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From: John M. <no...@gi...> - 2026-04-24 12:10:33
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: ceacd52d367483652d79f8a90f31b027b50ed002 https://github.com/cdk/cdk/commit/ceacd52d367483652d79f8a90f31b027b50ed002 Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesState.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java Log Message: ----------- Allow coordinate bonds to be parsed from CXSMILES - https://github.com/cdk/depict/issues/102 Commit: df1a0034c9c35cfe3491ac84ab56fc359467179f https://github.com/cdk/cdk/commit/df1a0034c9c35cfe3491ac84ab56fc359467179f Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java Log Message: ----------- Missed change to the BeamToCdk part Compare: https://github.com/cdk/cdk/compare/516927c7950d...df1a0034c9c3 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-24 11:35:59
|
Branch: refs/heads/cx-coord-bonds Home: https://github.com/cdk/cdk Commit: f8e1b9a7df5c39045908dda05a53b0eca98467bc https://github.com/cdk/cdk/commit/f8e1b9a7df5c39045908dda05a53b0eca98467bc Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java Log Message: ----------- Missed change to the BeamToCdk part To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-24 10:19:00
|
Branch: refs/heads/cx-coord-bonds Home: https://github.com/cdk/cdk Commit: 5bcb9715a3380412015db3ae9d5e3ae9f79eff5c https://github.com/cdk/cdk/commit/5bcb9715a3380412015db3ae9d5e3ae9f79eff5c Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesState.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java Log Message: ----------- Allow coordinate bonds to be parsed from CXSMILES - https://github.com/cdk/depict/issues/102 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-24 09:44:47
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 35bd46743947ba8b570114fa3b44a06963fa78a6 https://github.com/cdk/cdk/commit/35bd46743947ba8b570114fa3b44a06963fa78a6 Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java M app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java Log Message: ----------- Reuse the usmigen field when creating abbreviations, this allows hydrogen isotopes in the abbreviated structure. Commit: 516927c7950d622983af601a19707d5d2d39d651 https://github.com/cdk/cdk/commit/516927c7950d622983af601a19707d5d2d39d651 Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java Log Message: ----------- Spotted in molwitch-cdk, this check should only be warning (and skipping) if hashed wedge is between two stereocenters! Compare: https://github.com/cdk/cdk/compare/12ef701869b7...516927c7950d To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-24 09:23:57
|
Branch: refs/heads/2026-04-24 Home: https://github.com/cdk/cdk Commit: 9aa5c9aec5ba3f50b821cedec6091380000b37c8 https://github.com/cdk/cdk/commit/9aa5c9aec5ba3f50b821cedec6091380000b37c8 Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java M app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java Log Message: ----------- Reuse the usmigen field when creating abbreviations, this allows hydrogen isotopes in the abbreviated structure. Commit: 7fcfee042311bc2b30a1235b088ab5ef3aa4db76 https://github.com/cdk/cdk/commit/7fcfee042311bc2b30a1235b088ab5ef3aa4db76 Author: John Mayfield <jo...@ne...> Date: 2026-04-24 (Fri, 24 Apr 2026) Changed paths: M base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java Log Message: ----------- Spotted in molwitch-cdk, this check should only be warning (and skipping) if hashed wedge is between two stereocenters! Compare: https://github.com/cdk/cdk/compare/9aa5c9aec5ba%5E...7fcfee042311 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-24 09:20:46
|
Branch: refs/heads/iordf-removal Home: https://github.com/cdk/cdk To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-13 09:39:15
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 379efb2b4abb5120f82762f5b785c865a39e0007 https://github.com/cdk/cdk/commit/379efb2b4abb5120f82762f5b785c865a39e0007 Author: Egon Willighagen <ego...@gm...> Date: 2026-04-12 (Sun, 12 Apr 2026) Changed paths: M pom.xml Log Message: ----------- Updated Log4J, CMLXOM, and XOM Commit: 12ef701869b75fa35bf3dd3e292113803f418337 https://github.com/cdk/cdk/commit/12ef701869b75fa35bf3dd3e292113803f418337 Author: John Mayfield <jo...@ne...> Date: 2026-04-13 (Mon, 13 Apr 2026) Changed paths: M pom.xml Log Message: ----------- Merge pull request #1286 from cdk/update/deps-202604 Updated Log4J, CMLXOM, and XOM Compare: https://github.com/cdk/cdk/compare/09e5a6427872...12ef701869b7 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: dependabot[bot] <no...@gi...> - 2026-04-12 12:58:07
|
Branch: refs/heads/dependabot/maven/org.apache.logging.log4j-log4j-core-2.25.4 Home: https://github.com/cdk/cdk To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: Egon W. <no...@gi...> - 2026-04-12 12:56:50
|
Branch: refs/heads/update/deps-202604 Home: https://github.com/cdk/cdk Commit: 379efb2b4abb5120f82762f5b785c865a39e0007 https://github.com/cdk/cdk/commit/379efb2b4abb5120f82762f5b785c865a39e0007 Author: Egon Willighagen <ego...@gm...> Date: 2026-04-12 (Sun, 12 Apr 2026) Changed paths: M pom.xml Log Message: ----------- Updated Log4J, CMLXOM, and XOM To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: dependabot[bot] <no...@gi...> - 2026-04-10 23:51:54
|
Branch: refs/heads/dependabot/maven/org.apache.logging.log4j-log4j-core-2.25.4 Home: https://github.com/cdk/cdk Commit: d717ba6709058ccc4b96ace338bbe03dce8da94a https://github.com/cdk/cdk/commit/d717ba6709058ccc4b96ace338bbe03dce8da94a Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: 2026-04-10 (Fri, 10 Apr 2026) Changed paths: M pom.xml Log Message: ----------- Bump org.apache.logging.log4j:log4j-core from 2.25.3 to 2.25.4 Bumps org.apache.logging.log4j:log4j-core from 2.25.3 to 2.25.4. --- updated-dependencies: - dependency-name: org.apache.logging.log4j:log4j-core dependency-version: 2.25.4 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <su...@gi...> To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-04-03 17:46:29
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 09e5a64278728722486c76dd6aca1d5714319c91 https://github.com/cdk/cdk/commit/09e5a64278728722486c76dd6aca1d5714319c91 Author: John Mayfield <jo...@ne...> Date: 2026-04-03 (Fri, 03 Apr 2026) Changed paths: M bundle/pom.xml R storage/iordf/pom.xml R storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLReader.java R storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java R storage/iordf/src/main/java/org/openscience/cdk/libio/jena/CDK.java R storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java R storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLReaderTest.java R storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java R storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java R storage/iordf/src/test/resources/org/openscience/cdk/io/rdf/molecule.n3 M storage/pom.xml Log Message: ----------- Remove the iordf module as the JENA dependency brings in too many and exposed dependencies, the CDKOWLReader/Writer should be moved to a separate project. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
|
From: John M. <no...@gi...> - 2026-04-03 07:14:09
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: c50ce68df4ccbf18e31829ed91f9ef51a265122e https://github.com/cdk/cdk/commit/c50ce68df4ccbf18e31829ed91f9ef51a265122e Author: Felix Bänsch <168...@us...> Date: 2026-04-02 (Thu, 02 Apr 2026) Changed paths: M storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java M storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java Log Message: ----------- Introduce separate base counter for /F: layer parsing; Commit: 35f4d6b075e21dcafa30c9780f0950551dcefb5f https://github.com/cdk/cdk/commit/35f4d6b075e21dcafa30c9780f0950551dcefb5f Author: John Mayfield <jo...@ne...> Date: 2026-04-03 (Fri, 03 Apr 2026) Changed paths: M storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java M storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java Log Message: ----------- Merge pull request #1284 from fbaensch-beilstein/SeparateBaseCursor Introduce separate base counter for /F: layer parsing in InChINumbersTools.parseUSmilesNumbers Compare: https://github.com/cdk/cdk/compare/5b0d72fa6753...35f4d6b075e2 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-04-02 08:12:12
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Branch: refs/heads/iordf-removal Home: https://github.com/cdk/cdk Commit: f64b8e06aaeb4b09015f8316de376b00690047f3 https://github.com/cdk/cdk/commit/f64b8e06aaeb4b09015f8316de376b00690047f3 Author: John Mayfield <jo...@ne...> Date: 2026-04-02 (Thu, 02 Apr 2026) Changed paths: M bundle/pom.xml R storage/iordf/pom.xml R storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLReader.java R storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java R storage/iordf/src/main/java/org/openscience/cdk/libio/jena/CDK.java R storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java R storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLReaderTest.java R storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java R storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java R storage/iordf/src/test/resources/org/openscience/cdk/io/rdf/molecule.n3 M storage/pom.xml Log Message: ----------- Remove the iordf module as the JENA dependency brings in too many and exposed dependencies, the CDKOWLReader/Writer should be moved to a separate project. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-27 14:15:28
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 74c22e6cdefca464284fab153140c7a08c0c4906 https://github.com/cdk/cdk/commit/74c22e6cdefca464284fab153140c7a08c0c4906 Author: Uli <981...@us...> Date: 2026-03-25 (Wed, 25 Mar 2026) Changed paths: M base/core/src/main/java/org/openscience/cdk/CDKConstants.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven.mol Log Message: ----------- support reacting center status in MDL V2000 reader and writer; introduce tests for reacting center status handling Commit: 8198b825dca6f2ec3b9d6d0a6f09a0ca6746c8d5 https://github.com/cdk/cdk/commit/8198b825dca6f2ec3b9d6d0a6f09a0ca6746c8d5 Author: Uli <981...@us...> Date: 2026-03-25 (Wed, 25 Mar 2026) Changed paths: M .github/workflows/maven.yml M README.md M app/depict/pom.xml M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java M app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java M app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java M app/pom.xml M base/atomtype/pom.xml M base/core/pom.xml M base/core/src/main/java/org/openscience/cdk/CDKConstants.java M base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java A base/core/src/main/java/org/openscience/cdk/renderer/selection/AtomBondSelection.java M base/data/pom.xml M base/data/src/main/java/org/openscience/cdk/Atom.java M base/data/src/main/java/org/openscience/cdk/AtomType.java M base/data/src/main/java/org/openscience/cdk/Bond.java M base/data/src/main/java/org/openscience/cdk/Isotope.java M base/datadebug/pom.xml M base/dict/pom.xml M base/dict/src/test/java/org/openscience/cdk/dict/AbstractEntryTest.java M base/dict/src/test/java/org/openscience/cdk/dict/DictDBReactTest.java M base/dict/src/test/java/org/openscience/cdk/dict/DictDBTest.java M base/interfaces/pom.xml M base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java M base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObject.java A base/interfaces/src/main/java/org/openscience/cdk/renderer/selection/IChemObjectSelection.java M base/isomorphism/pom.xml M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/DfState.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryBond.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupList.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupQuery.java A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupQueryManipulator.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/RGroupListTest.java M base/pom.xml M base/reaction/pom.xml M base/reaction/src/test/java/org/openscience/cdk/atomtype/ReactionStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/atomtype/ResonanceStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionEngineTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionMechanismTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionSpecificationTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/ParameterReactTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/SetReactionCenterTest.java M base/reaction/src/test/java/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java M base/silent/pom.xml M base/silent/src/main/java/org/openscience/cdk/silent/Atom.java M base/silent/src/main/java/org/openscience/cdk/silent/AtomType.java M base/silent/src/main/java/org/openscience/cdk/silent/Bond.java M base/silent/src/main/java/org/openscience/cdk/silent/Isotope.java M base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java M base/standard/pom.xml M base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticType.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java M base/standard/src/main/java/org/openscience/cdk/graph/ConnectivityChecker.java M base/standard/src/main/java/org/openscience/cdk/layout/AtomPlacer.java M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java A base/standard/src/main/java/org/openscience/cdk/tools/manipulator/HydrogenState.java A base/standard/src/main/java/org/openscience/cdk/tools/manipulator/Hydrogens.java M base/test-atomtype/pom.xml M base/test-core/pom.xml M base/test-standard/pom.xml M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/graph/ConnectivityCheckerTest.java A base/test-standard/src/test/java/org/openscience/cdk/isomorphism/matchers/RGroupQueryManipulatorTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java M base/test-valencycheck/pom.xml M base/test/pom.xml M base/test/src/test/java/org/openscience/cdk/test/tools/AbstractLoggingToolTest.java M base/valencycheck/pom.xml M bundle/pom.xml M descriptor/cip/pom.xml M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPSMILESTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPToolTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImmutableHydrogenTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigancyFourChiralityTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/TerminalLigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/AtomicNumberRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/MassNumberRuleTest.java M descriptor/fingerprint/pom.xml M descriptor/ionpot/pom.xml M descriptor/pom.xml M descriptor/qsar/pom.xml M descriptor/qsar/src/test/java/org/openscience/cdk/qsar/DescriptorExceptionTest.java M descriptor/qsar/src/test/java/org/openscience/cdk/tools/AtomicPropertiesTest.java M descriptor/qsaratomic/pom.xml M descriptor/qsarbond/pom.xml M descriptor/qsarcml/pom.xml M descriptor/qsarionpot/pom.xml M descriptor/qsarmolecular/pom.xml M descriptor/qsarprotein/pom.xml M descriptor/qsarsubstance/pom.xml M descriptor/signature/pom.xml M descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeSignatureTest.java M descriptor/signature/src/test/java/org/openscience/cdk/similarity/SignatureFingerprintTanimotoTest.java M display/pom.xml M display/render/pom.xml R display/render/src/main/java/org/openscience/cdk/renderer/selection/IChemObjectSelection.java M display/renderawt/pom.xml M display/renderbasic/pom.xml M display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java M display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/ElementGroup.java M display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AtomSymbol.java M display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java M display/renderextra/pom.xml M legacy/pom.xml M legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/CTFileQueryBond.java M misc/control/pom.xml M misc/diff/pom.xml M misc/extra/pom.xml M misc/extra/src/test/java/org/openscience/cdk/AssociationTest.java M misc/extra/src/test/java/org/openscience/cdk/CloneAtomContainerTest.java R misc/extra/src/test/java/org/openscience/cdk/ReactionChainTest.java M misc/extra/src/test/java/org/openscience/cdk/atomtype/AtomTypeFactoryTest.java M misc/extra/src/test/java/org/openscience/cdk/config/XMLIsotopeFactoryTest.java M misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeHandlerTest.java M misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeReaderTest.java M misc/extra/src/test/java/org/openscience/cdk/dict/DictionaryTest.java M misc/extra/src/test/java/org/openscience/cdk/geometry/RDFCalculatorTest.java M misc/extra/src/test/java/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java M misc/extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java M misc/extra/src/test/java/org/openscience/cdk/index/CASNumberTest.java M misc/extra/src/test/java/org/openscience/cdk/io/ShelXWriterTest.java M misc/extra/src/test/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java M misc/extra/src/test/java/org/openscience/cdk/io/random/RandomAccessTest.java M misc/extra/src/test/java/org/openscience/cdk/limitations/SaturationCheckerTest.java A misc/extra/src/test/java/org/openscience/cdk/reaction/ReactionChainTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/BremserPredictorTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/HOSECodeAnalyserTest.java M misc/extra/src/test/java/org/openscience/cdk/validate/Geometry3DValidatorTest.java M misc/log4j/pom.xml M misc/pom.xml M misc/qm/pom.xml M misc/slf4j/pom.xml M pom.xml M storage/ctab/pom.xml M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/RGroupQueryReader.java M storage/ctab/src/main/java/org/openscience/cdk/io/RGroupQueryWriter.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/RGroupQueryReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/SDFWriterTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java M storage/inchi/pom.xml M storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java M storage/io/pom.xml M storage/io/src/main/java/org/openscience/cdk/io/iterator/event/EventCMLHandler.java M storage/ioformats/pom.xml M storage/ioformats/src/main/resources/org/openscience/cdk/tools/DataFeaturesTest.java M storage/ioformats/src/test/java/org/openscience/cdk/io/FormatFactoryTest.java M storage/iordf/pom.xml M storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java M storage/jniinchi-support/pom.xml M storage/libiocml/pom.xml M storage/libiomd/pom.xml M storage/libiomd/src/test/java/org/openscience/cdk/libio/md/MDMoleculeTest.java M storage/pdb/pom.xml M storage/pdb/src/test/java/org/openscience/cdk/templates/AminoAcidsTest.java M storage/pdb/src/test/java/org/openscience/cdk/tools/ProteinBuilderToolTest.java M storage/pdbcml/pom.xml M storage/pdbcml/src/test/java/org/openscience/cdk/io/cml/PDBAtomCustomizerTest.java M storage/pom.xml M storage/rinchi/pom.xml M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/InChILayersTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/KeyBase26Test.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIDecompositionTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIGeneratorTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIHashTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIToReactionTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/StatusMessagesOutputTest.java M storage/smiles/pom.xml M storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesState.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java M tool/builder3d/pom.xml M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java M tool/builder3dtools/pom.xml M tool/charges/pom.xml M tool/charges/src/test/java/org/openscience/cdk/charges/AtomTypeChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/InductivePartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PiElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PolarizabilityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/StabilizationChargesTest.java M tool/forcefield/pom.xml M tool/forcefield/src/test/java/org/openscience/cdk/charges/MMFF94PartialChargesTest.java M tool/formula/pom.xml M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopeContainerTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternGeneratorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternSimilarityTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaGeneratorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaRangeTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/rules/FormulaRuleTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulatorTest.java M tool/fragment/pom.xml A tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java A tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/ExhaustiveFragmenterTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/FragmentUtilsTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java M tool/group/pom.xml M tool/group/src/test/java/org/openscience/cdk/group/AbstractDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomGroupTests.java M tool/group/src/test/java/org/openscience/cdk/group/AtomPermutationTests.java M tool/group/src/test/java/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/BondGroupTests.java M tool/group/src/test/java/org/openscience/cdk/group/EquitablePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/PartitionTest.java M tool/group/src/test/java/org/openscience/cdk/group/PermutationGroupTest.java M tool/group/src/test/java/org/openscience/cdk/group/PermutationTest.java M tool/hash/pom.xml M tool/model/pom.xml M tool/pcore/pom.xml M tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.java M tool/pom.xml M tool/sdg/pom.xml M tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java M tool/sdg/src/main/java/org/openscience/cdk/layout/LayoutRefiner.java M tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java M tool/sdg/src/main/resources/org/openscience/cdk/layout/custom-templates.smi A tool/sdg/src/test/java/org/openscience/cdk/layout/Assertions2d.java M tool/sdg/src/test/java/org/openscience/cdk/layout/HydrogenPlacerTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/OverlapResolverTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/TemplateHandlerTest.java M tool/smarts/pom.xml M tool/smarts/src/main/java/org/openscience/cdk/smarts/CxSmartsParser.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smarts/ParserTest.java A tool/smarts/src/test/java/org/openscience/cdk/smarts/QueryManipulationTest.java M tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsPatternTest.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java M tool/structgen/pom.xml M tool/structgen/src/test/java/org/openscience/cdk/atomtype/StructGenAtomTypeGuesserTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/MathToolsTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/RandomStructureGeneratorTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/VicinitySamplerTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMergerTest.java R tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/ChemGraphTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachineTest.java M tool/tautomer/pom.xml M tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java M tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java Log Message: ----------- Merge branch 'main' into add-ctfile-reacting-center-status Commit: a75b4faadf438391c2eaab1c9016d2ca03762e93 https://github.com/cdk/cdk/commit/a75b4faadf438391c2eaab1c9016d2ca03762e93 Author: Uli <981...@us...> Date: 2026-03-26 (Thu, 26 Mar 2026) Changed paths: M base/core/src/main/java/org/openscience/cdk/CDKConstants.java A storage/ctab/src/main/java/org/openscience/cdk/io/MDLReactingCenterStatus.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java Log Message: ----------- migrate values for reacting center status from CDKConstants to MDLReactingCenterStatus; update reacting center status handling in MDL V2000 reader and writer; adjusts tests Commit: c14f44c8d65e6289369f67b83111c5bc6dabe2d5 https://github.com/cdk/cdk/commit/c14f44c8d65e6289369f67b83111c5bc6dabe2d5 Author: Uli <981...@us...> Date: 2026-03-26 (Thu, 26 Mar 2026) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLReactingCenterStatus.java Log Message: ----------- add javadocs for MDLReactingCenterStatus enum and its methods Commit: 09eb5bbf008a12cd7350e0e2079b8723c22a53d9 https://github.com/cdk/cdk/commit/09eb5bbf008a12cd7350e0e2079b8723c22a53d9 Author: Uli <981...@us...> Date: 2026-03-26 (Thu, 26 Mar 2026) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java Log Message: ----------- update reacting center status handling to use MDLReactingCenterStatus enum in MDLV2000Reader and adjust tests Commit: 782a6fd7a202962484acd97c1bb64462da0515ef https://github.com/cdk/cdk/commit/782a6fd7a202962484acd97c1bb64462da0515ef Author: Uli <981...@us...> Date: 2026-03-27 (Fri, 27 Mar 2026) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java Log Message: ----------- add support for reacting center status in MDL V3000 reader and writer Commit: 8c11d14b2a2ac16e676c31c99dc627737db278bb https://github.com/cdk/cdk/commit/8c11d14b2a2ac16e676c31c99dc627737db278bb Author: Uli <981...@us...> Date: 2026-03-27 (Fri, 27 Mar 2026) Changed paths: M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java R storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V3000.mol R storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V3000.mol R storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V3000.mol Log Message: ----------- add tests for handling reacting center status in MDL V3000 reader and writer; adjust V2000 test paths; fix order of actual and expected in assertions Commit: e1e03f4a70ee946ee193d157e3df99e33f41524a https://github.com/cdk/cdk/commit/e1e03f4a70ee946ee193d157e3df99e33f41524a Author: Uli <981...@us...> Date: 2026-03-27 (Fri, 27 Mar 2026) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLReactingCenterStatus.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java Log Message: ----------- MDLV2000Reader: replace logger.warn with handleError; MDLReactingCenterStatus: implement switch-based value mapping in and add copyright notice Commit: 5b0d72fa6753ccbd5479c652909601c4fc3fd817 https://github.com/cdk/cdk/commit/5b0d72fa6753ccbd5479c652909601c4fc3fd817 Author: John Mayfield <jo...@ne...> Date: 2026-03-27 (Fri, 27 Mar 2026) Changed paths: M base/core/src/main/java/org/openscience/cdk/CDKConstants.java A storage/ctab/src/main/java/org/openscience/cdk/io/MDLReactingCenterStatus.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V3000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V3000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V2000.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V3000.mol Log Message: ----------- Merge pull request #1280 from uli-f/add-ctfile-reacting-center-status support reacting center status in MDL V2000 reader and writer Compare: https://github.com/cdk/cdk/compare/adf113c73a5c...5b0d72fa6753 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: Egon W. <no...@gi...> - 2026-03-25 17:39:29
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: adf113c73a5c0e74903cc336eb1e2fa9b72d637f https://github.com/cdk/cdk/commit/adf113c73a5c0e74903cc336eb1e2fa9b72d637f Author: Egon Willighagen <ego...@gm...> Date: 2026-03-25 (Wed, 25 Mar 2026) Changed paths: M storage/iordf/pom.xml Log Message: ----------- Revert "replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xml" This reverts commit a937e057617cc43abab82aa6800d425d9a5c620f. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: Uli <no...@gi...> - 2026-03-25 16:01:46
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: a937e057617cc43abab82aa6800d425d9a5c620f https://github.com/cdk/cdk/commit/a937e057617cc43abab82aa6800d425d9a5c620f Author: Uli <981...@us...> Date: 2026-03-25 (Wed, 25 Mar 2026) Changed paths: M storage/iordf/pom.xml Log Message: ----------- replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xml To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-23 19:23:36
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 38be24ab72145a0f892b5ae1af898ffd4257996b https://github.com/cdk/cdk/commit/38be24ab72145a0f892b5ae1af898ffd4257996b Author: Jonas Schaub <jon...@gm...> Date: 2026-03-09 (Mon, 09 Mar 2026) Changed paths: A tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java A tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- initial implementation of CircularFragmenter Commit: f10fafba86bcb6fea792b44da8f5f9cba3457bfe https://github.com/cdk/cdk/commit/f10fafba86bcb6fea792b44da8f5f9cba3457bfe Author: Jonas Schaub <jon...@gm...> Date: 2026-03-10 (Tue, 10 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- WIP, removed the properties for the return ACs Commit: 0db0cbe9176bc0d7527ec61cf6e4f63d2f94a3db https://github.com/cdk/cdk/commit/0db0cbe9176bc0d7527ec61cf6e4f63d2f94a3db Author: Jonas Schaub <jon...@gm...> Date: 2026-03-10 (Tue, 10 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- adds a utility to calculate a suitable initial collection size for internal use Commit: b02711f61108259bc2f89b515b8bda9bfcb65ec1 https://github.com/cdk/cdk/commit/b02711f61108259bc2f89b515b8bda9bfcb65ec1 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-12 (Thu, 12 Mar 2026) Changed paths: M tool/fragment/pom.xml M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- adds settings for the preservation of stereochem and saturation by pseudo atoms; now uses the deep copy methods taken from the SDU; fixes saturation in general Commit: 49c75931527a27a8c523e15d3eb4fa07cd0db1e9 https://github.com/cdk/cdk/commit/49c75931527a27a8c523e15d3eb4fa07cd0db1e9 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M tool/fragment/pom.xml M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- mostly work on tests Commit: d4d156affbf88ed7c488f6e11d81605a81c3b92e https://github.com/cdk/cdk/commit/d4d156affbf88ed7c488f6e11d81605a81c3b92e Author: Jonas Schaub <jon...@gm...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- Gemini optimisation and doc additions Commit: 45bd2c86eeba0beec5da095f6b8f40351aa198f5 https://github.com/cdk/cdk/commit/45bd2c86eeba0beec5da095f6b8f40351aa198f5 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- work on doc Commit: 31e5e32a3cf491c2750d6c3d16a8fc58ad67d87f https://github.com/cdk/cdk/commit/31e5e32a3cf491c2750d6c3d16a8fc58ad67d87f Author: Jonas Schaub <jon...@gm...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- catch NoSuchBondException as well and correct malformatted doc Commit: 6e7909e36290b6333e9a384cde404141511e279c https://github.com/cdk/cdk/commit/6e7909e36290b6333e9a384cde404141511e279c Author: Jonas Schaub <jon...@gm...> Date: 2026-03-19 (Thu, 19 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- adds a property to each fragment atom that contains its depth/sphere/level/height in the respective fragment Commit: 32272718d305d882547341106a8aa1af87c88129 https://github.com/cdk/cdk/commit/32272718d305d882547341106a8aa1af87c88129 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-19 (Thu, 19 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- make protected methods and public constants private Commit: 2ceab3cb79339b795f98f9571b1536ef3f11e118 https://github.com/cdk/cdk/commit/2ceab3cb79339b795f98f9571b1536ef3f11e118 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- replace pre-built atomIndexMap with atom.getIndex() Commit: f003fd5052a3ad2c6b6ff2530aabd9a6b011bcc9 https://github.com/cdk/cdk/commit/f003fd5052a3ad2c6b6ff2530aabd9a6b011bcc9 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- enhances public API for retrieving only the fragment centered on a specific atom Commit: caed519df5bf0bb84c6f5c2d4fb01164a66a5b0b https://github.com/cdk/cdk/commit/caed519df5bf0bb84c6f5c2d4fb01164a66a5b0b Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- replaces visitedIndeces set and originalAtomToDepthMap with one array Commit: 7b1b6da12cbb912cfcef51e0309c7b52e0d14462 https://github.com/cdk/cdk/commit/7b1b6da12cbb912cfcef51e0309c7b52e0d14462 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- queue only holds index instead of index and depth Commit: 542f43f285699e9336ca8a4b220e7d89e2b92f7d https://github.com/cdk/cdk/commit/542f43f285699e9336ca8a4b220e7d89e2b92f7d Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- avoid exceptions in stereo mapping Commit: de48fa3efa8f09852390c747b382d8f0db513969 https://github.com/cdk/cdk/commit/de48fa3efa8f09852390c747b382d8f0db513969 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- encapsulates the fragment atom container creation and stereo element mapping Commit: d9651acec5b0f77d87fe0d239897b3205b343f24 https://github.com/cdk/cdk/commit/d9651acec5b0f77d87fe0d239897b3205b343f24 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- a few cosmetic improvements Commit: d9d8516f1ad2f07b8c767dd1aa4cbdb6befa74a3 https://github.com/cdk/cdk/commit/d9d8516f1ad2f07b8c767dd1aa4cbdb6befa74a3 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- adds note on aromaticity detection and test for previous HOSE code generator bug Commit: db79a97f86bc015e58878fe4c7ee58c8e205c7c7 https://github.com/cdk/cdk/commit/db79a97f86bc015e58878fe4c7ee58c8e205c7c7 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- move tag in front of code example Commit: 39d7825fdd3f21f069db72025e21dd4606b7e7a8 https://github.com/cdk/cdk/commit/39d7825fdd3f21f069db72025e21dd4606b7e7a8 Author: Jonas Schaub <jon...@gm...> Date: 2026-03-23 (Mon, 23 Mar 2026) Changed paths: M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- adds safeguards against null values Commit: 2a1a138135e80e9e23cee6ed1f9785f17bca32ee https://github.com/cdk/cdk/commit/2a1a138135e80e9e23cee6ed1f9785f17bca32ee Author: Jonas Schaub <jon...@gm...> Date: 2026-03-23 (Mon, 23 Mar 2026) Changed paths: M tool/fragment/pom.xml M tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java Log Message: ----------- adds test scope to cdk-data and cdk-inchi dependencies; copy bonds are created via begin.getContainer().newBond() now Commit: dfff5dcff768a1b984561863b412f27a4e84ca7a https://github.com/cdk/cdk/commit/dfff5dcff768a1b984561863b412f27a4e84ca7a Author: Jonas Schaub <jon...@gm...> Date: 2026-03-23 (Mon, 23 Mar 2026) Changed paths: M tool/fragment/pom.xml Log Message: ----------- resolve merge conflict by steering clear of the now removed cdk-test dependency Commit: f548b7db4bb93a26f1fa5bc364621cda562c378a https://github.com/cdk/cdk/commit/f548b7db4bb93a26f1fa5bc364621cda562c378a Author: John Mayfield <jo...@ne...> Date: 2026-03-23 (Mon, 23 Mar 2026) Changed paths: M .github/workflows/maven.yml M README.md M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java M app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java M base/dict/pom.xml M base/dict/src/test/java/org/openscience/cdk/dict/AbstractEntryTest.java M base/dict/src/test/java/org/openscience/cdk/dict/DictDBReactTest.java M base/dict/src/test/java/org/openscience/cdk/dict/DictDBTest.java M base/isomorphism/pom.xml M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/RGroupListTest.java M base/reaction/src/test/java/org/openscience/cdk/atomtype/ReactionStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/atomtype/ResonanceStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionEngineTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionMechanismTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionSpecificationTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/ParameterReactTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/SetReactionCenterTest.java M base/reaction/src/test/java/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java M descriptor/cip/pom.xml M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPSMILESTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPToolTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImmutableHydrogenTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigancyFourChiralityTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/TerminalLigandTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/AtomicNumberRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRuleTest.java M descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/MassNumberRuleTest.java M descriptor/qsar/pom.xml M descriptor/qsar/src/test/java/org/openscience/cdk/qsar/DescriptorExceptionTest.java M descriptor/qsar/src/test/java/org/openscience/cdk/tools/AtomicPropertiesTest.java M descriptor/qsarcml/pom.xml M descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeSignatureTest.java M descriptor/signature/src/test/java/org/openscience/cdk/similarity/SignatureFingerprintTanimotoTest.java M misc/extra/src/test/java/org/openscience/cdk/AssociationTest.java M misc/extra/src/test/java/org/openscience/cdk/CloneAtomContainerTest.java R misc/extra/src/test/java/org/openscience/cdk/ReactionChainTest.java M misc/extra/src/test/java/org/openscience/cdk/atomtype/AtomTypeFactoryTest.java M misc/extra/src/test/java/org/openscience/cdk/config/XMLIsotopeFactoryTest.java M misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeHandlerTest.java M misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeReaderTest.java M misc/extra/src/test/java/org/openscience/cdk/dict/DictionaryTest.java M misc/extra/src/test/java/org/openscience/cdk/geometry/RDFCalculatorTest.java M misc/extra/src/test/java/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java M misc/extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java M misc/extra/src/test/java/org/openscience/cdk/index/CASNumberTest.java M misc/extra/src/test/java/org/openscience/cdk/io/ShelXWriterTest.java M misc/extra/src/test/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java M misc/extra/src/test/java/org/openscience/cdk/io/random/RandomAccessTest.java M misc/extra/src/test/java/org/openscience/cdk/limitations/SaturationCheckerTest.java A misc/extra/src/test/java/org/openscience/cdk/reaction/ReactionChainTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/BremserPredictorTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/HOSECodeAnalyserTest.java M misc/extra/src/test/java/org/openscience/cdk/validate/Geometry3DValidatorTest.java M storage/ctab/src/test/java/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java M storage/ioformats/pom.xml M storage/ioformats/src/main/resources/org/openscience/cdk/tools/DataFeaturesTest.java M storage/ioformats/src/test/java/org/openscience/cdk/io/FormatFactoryTest.java M storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java M storage/libiomd/pom.xml M storage/libiomd/src/test/java/org/openscience/cdk/libio/md/MDMoleculeTest.java M storage/pdb/src/test/java/org/openscience/cdk/templates/AminoAcidsTest.java M storage/pdb/src/test/java/org/openscience/cdk/tools/ProteinBuilderToolTest.java M storage/pdbcml/pom.xml M storage/pdbcml/src/test/java/org/openscience/cdk/io/cml/PDBAtomCustomizerTest.java M storage/rinchi/pom.xml M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/InChILayersTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/KeyBase26Test.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIDecompositionTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIGeneratorTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIHashTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIToReactionTest.java M storage/rinchi/src/test/java/org/openscience/cdk/rinchi/StatusMessagesOutputTest.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java M tool/builder3d/pom.xml M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java M tool/charges/pom.xml M tool/charges/src/test/java/org/openscience/cdk/charges/AtomTypeChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/InductivePartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PiElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PolarizabilityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/StabilizationChargesTest.java M tool/forcefield/pom.xml M tool/forcefield/src/test/java/org/openscience/cdk/charges/MMFF94PartialChargesTest.java M tool/formula/pom.xml M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopeContainerTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternGeneratorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternSimilarityTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaGeneratorTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaRangeTest.java M tool/formula/src/test/java/org/openscience/cdk/formula/rules/FormulaRuleTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulatorTest.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulatorTest.java M tool/fragment/pom.xml M tool/fragment/src/test/java/org/openscience/cdk/fragment/ExhaustiveFragmenterTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/FragmentUtilsTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java M tool/group/pom.xml M tool/group/src/test/java/org/openscience/cdk/group/AbstractDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomGroupTests.java M tool/group/src/test/java/org/openscience/cdk/group/AtomPermutationTests.java M tool/group/src/test/java/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/BondGroupTests.java M tool/group/src/test/java/org/openscience/cdk/group/EquitablePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/PartitionTest.java M tool/group/src/test/java/org/openscience/cdk/group/PermutationGroupTest.java M tool/group/src/test/java/org/openscience/cdk/group/PermutationTest.java M tool/model/pom.xml M tool/sdg/pom.xml A tool/sdg/src/test/java/org/openscience/cdk/layout/Assertions2d.java M tool/sdg/src/test/java/org/openscience/cdk/layout/HydrogenPlacerTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/OverlapResolverTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java M tool/sdg/src/test/java/org/openscience/cdk/layout/TemplateHandlerTest.java M tool/smarts/pom.xml M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smarts/ParserTest.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java M tool/structgen/src/test/java/org/openscience/cdk/atomtype/StructGenAtomTypeGuesserTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/MathToolsTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/RandomStructureGeneratorTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/VicinitySamplerTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMergerTest.java R tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/ChemGraphTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachineTest.java M tool/tautomer/pom.xml M tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java Log Message: ----------- Merge branch 'main' into circular_fragmenter Commit: 96732f64153126127f57096d690a4b93d06fe223 https://github.com/cdk/cdk/commit/96732f64153126127f57096d690a4b93d06fe223 Author: John Mayfield <jo...@ne...> Date: 2026-03-23 (Mon, 23 Mar 2026) Changed paths: M tool/fragment/pom.xml A tool/fragment/src/main/java/org/openscience/cdk/fragment/CircularFragmenter.java A tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.java Log Message: ----------- Merge pull request #1277 from JonasSchaub/circular_fragmenter Fragmenter for circular substructures analogous to HOSE code / Morgan fingerprints / molecular signatures Compare: https://github.com/cdk/cdk/compare/d460802f116a...96732f641531 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: Jonas S. <no...@gi...> - 2026-03-20 18:30:57
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: d460802f116a11c52eb12310bf7464f3b9086be5 https://github.com/cdk/cdk/commit/d460802f116a11c52eb12310bf7464f3b9086be5 Author: Jonas Schaub <448...@us...> Date: 2026-03-20 (Fri, 20 Mar 2026) Changed paths: M README.md Log Message: ----------- Update CDK version from 2.11 to 2.12 in README To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: Egon W. <no...@gi...> - 2026-03-14 16:05:26
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 6d69b0c96ad6b149667d8fe6832e797d7c081af6 https://github.com/cdk/cdk/commit/6d69b0c96ad6b149667d8fe6832e797d7c081af6 Author: Egon Willighagen <ego...@gm...> Date: 2026-03-14 (Sat, 14 Mar 2026) Changed paths: M .github/workflows/maven.yml Log Message: ----------- Updated the GitHub Actions To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: Egon W. <no...@gi...> - 2026-03-14 15:35:23
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 4089c06f94f3967bfafab4fe30ecd009c6ae5f1d https://github.com/cdk/cdk/commit/4089c06f94f3967bfafab4fe30ecd009c6ae5f1d Author: Egon Willighagen <ego...@gm...> Date: 2026-03-14 (Sat, 14 Mar 2026) Changed paths: M README.md Log Message: ----------- Bumped the year To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-13 11:05:18
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Branch: refs/heads/configure Home: https://github.com/cdk/cdk Commit: 0fc086f4e11e36087dea086b66dc308897e9224c https://github.com/cdk/cdk/commit/0fc086f4e11e36087dea086b66dc308897e9224c Author: John Mayfield <jo...@ne...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionPBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java M base/reaction/src/test/java/org/openscience/cdk/atomtype/ReactionStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java M base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java M base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherSMILESTest.java M base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AtomTypeModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/DaylightModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/ExocyclicAtomTypeModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/PiBondModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/geometry/volume/VABCVolumeTest.java M base/test-standard/src/test/java/org/openscience/cdk/isomorphism/IsomorphismTesterTest.java M base/test-standard/src/test/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/HOSECodeGeneratorTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/LonePairElectronCheckerTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/RingSetManipulatorTest.java M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/EStateFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/MACCSFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/PubchemFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizerTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/LingoSimilarityTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/TanimotoTest.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptorTest.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/JPlogPDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/DescriptorNamesTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AtomTyperTests.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/JPlogPDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptorTest.java M descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java M legacy/src/main/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java M legacy/src/main/java/org/openscience/cdk/iupac/parser/MoleculeBuilder.java M legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java M legacy/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptor.java M legacy/src/main/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptor.java M legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java M legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java M legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java M legacy/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCS.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/MolHandler.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/MoleculeSanityCheck.java M legacy/src/main/java/org/openscience/cdk/tools/CDKUtilities.java M legacy/src/test/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java M legacy/src/test/java/org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetectorTest.java M legacy/src/test/java/org/openscience/cdk/normalize/SMSDNormalizerTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/RecursiveTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandlerTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/Molecules.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFLibTest.java M legacy/src/test/java/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java M legacy/src/test/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulatorTest.java M legacy/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java M legacy/src/test/java/org/openscience/cdk/tools/IonizationPotentialToolTest.java M misc/extra/src/main/java/org/openscience/cdk/tools/SugarRemovalUtility.java M misc/extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/SugarRemovalUtilityTest.java M storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java M storage/io/src/test/java/org/openscience/cdk/io/Mol2WriterTest.java M storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CML2WriterTest.java M storage/pdb/src/main/java/org/openscience/cdk/templates/AminoAcids.java M storage/smiles/src/test/java/org/openscience/cdk/io/SMILES2Mol2WriterTest.java M storage/smiles/src/test/java/org/openscience/cdk/io/SMILESWriterTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PiElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/StabilizationChargesTest.java M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java M tool/fragment/src/main/java/org/openscience/cdk/fragment/FunctionalGroupsFinder.java M tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/FunctionalGroupsFinderTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java M tool/hash/src/test/java/org/openscience/cdk/hash/HashCodeScenariosTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/VicinitySamplerTest.java M tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java Log Message: ----------- Move all usages over from percieveAtomTypesAndConfigureAtoms[ConfigureUnsetProperties]() to [re]configure(). Some minor changes were needed: - to QSAR Bond as the hydrogen count is now set so we need to roll this back. - reaction mechanisms needed to wipe the hydrogen count to ensure correct atom typing - because we do not throw and exception we need to check the return value sometimes and then throw (i.e. in QSAR) To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-13 11:03:55
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Branch: refs/heads/configure Home: https://github.com/cdk/cdk Commit: 50176d9b2863f78ad7ef2dd2bd574b3e9d607a84 https://github.com/cdk/cdk/commit/50176d9b2863f78ad7ef2dd2bd574b3e9d607a84 Author: John Mayfield <jo...@ne...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java M base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java M legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java Log Message: ----------- Add a new configure method to replace the (misspelt) percieveAtomTypesAndConfigure(UnsetProperties)(). Commit: d4b832aa9346ebebe165d2fadbc96177ac81085c https://github.com/cdk/cdk/commit/d4b832aa9346ebebe165d2fadbc96177ac81085c Author: John Mayfield <jo...@ne...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionPBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java M base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java M base/reaction/src/test/java/org/openscience/cdk/atomtype/ReactionStructuresTest.java M base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java M base/reaction/src/test/java/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java M base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java M base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherSMILESTest.java M base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AtomTypeModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/DaylightModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/ExocyclicAtomTypeModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/PiBondModelTest.java M base/test-standard/src/test/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/geometry/volume/VABCVolumeTest.java M base/test-standard/src/test/java/org/openscience/cdk/isomorphism/IsomorphismTesterTest.java M base/test-standard/src/test/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/HOSECodeGeneratorTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/LonePairElectronCheckerTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java M base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/RingSetManipulatorTest.java M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/EStateFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/MACCSFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/PubchemFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizerTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/LingoSimilarityTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/TanimotoTest.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java M descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptorTest.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java M descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/JPlogPDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/DescriptorNamesTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AtomTyperTests.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/JPlogPDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptorTest.java M descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptorTest.java M descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java M legacy/src/main/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java M legacy/src/main/java/org/openscience/cdk/iupac/parser/MoleculeBuilder.java M legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java M legacy/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptor.java M legacy/src/main/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptor.java M legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java M legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java M legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java M legacy/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCS.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/MolHandler.java M legacy/src/main/java/org/openscience/cdk/smsd/tools/MoleculeSanityCheck.java M legacy/src/main/java/org/openscience/cdk/tools/CDKUtilities.java M legacy/src/test/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java M legacy/src/test/java/org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetectorTest.java M legacy/src/test/java/org/openscience/cdk/normalize/SMSDNormalizerTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java M legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/RecursiveTest.java M legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandlerTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSTest.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/Molecules.java M legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFLibTest.java M legacy/src/test/java/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java M legacy/src/test/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulatorTest.java M legacy/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java M legacy/src/test/java/org/openscience/cdk/tools/IonizationPotentialToolTest.java M misc/extra/src/main/java/org/openscience/cdk/tools/SugarRemovalUtility.java M misc/extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java M misc/extra/src/test/java/org/openscience/cdk/tools/SugarRemovalUtilityTest.java M storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java M storage/io/src/test/java/org/openscience/cdk/io/Mol2WriterTest.java M storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CML2WriterTest.java M storage/pdb/src/main/java/org/openscience/cdk/templates/AminoAcids.java M storage/smiles/src/test/java/org/openscience/cdk/io/SMILES2Mol2WriterTest.java M storage/smiles/src/test/java/org/openscience/cdk/io/SMILESWriterTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java M tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/PiElectronegativityTest.java M tool/charges/src/test/java/org/openscience/cdk/charges/StabilizationChargesTest.java M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java M tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java M tool/fragment/src/main/java/org/openscience/cdk/fragment/FunctionalGroupsFinder.java M tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/FunctionalGroupsFinderTest.java M tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java M tool/group/src/test/java/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java M tool/group/src/test/java/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java M tool/hash/src/test/java/org/openscience/cdk/hash/HashCodeScenariosTest.java M tool/structgen/src/test/java/org/openscience/cdk/structgen/VicinitySamplerTest.java M tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java Log Message: ----------- Move all usages over from percieveAtomTypesAndConfigureAtoms[ConfigureUnsetProperties]() to [re]configure(). Some minor changes were needed: - to QSAR Bond as the hydrogen count is now set so we need to roll this back. - reaction mechanisms needed to wipe the hydrogen count to ensure correct atom typing Compare: https://github.com/cdk/cdk/compare/a8f68071000a...d4b832aa9346 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-13 09:09:36
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Branch: refs/heads/configure Home: https://github.com/cdk/cdk Commit: a8f68071000ad42fb209a1aa93f3a8c4bf651801 https://github.com/cdk/cdk/commit/a8f68071000ad42fb209a1aa93f3a8c4bf651801 Author: John Mayfield <jo...@ne...> Date: 2026-03-13 (Fri, 13 Mar 2026) Changed paths: M base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java M base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java Log Message: ----------- Add a new configure method to replace the (misspelt) percieveAtomTypesAndConfigure(UnsetProperties)(). To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-12 07:59:23
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Branch: refs/heads/3.0 Home: https://github.com/cdk/cdk Commit: 8e65828c41b0267dfc299b7a7fc54493948acf36 https://github.com/cdk/cdk/commit/8e65828c41b0267dfc299b7a7fc54493948acf36 Author: John Mayfield <jo...@ne...> Date: 2026-03-12 (Thu, 12 Mar 2026) Changed paths: M .github/workflows/maven.yml M pom.xml M storage/io/src/main/java/org/openscience/cdk/io/XYZWriter.java Log Message: ----------- Move to Java 21, there was a single regression where FormatStringBuilder.toString() was somehow no longer called. We can explicitly call toString or better we switch to a StringBuilder. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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From: John M. <no...@gi...> - 2026-03-12 07:58:54
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Branch: refs/heads/reduce-cdktestcase Home: https://github.com/cdk/cdk To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
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