") carb_j1 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb1") oxy_j2 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy2") @@ -22,14 +54,24 @@ oxy_j4 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy4") carb_j4 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb4") -j1 = Junction(neopentane.get_atom("C1"), neopentane.get_atom("O1"), name = "branch1") -j2 = Junction(neopentane.get_atom("C3"), neopentane.get_atom("O2"), name = "branch2") -j3 = Junction(neopentane.get_atom("C4"), neopentane.get_atom("O3"), name = "branch3") -j4 = Junction(neopentane.get_atom("C5"), neopentane.get_atom("O4"), name = "branch4") - +# Junctions for the 'terminal' Monomer that will terminate the Polymer's arms +# Note how only 1 Junction is created for the terminal Monomer, as this will +# act to cap the Polymer and prevent further extension as there will be no +# remaining Junctions. +# The 'term' Junction will join to the final 'ethanol' Monomer Junction (carb*) term_j = Junction(methane.get_atom("C1"), methane.get_atom("O1"), name = "term") -# create monomers from their topologies and any specified junctions + +# ----- Create Monomers from their Topologies and any specified Junctions ----- + +# Note that a unique Monomer has been created for each of the 4 arms with +# different Junctions, which ensures that only Monomers of the same type are +# joined to create the same arm, which means that all 4 arms will be the same +# desired length. +# If all Monomers had Junctions with the same names the polymerisation would be +# random and each of the arms would be different lengths. The lengths of each +# branch would also vary each time you built the Polymer, which is terrible for +# scientific replicability! e1 = Monomer(ethanol, [oxy_j1, carb_j1]) e2 = Monomer(ethanol, [oxy_j2, carb_j2]) e3 = Monomer(ethanol, [oxy_j3, carb_j3]) @@ -39,10 +81,36 @@ terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm -# start the polymer with the central monomer + +# ----- Start the Polymer with one Monomer ----- + +# Only a Polymer object has access to the 'extend()' and 'extra_bond()' +# functions needed to join monomers together, so the first Monomer object must +# be converted to a Polymer object to build from. +# Since the polymer will be built starting from the 'central' Monomer and +# radiating outwards, the 'central' Monomer will be used to start the Polymer. four_polymer = Polymer(central) -# attach three ethanols to each of the four junctions (j1-j4) of the central monomer + +# ----- Extending the Polymer to reach the desired structure ----- + +# The extend() function joins an incoming Monomer object to the Polymer object +# that is invoking the method (in this case 'four_polymer'). +# The argument 'from_junction_name' specifies which Junction (by its name) in +# the Polymer will form a new bond to the incoming Monomer, while the argument +# 'to_junction_name' is the Junction in the incoming Monomer that will form a +# bond to the Polymer. Such that the Polymer Junction's 'monomer atom' will +# join to the Monomer Junction's 'monomer atom' and both of their 'leaving atoms' +# will be discarded. +# To ensure that you generate a valid topology, the two Junctions you join +# should have corresponding atoms and the same bond, angle and dihedral +# parameters, which will be ensured by using an appropriately extended topology +# and defining Junctions correctly. + +# attach three ethanols to each of the four junctions (branch1-branch4) of the +# central monomer, by extending each arm by 1 ethanol at a time. Extend from +# carb* or branch* Junctions to the matching numbered oxy* Junctions, and then +# finally from a carb* Junction to a "term" Junction. four_polymer.extend(e1, from_junction_name="branch1", to_junction_name="oxy1") four_polymer.extend(e2, from_junction_name="branch2", to_junction_name="oxy2") four_polymer.extend(e3, from_junction_name="branch3", to_junction_name="oxy3") @@ -63,11 +131,16 @@ four_polymer.extend(terminal, from_junction_name="carb3", to_junction_name="term") four_polymer.extend(terminal, from_junction_name="carb4", to_junction_name="term") -# check polymer charge and give it a descriptive name +# Optionally (but recommended), check the netcharge of the monomers is +# preserved and give it a descriptive name print(f"netcharge = {four_polymer.topology.netcharge}") -four_polymer.topology.title = "four arm star polymer - overlapped monomers" # rename your ITP header and image name +four_polymer.topology.title = "four arm star polymer" # rename your ITP header and image name + + +# ----- Save the polymer dendrimer to an itp file ----- -# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check -four_polymer.save_to_file('data/four_arm_star_overlapped_monomers.json') # text dump -four_polymer.topology.to_ITP('data/four_arm_star_overlapped_monomers.itp') -Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data/four_arm_star_overlapped_monomers.png',(400,300)) \ No newline at end of file +# Optionally, use Visualize to generate an image of the structure with RDKit +# for an easy visual structure check +four_polymer.save_to_file('data/four_arm_star.json') # optional, text dump in a dictionary format +four_polymer.topology.to_ITP('data/four_arm_star.itp') # write the itp to be used for simulation +Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data/four_arm_star.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file