diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 7853cb8..0a79db6 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: [ 8, 11, 17] + java: [ 8, 11, 17, 21, 25 ] name: Java ${{ matrix.java }} steps: diff --git a/README.md b/README.md index 5f274db..0c3498a 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,10 @@ # CDK-Scaffold Module ## Scaffold Functionalities for the Chemistry Development Kit (CDK) -Copyright © 2023 The CDK Development Team, especially +Copyright © 2023-2026 The CDK Development Team, especially [Julian Zander](mailto:zanderjulian@gmx.de), [Jonas Schaub](mailto:jonas.schaub@uni-jena.de), +[Egon Willighagen](https://github.com/egonw), [Achim Zielesny](mailto:achim.zielesny@w-hs.de), [Christoph Steinbeck](mailto:christoph.steinbeck@uni-jena.de) @@ -51,13 +52,13 @@ If you are using Maven, you can install the cdk-scaffold package using: cdk-scaffold org.openscience.cdk - 2.8 + 2.12 ``` ### Snapshot releases -For snapshot releases (currently `2.9-SNAPSHOT`) include the following fragment to define the +For snapshot releases (currently `2.13-SNAPSHOT`) include the following fragment to define the snapshot repository: ```xml diff --git a/pom.xml b/pom.xml index bd9db5f..21715a8 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.openscience.cdk cdk-scaffold cdk-scaffold - 2.9-SNAPSHOT + 2.12-SNAPSHOT jar https://github.com/cdk/cdk-scaffold @@ -26,7 +26,7 @@ ${maven.multiModuleProjectDirectory}/bundle/target/site/jacoco-aggregate/jacoco.xml https://sonarcloud.io - 2.9 + 2.13-SNAPSHOT 5.9.3 2.2 0.8.15 diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/NetworkNode.java b/src/main/java/org/openscience/cdk/tools/scaffold/NetworkNode.java index ffd6050..de5f3ee 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/NetworkNode.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/NetworkNode.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -35,7 +35,8 @@ * @param As MoleculeType, any data type can be defined. * In our scenario, the node contains a CDK IAtomContainer. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.0.0 */ public class NetworkNode extends ScaffoldNodeBase { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldGenerator.java b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldGenerator.java index 35d6fbb..eef6b45 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldGenerator.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldGenerator.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -69,7 +69,8 @@ * Mining for Bioactive Scaffolds with Scaffold Networks paper. * Different trees or networks can also be merged together. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.4.0 */ public class ScaffoldGenerator { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNetwork.java b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNetwork.java index 122e1ce..f25a56e 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNetwork.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNetwork.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -38,7 +38,8 @@ * Top-level class to organise the NetworkNodes * A network can have several roots and leaves. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.2.1 */ public class ScaffoldNetwork extends ScaffoldNodeCollectionBase { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeBase.java b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeBase.java index 310d710..11204a5 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeBase.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeBase.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -37,7 +37,8 @@ * @param As MoleculeType, any data type can be defined. * In our scenario, the node contains a CDK IAtomContainer. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.1.0 */ public abstract class ScaffoldNodeBase { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeCollectionBase.java b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeCollectionBase.java index 278049f..3a052d8 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeCollectionBase.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeCollectionBase.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -39,7 +39,8 @@ * Base class of node collection objects. * Top-level class to organise the ScaffoldNodeBase objects. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.2.0 */ public abstract class ScaffoldNodeCollectionBase { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldTree.java b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldTree.java index f82de3f..21358fa 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldTree.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldTree.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -35,7 +35,8 @@ * Top-level class to organise the TreeNodes as a tree. * A tree can have one root and several leaves. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.2.0 */ public class ScaffoldTree extends ScaffoldNodeCollectionBase { diff --git a/src/main/java/org/openscience/cdk/tools/scaffold/TreeNode.java b/src/main/java/org/openscience/cdk/tools/scaffold/TreeNode.java index 1998b30..021047d 100644 --- a/src/main/java/org/openscience/cdk/tools/scaffold/TreeNode.java +++ b/src/main/java/org/openscience/cdk/tools/scaffold/TreeNode.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -34,7 +34,8 @@ * @param As MoleculeType, any data type can be defined. * In our scenario, the node contains a CDK IAtomContainer. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.0.0 */ public class TreeNode extends ScaffoldNodeBase { diff --git a/src/test/java/org/openscience/cdk/tools/scaffold/GitHubWikiCodeExamplesTest.java b/src/test/java/org/openscience/cdk/tools/scaffold/GitHubWikiCodeExamplesTest.java index 903effd..a594363 100644 --- a/src/test/java/org/openscience/cdk/tools/scaffold/GitHubWikiCodeExamplesTest.java +++ b/src/test/java/org/openscience/cdk/tools/scaffold/GitHubWikiCodeExamplesTest.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck diff --git a/src/test/java/org/openscience/cdk/tools/scaffold/ScaffoldGeneratorTest.java b/src/test/java/org/openscience/cdk/tools/scaffold/ScaffoldGeneratorTest.java index d65295a..1ad750b 100644 --- a/src/test/java/org/openscience/cdk/tools/scaffold/ScaffoldGeneratorTest.java +++ b/src/test/java/org/openscience/cdk/tools/scaffold/ScaffoldGeneratorTest.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2022 Julian Zander + * Copyright (c) 2026 Julian Zander * Jonas Schaub * Achim Zielesny * Christoph Steinbeck @@ -57,7 +57,8 @@ /** * JUnit test class for the Scaffold Generator. * - * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de) + * @author Julian Zander (zanderjulian@gmx.de) + * @author Jonas Schaub (jonas.schaub@uni-jena.de) * @version 1.0.7.0 */ public class ScaffoldGeneratorTest extends ScaffoldGenerator { @@ -944,7 +945,7 @@ public void stereoFragmentationTest() throws Exception { "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCC(C4CCCC(CC(CC5CCNCC5)=C)C4)CC3)/C6CCCCCNC6)CCC1", "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCC(C4CCCCC4)CC3)/C5CCCCCNC5)CCC1", "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCCCC3)/C4CCCCCNC4)CCC1", - "C(=C(C1CCCNCCC1)C2CCCCCCC2)C3CCCCCNC3", + "C(=C(\\C1CCCNCCC1)/C2CCCCCCC2)\\C3CCCCCNC3", "C(C1CCCNCCC1)(C2CCCCCCC2)=C", "C1CCCNCCC1" };