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SimilarityMapsInCPP_Jan2014

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appveyor_tuning

build-documentation-update-for-c++17

dev/azure-windows-update

dev/build_java_win64

dev/support-azure-pipelines

dev/version-in-windows-dlls

feat/mol_interchange_options

fix/free-wilson-complicated-scaffolds

github8918

legacy/master

master

modern_cxx

revert-7217-docs_preview_builds

revert-7301-noCoordsAtropisomers

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templates_update_1e107fb

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2014_09_1beta1

2020_03_3

CanonicalizationPaper_Aug2015

KnimeNodes_2.4.0_Binary

KnimeNodes_Dec2014_Binary

KnimeNodes_Feb2015_Binary

Release_2010_09_1

Release_2010_12_1

Release_2010_12_1beta1

Release_2010_12_1beta3

Release_2011_03_1

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Release_2012_06_1beta1

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Release_test_for_zenodo

inactive/premodern_master

Mono Color

• cda1b1df2f Fixes #8997 (#9060) Greg Landrum 2026-01-29 18:49:21 +01:00
• 86902488e9 Store CIP-ranked anchors after CIP labeling. (#9056) Ricardo Rodriguez 2026-01-29 12:23:44 -05:00
• 2ae0a75a25 Handle chiral atoms with 2 hydrogens in SCSR parser (#8939) tadhurst-cdd 2026-01-29 01:08:14 -06:00
• d3d4170e7c CXSMILES: do not add separators for unserializable Substance Groups (#9048) Ricardo Rodriguez 2026-01-27 06:35:18 -05:00
• e598f608fe Transform::SetRotationFromQuaternion takes const. (#9063) David Cosgrove 2026-01-24 06:18:41 +00:00
• d4641c1f58 Fix removing (non)redundant bond dir specs when exporting SMILES (#9066) Ricardo Rodriguez 2026-01-24 01:15:00 -05:00
• 21225e63b3 Move some more tests over to catch2 (#9058) Greg Landrum 2026-01-24 07:03:04 +01:00
• 163dd42d4c implement hasPrimaryLabel (#9052) Ricardo Rodriguez 2026-01-19 08:53:03 -05:00
• e5989aa446 Fix deprecated literal operators and macro redefinition warnings for modern compilers (#9055) Chris Von Bargen 2026-01-19 02:14:52 -05:00
• c8f274f0d3 Update deprecation messages for valence methods (#9050) Philip Ullmann 2026-01-19 08:12:53 +01:00
• 14c66817ea added FABS to test for issue #4364 (#9053) tadhurst-cdd 2026-01-19 01:10:15 -06:00
• 4b92c2fa8c Performance improvement: Implement buffered reading for SDMolSupplier (#9010) Raul Sofia 2026-01-10 17:29:56 +00:00
• 658a1af8b2 Read SD property names till the last '>' (#9047) Ricardo Rodriguez 2026-01-09 05:23:26 +01:00
• 7dec637a3f MolAlign: brace-init BestAlignmentParams in wrapper (#9042) Yakov Pechersky 2026-01-08 01:31:22 -05:00
• 9558cb8114 Check for correctly sized propertylists to avoid dropping molecules (#8921) Brian Kelley 2026-01-08 00:08:54 -05:00
• cef43e8aef In verbose output, check that the query molecule exists before using it. (#9040) David Cosgrove 2026-01-08 05:06:52 +00:00
• da08e8d954 Allow molzip to position fragments when joining them (#9021) Greg Landrum 2026-01-07 16:33:03 +01:00
• e0f3ada0d7 Fixes #9033 (#9036) Greg Landrum 2026-01-03 06:42:29 +01:00
• f8b6776af1 Fixes #9020 (#9025) Greg Landrum 2026-01-03 06:42:09 +01:00
• 2dda19d0ee Improve POPCNT optimization flag handling (#9029) wszqkzqk 2026-01-02 13:18:06 +08:00
• 9b69dd2a40 release notes and version bump Release_2025_09_4 Greg Landrum 2025-12-30 07:55:07 +01:00
• 4a007d4a7a Github9007 (#9022) David Cosgrove 2025-12-29 20:08:10 +00:00
• 7293070a49 Better solid triangles (#8943) David Cosgrove 2025-11-18 08:47:24 +00:00
• edbb86d1b3 atropisomer bond atoms are checked explicitly for SP2 hybridization (#8974) Yakov Pechersky 2025-12-29 12:04:40 -05:00
• 374d3a8143 Allow spaces and special chars in SCSR fullname attrs (#8982) tadhurst-cdd 2025-12-29 10:54:56 -06:00
• b381491432 Some more cleaning up in SMILES Writing (#8991) Ricardo Rodriguez 2025-12-29 07:00:45 +01:00
• 13c603990f Support serializing/deserializing FP generators to JSON (#9000) Greg Landrum 2025-12-24 19:09:05 +01:00
• 288a3ff919 Fixes #9014 (#9016) Ricardo Rodriguez 2025-12-23 06:43:05 +01:00
• 9201881de6 move molzip to its own file (#9013) Greg Landrum 2025-12-22 16:42:23 +01:00
• 3677e70af0 Convert testMolSupplier to catch2 (#9015) Ricardo Rodriguez 2025-12-22 07:33:36 +01:00
• af710afed7 Fix sulfonamide SMARTS in fragment descriptors. (#9019) Kevin Boyd 2025-12-22 01:23:33 -05:00
• b81004602a Fixes Github9009 (#9012) David Cosgrove 2025-12-22 05:26:23 +00:00
• 4c3a8ccfd0 Shape overlay initial start aligned to principal axes (#8999) David Cosgrove 2025-12-20 07:35:28 +00:00
• 1c0d063278 A bunch of modernization of the ShapeHelpers code (#8954) Greg Landrum 2025-12-15 21:49:00 +01:00
• 2bcb51c510 Last leak fixes for 2025! (#9006) Ricardo Rodriguez 2025-12-13 14:22:59 -05:00
• 0199b62742 convert smiTest1 to catch (#9004) Ricardo Rodriguez 2025-12-13 14:21:00 -05:00
• afd5601e56 rename test, convert to catch (#9003) Ricardo Rodriguez 2025-12-13 14:18:40 -05:00
• a323d6ce9d Stop writing so many atom properties to cxsmiles (#9002) Greg Landrum 2025-12-13 04:35:57 +01:00
• 1ca7215ee8 Allow adding custom atom and bond matcher functions for substructure searching (#8994) Greg Landrum 2025-12-12 20:03:31 +01:00
• deeb9727fc Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization (#8972) Ricardo Rodriguez 2025-12-12 08:07:26 -05:00
• 08d9b42574 Small fix in ring stereo/canonicalization (#8962) Ricardo Rodriguez 2025-12-12 07:56:01 -05:00
• 48e1fc2b8d Add extract mol fragment api (#8811) Brian Kelley 2025-12-09 09:06:29 -05:00
• c86a691a4d Improve DetermineBonds and DetermineBondOrders performance (#8888) Chi Cheng 2025-12-08 05:17:41 +00:00
• 63f514455f Allow Hs to be ignored in the RMSD alignment functions (#8976) Greg Landrum 2025-12-04 18:37:59 +01:00
• c69a20d9f6 strip whitespace from embedParametersToJSON() (#8989) Greg Landrum 2025-12-04 06:57:08 +01:00
• 896b6e8f1e Minor clean up in SMILES Writing double bond canonicalization (#8971) Ricardo Rodriguez 2025-12-03 11:38:56 -05:00
• a79d21e8e4 some optimizations of AlignPoints() (#8987) Greg Landrum 2025-12-03 16:59:11 +01:00
• d7cc6b67bf Convert graphmolMolOpsTest to catch2 (#8978) Ricardo Rodriguez 2025-12-03 00:28:56 -05:00
• 1193d84047 allow h removal to be skipped in ShowFeats.py (#8986) Greg Landrum 2025-12-02 17:14:21 +01:00
• 3bc08f39de Embed Parameters to JSON (#8977) Niels Maeder 2025-11-29 05:19:44 +01:00
• 8ef091f306 Github9007 (#9022) David Cosgrove 2025-12-29 20:08:10 +00:00
• 08552e56b1 atropisomer bond atoms are checked explicitly for SP2 hybridization (#8974) Yakov Pechersky 2025-12-29 12:04:40 -05:00
• 0f03609221 Allow spaces and special chars in SCSR fullname attrs (#8982) tadhurst-cdd 2025-12-29 10:54:56 -06:00
• 1c16a91730 Some more cleaning up in SMILES Writing (#8991) Ricardo Rodriguez 2025-12-29 07:00:45 +01:00
• b4164ea2f2 Support serializing/deserializing FP generators to JSON (#9000) Greg Landrum 2025-12-24 19:09:05 +01:00
• 47f2b7c1b5 Fixes #9014 (#9016) Ricardo Rodriguez 2025-12-23 06:43:05 +01:00
• d6cf5c4a01 move molzip to its own file (#9013) Greg Landrum 2025-12-22 16:42:23 +01:00
• 2921deb254 Convert testMolSupplier to catch2 (#9015) Ricardo Rodriguez 2025-12-22 07:33:36 +01:00
• 69b731650d Fix sulfonamide SMARTS in fragment descriptors. (#9019) Kevin Boyd 2025-12-22 01:23:33 -05:00
• 4883485ac5 Fixes Github9009 (#9012) David Cosgrove 2025-12-22 05:26:23 +00:00
• 21b3c4e6f1 Shape overlay initial start aligned to principal axes (#8999) David Cosgrove 2025-12-20 07:35:28 +00:00
• dc84967df2 A bunch of modernization of the ShapeHelpers code (#8954) Greg Landrum 2025-12-15 21:49:00 +01:00
• 9160ef8943 Last leak fixes for 2025! (#9006) Ricardo Rodriguez 2025-12-13 14:22:59 -05:00
• fa68ea2ef2 convert smiTest1 to catch (#9004) Ricardo Rodriguez 2025-12-13 14:21:00 -05:00
• 7c2a6f4a3b rename test, convert to catch (#9003) Ricardo Rodriguez 2025-12-13 14:18:40 -05:00
• c2e48f41d8 Stop writing so many atom properties to cxsmiles (#9002) Greg Landrum 2025-12-13 04:35:57 +01:00
• ef90a4bedf Allow adding custom atom and bond matcher functions for substructure searching (#8994) Greg Landrum 2025-12-12 20:03:31 +01:00
• b6655a136d Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization (#8972) Ricardo Rodriguez 2025-12-12 08:07:26 -05:00
• e786ca231d Stop using raw pointers in the canonicalization interface (#8990) Greg Landrum 2025-12-12 14:00:23 +01:00
• a8a00a1d99 Small fix in ring stereo/canonicalization (#8962) Ricardo Rodriguez 2025-12-12 07:56:01 -05:00
• 70540c2eed Add extract mol fragment api (#8811) Brian Kelley 2025-12-09 09:06:29 -05:00
• 2d25752fe0 Improve DetermineBonds and DetermineBondOrders performance (#8888) Chi Cheng 2025-12-08 05:17:41 +00:00
• 436ecbebac Allow Hs to be ignored in the RMSD alignment functions (#8976) Greg Landrum 2025-12-04 18:37:59 +01:00
• af4e6c05ec strip whitespace from embedParametersToJSON() (#8989) Greg Landrum 2025-12-04 06:57:08 +01:00
• 39c4083bbf Minor clean up in SMILES Writing double bond canonicalization (#8971) Ricardo Rodriguez 2025-12-03 11:38:56 -05:00
• 6e331accc0 some optimizations of AlignPoints() (#8987) Greg Landrum 2025-12-03 16:59:11 +01:00
• 22a9814655 Convert graphmolMolOpsTest to catch2 (#8978) Ricardo Rodriguez 2025-12-03 00:28:56 -05:00
• 9e073b8dd6 allow h removal to be skipped in ShowFeats.py (#8986) Greg Landrum 2025-12-02 17:14:21 +01:00
• bc4fffda7b Embed Parameters to JSON (#8977) Niels Maeder 2025-11-29 05:19:44 +01:00
• 4ef6ad1c62 [bot] Update molecular templates header templates_update_3d944c0 github-actions[bot] 2025-11-29 01:43:05 +00:00
• fd677c59b2 tag release Release_2025_09_3 greg landrum 2025-11-28 04:56:43 +01:00
• abfddf2a79 add more benchmarking (#8878) Andrew Dirksen 2025-11-27 05:25:57 -08:00
• 12b16e56ff stop ignoring confId in CalcMolDescriptors3D() (#8967) Greg Landrum 2025-11-27 13:11:11 +01:00
• 1232f08187 Valence error in scsr temlates for nitro and metal complexes (#8969) tadhurst-cdd 2025-11-27 06:10:01 -06:00
• 84ab326f3c count stereo features (#8963) Ricardo Rodriguez 2025-11-23 01:15:30 -05:00
• 1da163da0d Modern stereo: fix stereo inversion in rings (#8957) Rachel Walker 2025-11-20 22:50:16 -08:00
• a3854088fb Add test to watch the state of canonicalization problems reported in #8775 (#8958) Ricardo Rodriguez 2025-11-20 13:21:06 -05:00
• fb9e4237df Feat/flat matrix utils (#8955) Niels Maeder 2025-11-20 15:10:25 +01:00
• 9e7a88e68c Python Bond Inversion (#8951) paconius 2025-11-18 23:54:04 -05:00
• b13e703d1f Add function to compute shape scores without overlay. (#8950) David Cosgrove 2025-11-19 16:02:38 +00:00
• 65830d2b4c Do not add a __computedProps property to molecules when initializing them (#8931) Greg Landrum 2025-11-19 01:09:36 +01:00
• 136e128d95 Fix for issue with deprecated boost functions for MacOS build from source (#8929) Rachael Pirie 2025-11-18 16:15:28 +00:00
• 29e9f76a65 Valence error when parsing SCSR (#8948) tadhurst-cdd 2025-11-18 10:09:04 -06:00
• f66ffac70b remove rapidjson patch file (#8953) Greg Landrum 2025-11-18 17:02:53 +01:00
• ae74774799 yaehmop version bump (#8952) Greg Landrum 2025-11-18 17:02:04 +01:00
• 02f0226d6e Fixes #8945 (#8946) Greg Landrum 2025-11-13 15:18:03 +01:00
• 44cc1e0d55 Fixed Typo in Getting Started Docs (#8947) PatrickPenner 2025-11-13 05:21:48 +00:00
• d03f8cbe50 Make incremental search callback take ownership of mols (#8940) Justin Gullingsrud 2025-11-11 11:10:29 -05:00
• ff6b3b29b5 Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available (#8924) Phong Lam 2025-11-11 17:05:30 +01:00
• 764b3b8c3e Fix potential iterator invalidation (#8944) Max Rietmann 2025-11-11 17:03:05 +01:00