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From: Egon W. <no...@gi...> - 2024-07-14 12:19:09
|
Branch: refs/heads/cdk2024/wp1/testing5 Home: https://github.com/cdk/cdk Commit: 68ba5387866371b81935277e7e6935c11005e5d1 https://github.com/cdk/cdk/commit/68ba5387866371b81935277e7e6935c11005e5d1 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-14 (Sun, 14 Jul 2024) Changed paths: M base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactoryTest.java Log Message: ----------- Removed the redundant 'public' qualifier To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-07-14 12:05:17
|
Branch: refs/heads/cdk2024/wp1/testing5 Home: https://github.com/cdk/cdk Commit: eaaec8e582258a8fd79e1288b8139d3760c5189f https://github.com/cdk/cdk/commit/eaaec8e582258a8fd79e1288b8139d3760c5189f Author: Egon Willighagen <ego...@gm...> Date: 2024-07-14 (Sun, 14 Jul 2024) Changed paths: M base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractIsotopeTest.java Log Message: ----------- Test the output of additional isotope info Commit: bdf563f29464596783a083cd5d2936a2c67ced97 https://github.com/cdk/cdk/commit/bdf563f29464596783a083cd5d2936a2c67ced97 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-14 (Sun, 14 Jul 2024) Changed paths: A base/data/src/test/java/org/openscience/cdk/templates/TestMoleculeFactoryTest.java Log Message: ----------- Added a test class to check methods not tested otherwise (in this module) Commit: e28079b1d93f269b11f0b4b0f84c43dc0121d45d https://github.com/cdk/cdk/commit/e28079b1d93f269b11f0b4b0f84c43dc0121d45d Author: Egon Willighagen <ego...@gm...> Date: 2024-07-14 (Sun, 14 Jul 2024) Changed paths: M base/data/src/test/java/org/openscience/cdk/DefaultChemObjectBuilderTest.java Log Message: ----------- Added more builder methods Commit: 73192fdf33d00a7dc14be84067a171e5ef2e1181 https://github.com/cdk/cdk/commit/73192fdf33d00a7dc14be84067a171e5ef2e1181 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-14 (Sun, 14 Jul 2024) Changed paths: M base/silent/src/test/java/org/openscience/cdk/silent/SilentChemObjectBuilderTest.java Log Message: ----------- Added more builder methods Compare: https://github.com/cdk/cdk/compare/eaaec8e58225%5E...73192fdf33d0 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-07-13 16:27:22
|
Branch: refs/heads/cdk2024/wp1/testing4 Home: https://github.com/cdk/cdk Commit: 4eac8c6c6ff10d433338116d2d13f60545968a51 https://github.com/cdk/cdk/commit/4eac8c6c6ff10d433338116d2d13f60545968a51 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensTest.java Log Message: ----------- Also create and add the hydrogen Commit: 5d7650da60629f56e81a9a8fa5e84a2b9409dfce https://github.com/cdk/cdk/commit/5d7650da60629f56e81a9a8fa5e84a2b9409dfce Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensTest.java Log Message: ----------- Add atoms before bonds to hydrogens are created Commit: 1c23e4dd47f4fbee9ab65403ef0bffbb447f8a6d https://github.com/cdk/cdk/commit/1c23e4dd47f4fbee9ab65403ef0bffbb447f8a6d Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensTest.java Log Message: ----------- Use the cleaner newAtom() API Compare: https://github.com/cdk/cdk/compare/af49a64d7f3e...1c23e4dd47f4 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-07-13 15:59:46
|
Branch: refs/heads/cdk2024/wp1/testing4 Home: https://github.com/cdk/cdk Commit: 7aac699c228df0be11a81533706defb1c0da5909 https://github.com/cdk/cdk/commit/7aac699c228df0be11a81533706defb1c0da5909 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java Log Message: ----------- Cleaner code by newer API Commit: af49a64d7f3ec83ff8a49d0f827a4ee87e5429db https://github.com/cdk/cdk/commit/af49a64d7f3ec83ff8a49d0f827a4ee87e5429db Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: R base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogens.java A base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensTest.java Log Message: ----------- Renamed so that the test is actually run (and it fails) Compare: https://github.com/cdk/cdk/compare/06fec5705874...af49a64d7f3e To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-07-13 15:34:19
|
Branch: refs/heads/cdk2024/wp1/testing3 Home: https://github.com/cdk/cdk Commit: 8221a911dc32ecf9d967fc80785392d0284d7877 https://github.com/cdk/cdk/commit/8221a911dc32ecf9d967fc80785392d0284d7877 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-core/src/test/java/org/openscience/cdk/CDKConstantsTest.java Log Message: ----------- Use interfaces instead of instances and use silent To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-07-13 14:54:36
|
Branch: refs/heads/cdk2024/wp1/testing4 Home: https://github.com/cdk/cdk Commit: a7f2400262391c1f1ce209640c34f1ebf117053c https://github.com/cdk/cdk/commit/a7f2400262391c1f1ce209640c34f1ebf117053c Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/pom.xml M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogens.java Log Message: ----------- Remove explicit use of 'data' classes Commit: 11f93533b1faf30de8322e81cb76c76f70b877a1 https://github.com/cdk/cdk/commit/11f93533b1faf30de8322e81cb76c76f70b877a1 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/SaturationCheckerTest.java Log Message: ----------- setUp is not a test Commit: 8259df90f3639198166967cd4236cc73bdbf22a7 https://github.com/cdk/cdk/commit/8259df90f3639198166967cd4236cc73bdbf22a7 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/SaturationCheckerTest.java Log Message: ----------- There is no exception thrown Commit: 06fec57058743de058370e92069b961c4f3ad7d8 https://github.com/cdk/cdk/commit/06fec57058743de058370e92069b961c4f3ad7d8 Author: Egon Willighagen <ego...@gm...> Date: 2024-07-13 (Sat, 13 Jul 2024) Changed paths: M base/test-valencycheck/src/test/java/org/openscience/cdk/tools/SaturationCheckerTest.java Log Message: ----------- Better assertion Compare: https://github.com/cdk/cdk/compare/a7f240026239%5E...06fec5705874 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 19:22:10
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: fe02761e5854fc2fd0a1163a65e8074768f9cf15 https://github.com/cdk/cdk/commit/fe02761e5854fc2fd0a1163a65e8074768f9cf15 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsPattern.java Log Message: ----------- Actually use the new smart "requires" flag. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 19:18:23
|
Branch: refs/heads/sd-tautomer Home: https://github.com/cdk/cdk Commit: 63d7c2ba5e5f6eb7f1768e6ae4f4726a214d1c31 https://github.com/cdk/cdk/commit/63d7c2ba5e5f6eb7f1768e6ae4f4726a214d1c31 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java M storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java M storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java Log Message: ----------- Beam improvements. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 19:18:07
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: 71d2d9802c28f08419dc21eb16732cd50d74c798 https://github.com/cdk/cdk/commit/71d2d9802c28f08419dc21eb16732cd50d74c798 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsPattern.java Log Message: ----------- Aromaticity is no longer needed here Commit: 8da8ab502fdb345c559e18a8f9225d8c76c0d187 https://github.com/cdk/cdk/commit/8da8ab502fdb345c559e18a8f9225d8c76c0d187 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsPattern.java M tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsPatternTest.java Log Message: ----------- Smarter SmartsPattern - only do the ring/arom finding if the query actually needs it. Compare: https://github.com/cdk/cdk/compare/5409fcc2ee71...8da8ab502fdb To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 18:49:23
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: 5409fcc2ee7125dd800310ef1f4f40bdafeca51b https://github.com/cdk/cdk/commit/5409fcc2ee7125dd800310ef1f4f40bdafeca51b Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java Log Message: ----------- Fix some code smells. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 10:22:54
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: 660acd8e8097be1895f18911e0f7822bf6a0ea75 https://github.com/cdk/cdk/commit/660acd8e8097be1895f18911e0f7822bf6a0ea75 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Make sure aromatic flags are always cleared. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 10:12:00
|
Branch: refs/heads/cdk-arom-atom-type 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...> - 2024-07-10 10:11:04
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: aaeb8a5ae113bdf452148e7c39e5fac05d415309 https://github.com/cdk/cdk/commit/aaeb8a5ae113bdf452148e7c39e5fac05d415309 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticType.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java A base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.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 tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsPattern.java Log Message: ----------- Overhaul and optimise the aromaticity procedures in CDK. 1. The ElectronDontation models now no longer requires a RingSearch instance and instead use the ring flags on atom/bonds, this avoid doing twice the work if we already have done the ring perception. 2. Models/calling of the aromaticity varied but a good set of cycles was Cycles.or(Cycles.all(), Cycles.all(6)) which meant "try all cycles or fall back and only do small cycles (up to size 6). We now do this by default but in reverse. Check small cycles first and only then if there is more work to do we check longer cycles. This is now done internally with a backtracking searching. Intractability is checked with a state counter and the return value rather than an exception. An exception is still thrown on the existing API ``apply(mol)``. If the user provides Cycles.all() we detect this and use the backtracking search. 3. Add a new configurable aromaticity type model. This more efficient model does the aromatic atom type on-the-fly and returns an Enum type. Thought was given to make this a fully fledged AtomTypeMatcher but it would require returning/implementing IAtomType instances which is too heavy weight for this use case. Also for now the model is keep package-private. Overall this gives us a ~5x performance improvement. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 10:10:48
|
Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: be34f0c8afec5a555791c4b91482f2023f4ecf9f https://github.com/cdk/cdk/commit/be34f0c8afec5a555791c4b91482f2023f4ecf9f Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java Log Message: ----------- Fixup To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 09:40:40
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Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: 6724d5fa8fe45b720ea06f5df99c26baa2d9599f https://github.com/cdk/cdk/commit/6724d5fa8fe45b720ea06f5df99c26baa2d9599f Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticType.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java A base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.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 tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsPattern.java Log Message: ----------- Overhaul and optimise the aromaticity procedures in CDK. 1. The ElectronDontation models now no longer requires a RingSearch instance and instead use the ring flags on atom/bonds, this avoid doing twice the work if we already have done the ring perception. 2. Models/calling of the aromaticity varied but a good set of cycles was Cycles.or(Cycles.all(), Cycles.all(6)) which meant "try all cycles or fall back and only do small cycles (up to size 6). We now do this by default but in reverse. Check small cycles first and only then if there is more work to do we check longer cycles. This is now done internally with a backtracking searching. Intractability is checked with a state counter and the return value rather than an exception. An exception is still thrown on the existing API ``apply(mol)``. If the user provides Cycles.all() we detect this and use the backtracking search. 3. Add a new configurable aromaticity type model. This more efficient model does the aromatic atom type on-the-fly and returns an Enum type. Thought was given to make this a fully fledged AtomTypeMatcher but it would require returning/implementing IAtomType instances which is too heavy weight for this use case. Also for now the model is keep package-private. Overall this gives us a ~5x performance improvement. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-10 09:11:47
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Branch: refs/heads/aromaticity-new Home: https://github.com/cdk/cdk Commit: 6fba40adca5ac801d2c79032f4b590c24c6ae1a9 https://github.com/cdk/cdk/commit/6fba40adca5ac801d2c79032f4b590c24c6ae1a9 Author: John Mayfield <jo...@ne...> Date: 2024-03-05 (Tue, 05 Mar 2024) Changed paths: A base/core/src/main/java/org/openscience/cdk/graph/BiconnectedComponents.java M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- More efficient determination of ring flags/count. Commit: 4d2cfab1aa3f21b1b4924e31f5b67f22681683f9 https://github.com/cdk/cdk/commit/4d2cfab1aa3f21b1b4924e31f5b67f22681683f9 Author: John Mayfield <jo...@ne...> Date: 2024-03-05 (Tue, 05 Mar 2024) Changed paths: M base/test-core/src/test/java/org/openscience/cdk/graph/CyclesTest.java Log Message: ----------- Some unit tests for the marking of ring/atoms bonds. Commit: f5cf1ef44df8e1b39a5d0924969b617080ed4606 https://github.com/cdk/cdk/commit/f5cf1ef44df8e1b39a5d0924969b617080ed4606 Author: John Mayfield <jo...@ne...> Date: 2024-03-05 (Tue, 05 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- Deprecate the method that took in the GraphUtil/EdgeMap cache Commit: e8961174f7668d82aac9f5b94763f81169837cf6 https://github.com/cdk/cdk/commit/e8961174f7668d82aac9f5b94763f81169837cf6 Author: John Mayfield <jo...@ne...> Date: 2024-03-05 (Tue, 05 Mar 2024) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- Actually deprecate. Commit: 6d682c52c13f480d3dcea7aa29a977ccd6ddc785 https://github.com/cdk/cdk/commit/6d682c52c13f480d3dcea7aa29a977ccd6ddc785 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: A base/core/src/main/java/org/openscience/cdk/atomtype/AromaticAtomTyper.java A base/core/src/main/java/org/openscience/cdk/atomtype/AromaticType.java Log Message: ----------- Faster aromaticity Commit: 690055f2b9e36b1a5d9972c4fe0c21a53f7d21f0 https://github.com/cdk/cdk/commit/690055f2b9e36b1a5d9972c4fe0c21a53f7d21f0 Author: John Mayfield <jo...@ne...> Date: 2024-03-09 (Sat, 09 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/atomtype/AromaticAtomTyper.java M base/core/src/main/java/org/openscience/cdk/atomtype/AromaticType.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java A base/test-core/src/test/java/org/openscience/cdk/atomtype/AromaticAtomTyperTest.java Log Message: ----------- WIP Commit: 12faf51c809d23e0a740d91f97b73aaf9755bb5c https://github.com/cdk/cdk/commit/12faf51c809d23e0a740d91f97b73aaf9755bb5c Author: John Mayfield <jo...@ne...> Date: 2024-03-13 (Wed, 13 Mar 2024) Changed paths: R base/core/src/main/java/org/openscience/cdk/atomtype/AromaticAtomTyper.java R base/core/src/main/java/org/openscience/cdk/atomtype/AromaticType.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticType.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java A base/test-core/src/test/java/org/openscience/cdk/atomtype/AromTyperTest.java R base/test-core/src/test/java/org/openscience/cdk/atomtype/AromaticAtomTyperTest.java A base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.java A base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityIntegrationTest.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 A base/test-standard/src/test/java/org/openscience/cdk/aromaticity/GenerateAromTypeModels.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/PiBondModelTest.java A base/test-standard/src/test/resources/org/openscience/cdk/aromaticity/arom_examples.smi Log Message: ----------- WIP Commit: a26429b507f7cafad473eb631cb472c78b27005e https://github.com/cdk/cdk/commit/a26429b507f7cafad473eb631cb472c78b27005e Author: John Mayfield <jo...@ne...> Date: 2024-03-15 (Fri, 15 Mar 2024) Changed paths: 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/aromaticity/Aromaticity.java A base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticityAllPaths.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityIntegrationTest.java Log Message: ----------- Updating aromaticity Commit: 76cd9737897a2ab8ea9d49207d4f9e49dc806f63 https://github.com/cdk/cdk/commit/76cd9737897a2ab8ea9d49207d4f9e49dc806f63 Author: John Mayfield <jo...@ne...> Date: 2024-07-07 (Sun, 07 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Fixup Commit: de964fd372d0823c168912d5979c4d17c24e96a3 https://github.com/cdk/cdk/commit/de964fd372d0823c168912d5979c4d17c24e96a3 Author: John Mayfield <jo...@ne...> Date: 2024-07-09 (Tue, 09 Jul 2024) Changed paths: 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/aromaticity/Aromaticity.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityIntegrationTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Cleanup the new implementation Commit: e363cf5fa7eeefc4115c8df9d06d8666df9d63c9 https://github.com/cdk/cdk/commit/e363cf5fa7eeefc4115c8df9d06d8666df9d63c9 Author: John Mayfield <jo...@ne...> Date: 2024-07-10 (Wed, 10 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java R base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityIntegrationTest.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Finalize improved aromaticity Compare: https://github.com/cdk/cdk/compare/6fba40adca5a%5E...e363cf5fa7ee To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-09 15:26:14
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 5777492dafb6c63d23f9b65f9121a88c5fa45786 https://github.com/cdk/cdk/commit/5777492dafb6c63d23f9b65f9121a88c5fa45786 Author: John Mayfield <jo...@ne...> Date: 2024-07-09 (Tue, 09 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AtomTypeModelTest.java Log Message: ----------- Stabilise the CDK atom type based aromaticity model. This causes a small fraction of ChEMBL to change but overall is actually a bit close to the Daylight aromatic model. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-09 11:51:59
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Branch: refs/heads/cdk-arom-atom-type Home: https://github.com/cdk/cdk Commit: 51983aa88cd2cbf0c042f263dea6d04414cca6d4 https://github.com/cdk/cdk/commit/51983aa88cd2cbf0c042f263dea6d04414cca6d4 Author: John Mayfield <jo...@ne...> Date: 2024-07-09 (Tue, 09 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AtomTypeModelTest.java Log Message: ----------- Stabilise the CDK atom type based aromaticity model. This causes a small fraction of ChEMBL to change but overall is actually a bit close to the Daylight aromatic model. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-08 10:36:33
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Branch: refs/heads/sd-tautomer Home: https://github.com/cdk/cdk Commit: 0f24cf73752cf082a4d5c2b107e900fa8cda185b https://github.com/cdk/cdk/commit/0f24cf73752cf082a4d5c2b107e900fa8cda185b Author: John Mayfield <jo...@ne...> Date: 2024-07-08 (Mon, 08 Jul 2024) Changed paths: M tool/tautomer/src/test/java/org/openscience/cdk/tautomer/TautomersTest.java Log Message: ----------- Test the identity return To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-08 10:36:05
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Branch: refs/heads/sd-tautomer Home: https://github.com/cdk/cdk Commit: 6afc540bff4dbbe240727f6981fc158ceaacca07 https://github.com/cdk/cdk/commit/6afc540bff4dbbe240727f6981fc158ceaacca07 Author: John Mayfield <jo...@ne...> Date: 2024-07-08 (Mon, 08 Jul 2024) Changed paths: M tool/tautomer/src/main/java/org/openscience/cdk/tautomer/SayleDelanyState.java M tool/tautomer/src/main/java/org/openscience/cdk/tautomer/Tautomers.java Log Message: ----------- Always return the input molecule when there are no tautomeric atom types. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-08 10:15:05
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Branch: refs/heads/sd-tautomer Home: https://github.com/cdk/cdk Commit: 393b2fd9b9de2ee494d459ffa63af7ad6d7f8b79 https://github.com/cdk/cdk/commit/393b2fd9b9de2ee494d459ffa63af7ad6d7f8b79 Author: John Mayfield <jo...@ne...> Date: 2024-07-08 (Mon, 08 Jul 2024) Changed paths: A tool/tautomer/src/main/java/org/openscience/cdk/tautomer/AtomTypeMatcher.java R tool/tautomer/src/main/java/org/openscience/cdk/tautomer/BasicRoleTyper.java R tool/tautomer/src/main/java/org/openscience/cdk/tautomer/Role.java R tool/tautomer/src/main/java/org/openscience/cdk/tautomer/SDTautomerState.java R tool/tautomer/src/main/java/org/openscience/cdk/tautomer/SDTautomerStream.java A tool/tautomer/src/main/java/org/openscience/cdk/tautomer/SayleDelanyState.java A tool/tautomer/src/main/java/org/openscience/cdk/tautomer/Tautomers.java R tool/tautomer/src/test/java/org/openscience/cdk/tautomer/SDTautomerStreamTest.java A tool/tautomer/src/test/java/org/openscience/cdk/tautomer/SayleDelanyStateTest.java A tool/tautomer/src/test/java/org/openscience/cdk/tautomer/TautomersTest.java Log Message: ----------- Cleanup the API and add more tests To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-07-05 19:39:09
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 38e7a206c51a623667530276a2bb07c9c5f4f44d https://github.com/cdk/cdk/commit/38e7a206c51a623667530276a2bb07c9c5f4f44d Author: John Mayfield <jo...@ne...> Date: 2024-07-05 (Fri, 05 Jul 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java M base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java Log Message: ----------- Update the fingerprint documentation to reflect the improved behaviour. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-06-28 13:24:17
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: edd9333a4a1a44fb3f8086851eb9de934f61c58d https://github.com/cdk/cdk/commit/edd9333a4a1a44fb3f8086851eb9de934f61c58d Author: John Mayfield <jo...@ne...> Date: 2024-06-28 (Fri, 28 Jun 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ExtendedFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java Log Message: ----------- The path based fingerprint should be identical with/without explicit hydrogens. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-06-28 11:09:57
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Branch: refs/heads/hydrogen-rep-fps Home: https://github.com/cdk/cdk Commit: a97b204d3d2872de2bbfa43e4638d8ec1b7d04a5 https://github.com/cdk/cdk/commit/a97b204d3d2872de2bbfa43e4638d8ec1b7d04a5 Author: John Mayfield <jo...@ne...> Date: 2024-06-28 (Fri, 28 Jun 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ExtendedFingerprinterTest.java M descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java Log Message: ----------- The path based fingerprint should be identical with/without explicit hydrogens. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-06-27 21:09:00
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 5e2d601b882a9351d677fce246098b05a5fd9633 https://github.com/cdk/cdk/commit/5e2d601b882a9351d677fce246098b05a5fd9633 Author: Egon Willighagen <ego...@gm...> Date: 2024-06-27 (Thu, 27 Jun 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java M descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java M legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java M storage/io/src/main/java/org/openscience/cdk/io/XYZReader.java M storage/io/src/main/java/org/openscience/cdk/io/program/GaussianInputWriter.java M storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java M tool/charges/src/main/java/org/openscience/cdk/charges/AtomTypeCharges.java M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java M tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReaderTest.java M tool/hash/src/test/java/org/openscience/cdk/hash/BasicAtomEncoderTest.java Log Message: ----------- Replaced deprecated API calls (cherry picked from commit 9a48d3d5552edae4044a67d5a42d17a8c9114438) To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |