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From: John M. <no...@gi...> - 2024-05-05 12:39:19
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 031ba966e2cf2551197e09324ea272957e1942b2 https://github.com/cdk/cdk/commit/031ba966e2cf2551197e09324ea272957e1942b2 Author: John Mayfield <jo...@ne...> Date: 2024-05-05 (Sun, 05 May 2024) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java Log Message: ----------- Increase the max fragment count when generating abbreviations. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-05-03 09:01:10
|
Branch: refs/heads/abbr-max-frag Home: https://github.com/cdk/cdk Commit: 8018990a7fba162e385cdf52661d0fcf212ec457 https://github.com/cdk/cdk/commit/8018990a7fba162e385cdf52661d0fcf212ec457 Author: John Mayfield <jo...@ne...> Date: 2024-05-03 (Fri, 03 May 2024) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java Log Message: ----------- Increase the max fragment count when generating abbreviations. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-04-22 08:02:01
|
Branch: refs/heads/pubchemfp-params Home: https://github.com/cdk/cdk Commit: 373659f900c22f7efb1ad213722865484da760e0 https://github.com/cdk/cdk/commit/373659f900c22f7efb1ad213722865484da760e0 Author: John Mayfield <jo...@ne...> Date: 2024-04-22 (Mon, 22 Apr 2024) Changed paths: M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java Log Message: ----------- Ensure the ESSSR parameter is reported in the FP version info. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-04-10 18:54:17
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 2b453c55598a63928d7b9780097902936c5941aa https://github.com/cdk/cdk/commit/2b453c55598a63928d7b9780097902936c5941aa Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: 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/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java A storage/ctab/src/test/resources/org/openscience/cdk/io/pubchem_paracetamol.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/pubchem_paracetamol_delimnoise.mol A storage/ctab/src/test/resources/org/openscience/cdk/io/pubchem_paracetamol_nodelim.mol Log Message: ----------- Read in SDfile properties from single V3000 files to be consistent with V2000. We also make sure we are consistent with the $$$$ handling and enforce it must only "start with" this tag. Commit: 3f34e5a34a612652b573e160715c63448a3ffef9 https://github.com/cdk/cdk/commit/3f34e5a34a612652b573e160715c63448a3ffef9 Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java Log Message: ----------- Now the V2000/V3000 read the SD properties we can simplify the IteratingSdfReader. Commit: ce72a79148af2ce6aee3c85ebc6dd34d727cbb8c https://github.com/cdk/cdk/commit/ce72a79148af2ce6aee3c85ebc6dd34d727cbb8c Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/test/resources/org/openscience/cdk/io/pubchem_paracetamol.mol M storage/ctab/src/test/resources/org/openscience/cdk/io/pubchem_paracetamol_nodelim.mol Log Message: ----------- Missed changes for test files. Commit: 5c301c92bd8592ee915a1b2e8d575a848485071a https://github.com/cdk/cdk/commit/5c301c92bd8592ee915a1b2e8d575a848485071a Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java Log Message: ----------- Null check needed for reaction (RXN) readers - should probably also read the properties there as well. Commit: cb74c6ff8c51d68aa451f18afc316fd4120e8e56 https://github.com/cdk/cdk/commit/cb74c6ff8c51d68aa451f18afc316fd4120e8e56 Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java Log Message: ----------- Cleaner Iterating SDF loop Commit: 0d01aeb7659ff2dc126161488b7ea5bdaf728c09 https://github.com/cdk/cdk/commit/0d01aeb7659ff2dc126161488b7ea5bdaf728c09 Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java Log Message: ----------- Move the writing of non-structural data to the V2000 writer. Commit: 575c50e7def8bcffadcbfd7ebfb3618141c1c97e https://github.com/cdk/cdk/commit/575c50e7def8bcffadcbfd7ebfb3618141c1c97e Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java M storage/ctab/src/test/java/org/openscience/cdk/io/SDFWriterTest.java Log Message: ----------- Options to write out the SD tags from the V2000/V3000 writer. Commit: c47141ce78ca6b146969b824a281759e30ab2154 https://github.com/cdk/cdk/commit/c47141ce78ca6b146969b824a281759e30ab2154 Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/io/ChemObjectIO.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java Log Message: ----------- Clean up how option overiding works, when we add a single setting we should check if it already exists. This allows the base V2000/3000 writers to not emit SD tags by default, but when they are used in the SDWriter then they can emit the tags Commit: bbdafb43d4df0f63511d1160dff41812e52542ae https://github.com/cdk/cdk/commit/bbdafb43d4df0f63511d1160dff41812e52542ae Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java M storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java Log Message: ----------- Code Smell: Variable renaming. Commit: 01d7ab0ea4f5f0f590b42cbb2c45e32e2cf41066 https://github.com/cdk/cdk/commit/01d7ab0ea4f5f0f590b42cbb2c45e32e2cf41066 Author: John Mayfield <jo...@ne...> Date: 2024-04-10 (Wed, 10 Apr 2024) Changed paths: M storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java M storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java Log Message: ----------- Additional code smells - unused functions. Compare: https://github.com/cdk/cdk/compare/99548a9001ab...01d7ab0ea4f5 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-04-04 11:36:18
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 99548a9001ab0be1c5ad437d802f511b91d74210 https://github.com/cdk/cdk/commit/99548a9001ab0be1c5ad437d802f511b91d74210 Author: Egon Willighagen <ego...@gm...> Date: 2024-04-04 (Thu, 04 Apr 2024) Changed paths: M README.md Log Message: ----------- List the latest release To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-21 14:42:26
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 6f66c39a1b1bfde41d9a104ffbf3d6ce2cca7f83 https://github.com/cdk/cdk/commit/6f66c39a1b1bfde41d9a104ffbf3d6ce2cca7f83 Author: Jonas Schaub <448...@us...> Date: 2024-03-21 (Thu, 21 Mar 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java Log Message: ----------- small doc fix for cdkAllowingExocyclic() Commit: 904c8f6093794b6de1114876f191eeb021923118 https://github.com/cdk/cdk/commit/904c8f6093794b6de1114876f191eeb021923118 Author: John Mayfield <jo...@ne...> Date: 2024-03-21 (Thu, 21 Mar 2024) Changed paths: M base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java Log Message: ----------- Merge pull request #1060 from JonasSchaub/ElectronDonation-small-doc-fix small doc fix for cdkAllowingExocyclic() Compare: https://github.com/cdk/cdk/compare/267f3b67efe5...904c8f609379 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-15 20:48:13
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 267f3b67efe554d1ffbfb308514ef04141e9f0be https://github.com/cdk/cdk/commit/267f3b67efe554d1ffbfb308514ef04141e9f0be Author: John Mayfield <jo...@ne...> Date: 2024-03-15 (Fri, 15 Mar 2024) Changed paths: M display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java Log Message: ----------- Fix a corner case when depicting cc(C)c To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-15 14:47:19
|
Branch: refs/heads/fix-1057 Home: https://github.com/cdk/cdk Commit: a650de99cd77a259e2e5b3a78943196e22b3350d https://github.com/cdk/cdk/commit/a650de99cd77a259e2e5b3a78943196e22b3350d Author: John Mayfield <jo...@ne...> Date: 2024-03-15 (Fri, 15 Mar 2024) Changed paths: M display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java Log Message: ----------- Fix a corner case when depicting cc(C)c To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-11 08:39:17
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 2ca780210fcde16796a8dcc3123e5df9dae4ea59 https://github.com/cdk/cdk/commit/2ca780210fcde16796a8dcc3123e5df9dae4ea59 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: A CITATION.cff Log Message: ----------- Create CITATION.cff Commit: c5572eecca16eded598f803259e36372137e3cf2 https://github.com/cdk/cdk/commit/c5572eecca16eded598f803259e36372137e3cf2 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-11 (Mon, 11 Mar 2024) Changed paths: M CITATION.cff Log Message: ----------- Applied suggested changes - preferred-citation is now an object Commit: bb49c4520acf046d964185dcadb311ae5066d8a4 https://github.com/cdk/cdk/commit/bb49c4520acf046d964185dcadb311ae5066d8a4 Author: John Mayfield <jo...@ne...> Date: 2024-03-11 (Mon, 11 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Merge branch 'main' into update/CITATION.cff Commit: 16f6bc2eb6a84b19a75be7c0284c3ef46a3c7a3a https://github.com/cdk/cdk/commit/16f6bc2eb6a84b19a75be7c0284c3ef46a3c7a3a Author: John Mayfield <jo...@ne...> Date: 2024-03-11 (Mon, 11 Mar 2024) Changed paths: A CITATION.cff Log Message: ----------- Merge pull request #1055 from cdk/update/CITATION.cff Create CITATION.cff Compare: https://github.com/cdk/cdk/compare/9ccb3b19ba30...16f6bc2eb6a8 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-11 08:38:57
|
Branch: refs/heads/update/CITATION.cff Home: https://github.com/cdk/cdk Commit: cda2eb39298d6bb489507203719511d27429e738 https://github.com/cdk/cdk/commit/cda2eb39298d6bb489507203719511d27429e738 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Updated JNA-InChI (updating the JNA dependency) Commit: 9ccb3b19ba3090ff2997e9d4730099124a256698 https://github.com/cdk/cdk/commit/9ccb3b19ba3090ff2997e9d4730099124a256698 Author: John Mayfield <jo...@ne...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Merge pull request #1054 from egonw/update/jna-inchi Updated JNA-InChI (JNA compatibility) Commit: bb49c4520acf046d964185dcadb311ae5066d8a4 https://github.com/cdk/cdk/commit/bb49c4520acf046d964185dcadb311ae5066d8a4 Author: John Mayfield <jo...@ne...> Date: 2024-03-11 (Mon, 11 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Merge branch 'main' into update/CITATION.cff Compare: https://github.com/cdk/cdk/compare/c5572eecca16...bb49c4520acf To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-03-11 08:31:26
|
Branch: refs/heads/update/CITATION.cff Home: https://github.com/cdk/cdk Commit: c5572eecca16eded598f803259e36372137e3cf2 https://github.com/cdk/cdk/commit/c5572eecca16eded598f803259e36372137e3cf2 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-11 (Mon, 11 Mar 2024) Changed paths: M CITATION.cff Log Message: ----------- Applied suggested changes - preferred-citation is now an object To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-10 21:17:17
|
Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: cda2eb39298d6bb489507203719511d27429e738 https://github.com/cdk/cdk/commit/cda2eb39298d6bb489507203719511d27429e738 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Updated JNA-InChI (updating the JNA dependency) Commit: 9ccb3b19ba3090ff2997e9d4730099124a256698 https://github.com/cdk/cdk/commit/9ccb3b19ba3090ff2997e9d4730099124a256698 Author: John Mayfield <jo...@ne...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M storage/inchi/pom.xml Log Message: ----------- Merge pull request #1054 from egonw/update/jna-inchi Updated JNA-InChI (JNA compatibility) Compare: https://github.com/cdk/cdk/compare/8d039b0b5217...9ccb3b19ba30 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: Egon W. <no...@gi...> - 2024-03-10 18:51:29
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Branch: refs/heads/update/CITATION.cff Home: https://github.com/cdk/cdk Commit: 2ca780210fcde16796a8dcc3123e5df9dae4ea59 https://github.com/cdk/cdk/commit/2ca780210fcde16796a8dcc3123e5df9dae4ea59 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: A CITATION.cff Log Message: ----------- Create CITATION.cff To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-10 08:58:40
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 8b15a8fdf289717a0f74d4841c93ebe3bba47abc https://github.com/cdk/cdk/commit/8b15a8fdf289717a0f74d4841c93ebe3bba47abc Author: Uli Fechner <ma...@ul...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- added test case for initial cycles oom Commit: 1bb187266dec18598a64827fa6651b589b1635f7 https://github.com/cdk/cdk/commit/1bb187266dec18598a64827fa6651b589b1635f7 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Added the catching and exception of the Intractable exception Commit: 8d039b0b521759a956a551ed114e28a95e34b888 https://github.com/cdk/cdk/commit/8d039b0b521759a956a551ed114e28a95e34b888 Author: John Mayfield <jo...@ne...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Add missing import Compare: https://github.com/cdk/cdk/compare/635049017b1c...8d039b0b5217 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-10 07:04:57
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Branch: refs/heads/binconnected 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...> - 2024-03-10 07:03:39
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Branch: refs/heads/relavent-cycles-limit-test Home: https://github.com/cdk/cdk Commit: 58f50f6532bf09aaa32a78a12f5265fef1e409a1 https://github.com/cdk/cdk/commit/58f50f6532bf09aaa32a78a12f5265fef1e409a1 Author: Uli Fechner <ma...@ul...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- added test case for initial cycles oom Commit: bdcab397b6e2ebe50e0699df0bbea8f3d75673c1 https://github.com/cdk/cdk/commit/bdcab397b6e2ebe50e0699df0bbea8f3d75673c1 Author: Egon Willighagen <ego...@gm...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Added the catching and exception of the Intractable exception Commit: 5506b39d3af6b8a8c19f3e17db0b0dbadd06d3e1 https://github.com/cdk/cdk/commit/5506b39d3af6b8a8c19f3e17db0b0dbadd06d3e1 Author: John Mayfield <jo...@ne...> Date: 2024-03-10 (Sun, 10 Mar 2024) Changed paths: M base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java Log Message: ----------- Add missing import Compare: https://github.com/cdk/cdk/compare/58f50f6532bf%5E...5506b39d3af6 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-09 13:03:08
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 635049017b1c15f83f259d70ded690f3d611b36d https://github.com/cdk/cdk/commit/635049017b1c15f83f259d70ded690f3d611b36d Author: John Mayfield <jo...@ne...> Date: 2024-03-09 (Sat, 09 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- The number of essential/relevant cycles can be exponential for some molecules - e.g. cyclo-phanes. We know how many there are before generating them so we can et a reasonable limit which just fails if this limit is reached. This limit can be configured by a system property. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-09 08:57:46
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Branch: refs/heads/relavent-cycles-limit Home: https://github.com/cdk/cdk Commit: 02a7fdb4e666718a5a83fac16524eb91e6e5b9fd https://github.com/cdk/cdk/commit/02a7fdb4e666718a5a83fac16524eb91e6e5b9fd Author: John Mayfield <jo...@ne...> Date: 2024-03-09 (Sat, 09 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- The number of essential/relevant cycles can be exponential for some molecules - e.g. cyclo-phanes. We know how many there are before generating them so we can et a reasonable limit which just fails if this limit is reached. This limit can be configured by a system property. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-09 08:56:18
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Branch: refs/heads/relavent-cycles-limit Home: https://github.com/cdk/cdk Commit: 29828f985cae8b0db33d6795348df895d4d34f24 https://github.com/cdk/cdk/commit/29828f985cae8b0db33d6795348df895d4d34f24 Author: John Mayfield <jo...@ne...> Date: 2024-03-09 (Sat, 09 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- use a logger rather than System Error To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-09 08:38:45
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Branch: refs/heads/relavent-cycles-limit Home: https://github.com/cdk/cdk Commit: d4949f583882a195c3e1050d014bb01e15c303c0 https://github.com/cdk/cdk/commit/d4949f583882a195c3e1050d014bb01e15c303c0 Author: John Mayfield <jo...@ne...> Date: 2024-03-09 (Sat, 09 Mar 2024) Changed paths: M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java Log Message: ----------- The number of essential/relevant cycles can be exponential for some molecules - e.g. cyclo-phanes. We know how many there are before generating them so we can et a reasonable limit which just fails if this limit is reached. This limit can be configured by a system property. To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-09 08:38:18
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Branch: refs/heads/relavent-cycles-limit 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...> - 2024-03-06 14:37:43
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Branch: refs/heads/main Home: https://github.com/cdk/cdk Commit: 19f18c2e1374eb18a1f8af56338362d427aa491b https://github.com/cdk/cdk/commit/19f18c2e1374eb18a1f8af56338362d427aa491b Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java A base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java A tool/smarts/src/main/java/org/openscience/cdk/smirks/BinaryExprValue.java A tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java A tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksTransform.java A tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add transform/SMIRKS support to CDK. This patch provides the generic/low-level data structures and representations to describe a molecular transform. A conveient way of describing transforms is the SMIRKS syntax which is supported via functionality in the 'cdk-smarts' module. Transforms are useful for standardisation, library generation, and retro synthesis. Commit: 101f7f901ad9efdfca89f15364ffd83b360c0671 https://github.com/cdk/cdk/commit/101f7f901ad9efdfca89f15364ffd83b360c0671 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- SonarCloud suggestions. - Fix SonarCloud "bug", which IntelliJ now warns about since the brackets are redundant. - IAtom.C => IElement.C - Add missing assertion - LOGGER instead of print to STDERR Commit: fff2eddb16013aaec3d960096dac2cda5f966d14 https://github.com/cdk/cdk/commit/fff2eddb16013aaec3d960096dac2cda5f966d14 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java Log Message: ----------- Correct bond index Commit: 5fb76939e4039b6a9fbfb0f5c56d40fe7d5008bd https://github.com/cdk/cdk/commit/5fb76939e4039b6a9fbfb0f5c56d40fe7d5008bd Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java Log Message: ----------- Remove stray print, allready got a debug here Commit: ec03ad5d7eff28b0e958d09c900557016fed7893 https://github.com/cdk/cdk/commit/ec03ad5d7eff28b0e958d09c900557016fed7893 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Fix an issue with beg/end ordering when pairing up bonds. Commit: 1e53c60a438d25d2dc74e6980419b71ffe9973fe https://github.com/cdk/cdk/commit/1e53c60a438d25d2dc74e6980419b71ffe9973fe Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Removed unused field, we deletage to the SmartsPattern. Commit: b09a5a4cc1769e850cbae34db9f0ccb7c64b96a5 https://github.com/cdk/cdk/commit/b09a5a4cc1769e850cbae34db9f0ccb7c64b96a5 Author: Uli Fechner <ma...@ul...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- added two test cases; reverted system.err to logger output; commented out some other system.err; removed unused local variables Commit: f8d0e194f86bcca599ad37fb8026693bc293b85f https://github.com/cdk/cdk/commit/f8d0e194f86bcca599ad37fb8026693bc293b85f Author: Uli Fechner <ma...@ul...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- added more test cases Commit: cd1209b109b731520c8be85ad1e142328810993a https://github.com/cdk/cdk/commit/cd1209b109b731520c8be85ad1e142328810993a Author: Uli Fechner <ma...@ul...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- added convenient method to SmirksTest to assert different Transform.Mode modes; added more test cases Commit: 2f79272296b6b7327005ec1266159e778d569baf https://github.com/cdk/cdk/commit/2f79272296b6b7327005ec1266159e778d569baf Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksTransform.java Log Message: ----------- Remove unused field (aromaticity) Commit: 2ab548c505ee2e8854aebc0c1a84bd4fd3871553 https://github.com/cdk/cdk/commit/2ab548c505ee2e8854aebc0c1a84bd4fd3871553 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Ensure a deep copy of the molecule occurs for iterative mapping modes. Commit: 645bd6f4a02f0bba6eedb9104c1f5c3a3824d230 https://github.com/cdk/cdk/commit/645bd6f4a02f0bba6eedb9104c1f5c3a3824d230 Author: Uli Fechner <ma...@ul...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- added more test cases Commit: 1f6aa3f6d74a3c4a5d71dde303acf003a10a99f9 https://github.com/cdk/cdk/commit/1f6aa3f6d74a3c4a5d71dde303acf003a10a99f9 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java Log Message: ----------- Make the results list unmodifiable, in future we will return an iterator. Commit: 13d21f13fb28f5d83a8d40a34c7ed36acd2e7d02 https://github.com/cdk/cdk/commit/13d21f13fb28f5d83a8d40a34c7ed36acd2e7d02 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Improved some corner cases w.r.t atom maps and warnings. Commit: 6780d3c2a2bd33eb29d19cef5d67ac5b67681445 https://github.com/cdk/cdk/commit/6780d3c2a2bd33eb29d19cef5d67ac5b67681445 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Better aromaticity semantics and warn on dubious patterns with an aromatic bond between aliphatic atoms. Some tests need to be adjusted since the patterns were not quite correct. Commit: 1ff8710bb483cec5a1b19b719680616e45095fda https://github.com/cdk/cdk/commit/1ff8710bb483cec5a1b19b719680616e45095fda Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java Log Message: ----------- Make sure AromaticBond gets printed. Commit: 11a1aeb8e9650507a26a42a590efb2e8650694e4 https://github.com/cdk/cdk/commit/11a1aeb8e9650507a26a42a590efb2e8650694e4 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Improved assertion error to show what the generated output was. Commit: 3e08c12104d34b4eb7a371579dcc9676932f23c2 https://github.com/cdk/cdk/commit/3e08c12104d34b4eb7a371579dcc9676932f23c2 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add a test case for "Retro-Wittig Like" Commit: b58eb455048830a56c891fa0b05de12a28aa8e04 https://github.com/cdk/cdk/commit/b58eb455048830a56c891fa0b05de12a28aa8e04 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Improved aromatic handling based on bond context. Fail if the pattern could be defined better. Commit: b03418dfcdc56df402920861cf9c501044669e77 https://github.com/cdk/cdk/commit/b03418dfcdc56df402920861cf9c501044669e77 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Fix an ordering issue in the op codes, we need a better comparator so this is a band aid for now. Commit: 2c4e7f57c6a14253fd2bc04250156c68d891a93f https://github.com/cdk/cdk/commit/2c4e7f57c6a14253fd2bc04250156c68d891a93f Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Another test case. Commit: 20813515a2014aed758bfb03eec28bdc168af5a1 https://github.com/cdk/cdk/commit/20813515a2014aed758bfb03eec28bdc168af5a1 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- AromaticBond implies aromatic atoms, aliphatic bond does not imply aliphatic atoms. Commit: 4344e50729cb8ead08deca42d4debffbc5be999a https://github.com/cdk/cdk/commit/4344e50729cb8ead08deca42d4debffbc5be999a Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java Log Message: ----------- When we optimize our op-codes (replace-atom) we need to remap the atom numbers in other op-codes. Commit: 95ab42db7e8c8e9af553a3cbd8c6b72492f7d260 https://github.com/cdk/cdk/commit/95ab42db7e8c8e9af553a3cbd8c6b72492f7d260 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add in the charge test Commit: b8ab4b4deb2cf140db0d3f220dcc3c54b639de73 https://github.com/cdk/cdk/commit/b8ab4b4deb2cf140db0d3f220dcc3c54b639de73 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add a failing test to remind us to fix something. Commit: 71c7bc4b7f1ac09e4784c91f65bcdb984a577c7f https://github.com/cdk/cdk/commit/71c7bc4b7f1ac09e4784c91f65bcdb984a577c7f Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Correct these two aromatic SMIKRS patterns, we may want to keep the originals for compatibility mode testing. Commit: 564d05c9e37799c736859a8e22c610700a1874a4 https://github.com/cdk/cdk/commit/564d05c9e37799c736859a8e22c610700a1874a4 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Another iffy aromatic pattern. Commit: 62de3665b5d8648505a1f745f5887177589a7c51 https://github.com/cdk/cdk/commit/62de3665b5d8648505a1f745f5887177589a7c51 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- New op: PromoteH to handle the case where we need to possible move and create an explicit H in the product. Commit: e2bc13962995e681ad1ee8a9af4f9d8555f8e9af https://github.com/cdk/cdk/commit/e2bc13962995e681ad1ee8a9af4f9d8555f8e9af Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Various code cleanup Commit: 30a36056f22a4ca743b769c12124337e3291c665 https://github.com/cdk/cdk/commit/30a36056f22a4ca743b769c12124337e3291c665 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Cleanup recommended by SonarCloud. Commit: fdc816c16dc04006f07695eb76713e6a80d5b965 https://github.com/cdk/cdk/commit/fdc816c16dc04006f07695eb76713e6a80d5b965 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Improve op-code test coverage, normally the delete atom/bond gets optimized so we need specific cases to test those op-codes. Commit: f870d27c1bf498de2ab29cf958bc64da78ded1e0 https://github.com/cdk/cdk/commit/f870d27c1bf498de2ab29cf958bc64da78ded1e0 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- SonarCloud - damn'd if you do damn'd if you don't Commit: 2902bf8106bf89072a962cc3f7ab85c34fcc604c https://github.com/cdk/cdk/commit/2902bf8106bf89072a962cc3f7ab85c34fcc604c Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Only call resyncStereo() once (after all ops have been applied) and make sure reactive centre gets marked correctly. These two tests are nice tests which should keep stereo but currently don't. Commit: d857a3edf64a003bfe204c25cd11dea57eb5a220 https://github.com/cdk/cdk/commit/d857a3edf64a003bfe204c25cd11dea57eb5a220 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java Log Message: ----------- Make the Unique/All application of transforms lazy with an iterator. Commit: 564e2a7c32bfd50df92f109a60dfe85992e79081 https://github.com/cdk/cdk/commit/564e2a7c32bfd50df92f109a60dfe85992e79081 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Lazy transforms and the ability to limit the number of matches. Commit: ff7f4beadf3ca271552f7f808b46eb779ec9d0af https://github.com/cdk/cdk/commit/ff7f4beadf3ca271552f7f808b46eb779ec9d0af Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Some extra test coverage. Commit: f7e3fce498d876034a61ca169242f255e0345d8c https://github.com/cdk/cdk/commit/f7e3fce498d876034a61ca169242f255e0345d8c Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: A base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformOpTest.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Additional unit tests Commit: f337a55cb0814c202d868b8ff9df834711e63e90 https://github.com/cdk/cdk/commit/f337a55cb0814c202d868b8ff9df834711e63e90 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Distinction between total vs implicit hydrogen count, fix default valences for new atoms. Commit: aed14fb8547ef52320602fa2ced7ead6af6b0638 https://github.com/cdk/cdk/commit/aed14fb8547ef52320602fa2ced7ead6af6b0638 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java M tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsResult.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Track atom/bond indexes from input SMARTS allowing better warning/error messages. Commit: 614f1f3cf57873c10549753dfccad421571287b8 https://github.com/cdk/cdk/commit/614f1f3cf57873c10549753dfccad421571287b8 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Make sure bond position arrays grow correctly. Use ORDER=1 for UP/DOWN stereobonds, this makes it possible for SMIRKS to avoid the warning. Some tweaks are needed to SMARTS writing. Commit: 81ddf6008e2473cbc9042c6a4b17350c75e03585 https://github.com/cdk/cdk/commit/81ddf6008e2473cbc9042c6a4b17350c75e03585 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- If we can't work out the bond order, make a guess (if possible). In strict/pedantic mode this will warn/fail. Commit: f708aeb516773d4a249745c6812a4c656fb3c5ab https://github.com/cdk/cdk/commit/f708aeb516773d4a249745c6812a4c656fb3c5ab Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Improved (but complicated) stereochemistry handling, there is likely a better abstraction to keep things more sane. Commit: 0102b0ded5609bfc216e0afda3868e5f96f86ca4 https://github.com/cdk/cdk/commit/0102b0ded5609bfc216e0afda3868e5f96f86ca4 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java Log Message: ----------- This temporary field should be private. Commit: 970edd3ccd2353697a8f9ede8e47dab2a32f2a9a https://github.com/cdk/cdk/commit/970edd3ccd2353697a8f9ede8e47dab2a32f2a9a Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java A tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksOption.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add in SMIRKS options, currently just a PEDANTIC mode which does additional checks. The valence checking is a WIP but the basics are there. Commit: ca4df6d7d875007e14126929f5727b4f33c30bd9 https://github.com/cdk/cdk/commit/ca4df6d7d875007e14126929f5727b4f33c30bd9 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Tweaks to our valence checking, store the "old" bond order in the BondOrder op-code. Commit: 945094e005cd4de0e786463f176bfe91ae664803 https://github.com/cdk/cdk/commit/945094e005cd4de0e786463f176bfe91ae664803 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Cleaner if condition for PEDANTIC erorr checking Commit: 7862a44135c0a0dd86562db9fb84e0511f8d1ff4 https://github.com/cdk/cdk/commit/7862a44135c0a0dd86562db9fb84e0511f8d1ff4 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Valence check only when pedantic. Commit: 91fb80863e546112dff51e626097be440b6900ff https://github.com/cdk/cdk/commit/91fb80863e546112dff51e626097be440b6900ff Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- The warning message changed. Commit: 9eb4c384754b0c4df4cd110b6a179bbed0e43195 https://github.com/cdk/cdk/commit/9eb4c384754b0c4df4cd110b6a179bbed0e43195 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksOption.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Allow reactions to be run backwards. Commit: 33c0a5e89ab8be58346ab935feb41f5dbf96ebf3 https://github.com/cdk/cdk/commit/33c0a5e89ab8be58346ab935feb41f5dbf96ebf3 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/BinaryExprValue.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksOption.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Preliminary work on some SMIRKS options and mimicking other implementations. Commit: bf68a5107aec09c77b78647e1700d683efbe5d85 https://github.com/cdk/cdk/commit/bf68a5107aec09c77b78647e1700d683efbe5d85 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Make sure the bonds are ordered correctly when setting DB stereo. Commit: dfded2b0227eb18c90741557ff3bb82dc7c96627 https://github.com/cdk/cdk/commit/dfded2b0227eb18c90741557ff3bb82dc7c96627 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksOption.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add the option to remove unmapped parts of a transformed molecule. Commit: 803214fd8171dd67923880bc320f6fe47e369835 https://github.com/cdk/cdk/commit/803214fd8171dd67923880bc320f6fe47e369835 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: 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 tool/smarts/pom.xml M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksOption.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Add in the option to recompute hydrogens. Commit: 7091ee49aa28ebc1d9a0b384d345f7319a3c2568 https://github.com/cdk/cdk/commit/7091ee49aa28ebc1d9a0b384d345f7319a3c2568 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- Make sure we fail currently on bond order unknown. Commit: ed3165e6c353266fb6f0b4405b1001781c857c32 https://github.com/cdk/cdk/commit/ed3165e6c353266fb6f0b4405b1001781c857c32 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Ensure correct error handling when not processing bonds. Commit: 68b4522c9cf8dde0a2add96208624982c61c941b https://github.com/cdk/cdk/commit/68b4522c9cf8dde0a2add96208624982c61c941b Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/data/src/main/java/org/openscience/cdk/AtomContainer.java M base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java Log Message: ----------- Fix an error mesg in the AtomContainer implementation Commit: fc5ea0cd288af89c080fb6c581bcfd63d9d264a8 https://github.com/cdk/cdk/commit/fc5ea0cd288af89c080fb6c581bcfd63d9d264a8 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Warning message changed Commit: 8739237fc6ce6cd0a81a8cfc7364862e8059761b https://github.com/cdk/cdk/commit/8739237fc6ce6cd0a81a8cfc7364862e8059761b Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Reinstate test which is fine but not perfect. Commit: 95a9f7d8f2c25b33b7c8f28d21211bcbeaa271b3 https://github.com/cdk/cdk/commit/95a9f7d8f2c25b33b7c8f28d21211bcbeaa271b3 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Tests are all now enabled. Commit: 16fdf19d40af67bd423314ff8058fa64cc2af8ac https://github.com/cdk/cdk/commit/16fdf19d40af67bd423314ff8058fa64cc2af8ac Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksTransform.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Address some SonarCloud issues Commit: f4948cd682c859d5df0d7e47430ee7e7ec0f946c https://github.com/cdk/cdk/commit/f4948cd682c859d5df0d7e47430ee7e7ec0f946c Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java Log Message: ----------- Fix test value Commit: 2af6236fd9873b1b489bdc4f4385d14654d9a5bf https://github.com/cdk/cdk/commit/2af6236fd9873b1b489bdc4f4385d14654d9a5bf Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- SonarCloud complains if the capturing groups are removed (Group parts of the regex together). Compare: https://github.com/cdk/cdk/compare/a0b6c7a983c0...2af6236fd987 To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-06 12:27:32
|
Branch: refs/heads/smirks Home: https://github.com/cdk/cdk Commit: 148ed985fdd0b25dea274ce73635f06118b82606 https://github.com/cdk/cdk/commit/148ed985fdd0b25dea274ce73635f06118b82606 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java Log Message: ----------- SonarCloud complains if the capturing groups are removed (Group parts of the regex together). To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-06 11:32:19
|
Branch: refs/heads/smirks Home: https://github.com/cdk/cdk Commit: dc8be8572c7df01692f0cf70c01d269caf4fc8f8 https://github.com/cdk/cdk/commit/dc8be8572c7df01692f0cf70c01d269caf4fc8f8 Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java Log Message: ----------- Fix test value To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |
From: John M. <no...@gi...> - 2024-03-06 11:07:13
|
Branch: refs/heads/smirks Home: https://github.com/cdk/cdk Commit: d66fe1bcba618ed2e1db577441c35ab140470bdc https://github.com/cdk/cdk/commit/d66fe1bcba618ed2e1db577441c35ab140470bdc Author: John Mayfield <jo...@ne...> Date: 2024-03-06 (Wed, 06 Mar 2024) Changed paths: M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/TransformTest.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java M tool/smarts/src/main/java/org/openscience/cdk/smirks/SmirksTransform.java M tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java Log Message: ----------- Address some SonarCloud issues To unsubscribe from these emails, change your notification settings at https://github.com/cdk/cdk/settings/notifications |