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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

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inactive/premodern_master

Mono Color

• a3b2e50ad3 A collection of small improvements from Roger S (#7566) Greg Landrum 2024-06-26 08:29:57 +02:00
• df0224fb7d Fixes #7552 (#7564) Greg Landrum 2024-06-26 04:42:33 +02:00
• c0eaba0c3f ConfGen: fix a logic error in one of the chiral volume tests (#7560) Greg Landrum 2024-06-26 04:41:07 +02:00
• 99288ff988 fix one case of undesired 1-3 charge recombination (#7561) Riccardo Vianello 2024-06-25 15:44:36 +02:00
• 724716b2c6 Switch to isoelectronic valence model (#7491) Greg Landrum 2024-06-25 15:38:49 +02:00
• 806a5e931a Add python Conformer.SetPositions wrapper (#7449) Brian Kelley 2024-06-24 20:38:31 -06:00
• e908c482cc fix #7543 (#7546) Paolo Tosco 2024-06-24 04:51:42 +02:00
• b7e999bfd8 Rascal exactConnectionsMatch bug (#7359) David Cosgrove 2024-06-23 06:05:35 +01:00
• 2b99ee477c Allow fragments to be grouped in cdxml (#7529) Brian Kelley 2024-06-23 01:02:19 -04:00
• 21df90304a Add getUIntVectProp to RDProps (#7507) Gareth Jones 2024-06-22 23:01:07 -06:00
• b5d4b54d20 - patch RapidJSON 1.1.0 release backporting a fix from the master branch to avoid a compilation error on newer compilers (fix #7485) (#7550) Paolo Tosco 2024-06-23 06:59:52 +02:00
• 0edde326ac - Restore mol writing functions in the RDKFuncs module (#7544) Paolo Tosco 2024-06-21 05:51:18 +02:00
• 50aea5cf62 Fix issues arising from useMolBlockWedging and the new atropisomer kekulization code (#7540) Paolo Tosco 2024-06-20 19:32:41 +02:00
• a4285a0524 Switch to using FindPotentialStereo() in EnumerateStereoisomers (#7524) Greg Landrum 2024-06-20 14:52:07 +02:00
• d3061b03ef Fixes github #7533 (#7539) Greg Landrum 2024-06-20 09:27:27 +02:00
• 3a8199e4ca Numpy 2 Support (#7531) Anna Brünisholz 2024-06-19 07:54:50 +02:00
• d6171aaade Fixes #7509 (#7513) Ricardo Rodriguez 2024-06-13 23:39:48 -04:00
• ea6fbeec30 add MolToV2KMolBlock() (#7511) Greg Landrum 2024-06-13 09:43:59 +02:00
• 256515f40d Optionally limit the MolStandardize::Uncharger to only alter the protonation state (#7458) Riccardo Vianello 2024-06-13 08:37:24 +02:00
• 4ce1a5640a Ring stereo atropisomers (#7486) tadhurst-cdd 2024-06-13 01:35:42 -05:00
• a7e1f3014e - avoid inconsistency between V2K and V3K MDL output wrt isotopic labelling of R groups (neither should be isotopically labelled) (#7504) Paolo Tosco 2024-06-09 07:32:16 +02:00
• 685e781b54 Allow creation of an empty forcefield (#7494) nmaeder 2024-06-08 05:18:22 +02:00
• 93e8a746bf Shrink the tautomeric zone for the v2 hash of things like imines (#7502) Greg Landrum 2024-06-07 05:09:57 +02:00
• 8c27805fa3 Allow wedged double and aromatic bonds (#7495) Greg Landrum 2024-06-07 05:09:33 +02:00
• c40fb8791c Favor nonwedged bonds in kekulization (#7456) Greg Landrum 2024-06-05 13:56:00 +02:00
• 67ef181233 install atrop header (#7487) Ricardo Rodriguez 2024-06-04 10:15:21 -04:00
• c651ca61de Dclv fix (#7480) Rachael Pirie 2024-06-04 15:14:05 +01:00
• fbad8f7399 fix: Add aromatic aluminium token (#7428) Inwan Yoo 2024-05-31 21:47:14 +09:00
• ba5f43fa6f Fixes #7438 (#7474) Greg Landrum 2024-05-31 14:41:22 +02:00
• 5d3c7f1df9 update release notes tag release Release_2024_03_3 greg landrum 2024-05-30 14:45:17 +02:00
• 29c03b9b70 Update MinimalLib for Function Exposure: runReactants (#7210) Syed Zayyan Masud 2024-05-09 18:30:49 +01:00
• fb0ec41b05 Remove unnecessary wrapped pointers (#7465) Brian Kelley 2024-05-30 08:12:33 -04:00
• f8ca18b3e9 MaeWriter: handle the R group label property and update the Maestro property prefixing (#7454) Ricardo Rodriguez 2024-05-30 08:11:19 -04:00
• 2a1f488582 Remove unnecessary wrapped pointers (#7465) Brian Kelley 2024-05-30 08:12:33 -04:00
• 9a9eacc8b6 MaeWriter: handle the R group label property and update the Maestro property prefixing (#7454) Ricardo Rodriguez 2024-05-30 08:11:19 -04:00
• e586514a17 No coords atropisomers - fix smiles output of atrop wedges after reordering (#7418) tadhurst-cdd 2024-05-07 10:06:33 -05:00
• 2361bb4888 Allow the substruct library to be deleted when refcount goes to 0 (#7462) Brian Kelley 2024-05-27 22:39:54 -04:00
• 0a9b839b1e Make CXSMILES writer use the default conformer ID (#7415) Greg Landrum 2024-05-09 14:43:49 +02:00
• 18905e1e83 Allow disabling output of dative bonds to SMILES (#7384) Greg Landrum 2024-05-25 06:48:55 +02:00
• 85cd0eab38 Fix a python 3.12 compatibility issue (#7450) Riccardo Vianello 2024-05-24 07:32:50 +02:00
• f60f297f4a Expose the property pickle options to SWIG (#7448) Greg Landrum 2024-05-24 07:37:06 +02:00
• 4a9096035f Handle query atoms and bonds in SWIG wrappers (#7431) Gareth Jones 2024-05-22 23:18:49 -06:00
• 14ee4711ea Expose a couple of additional functions to Python (#7444) Greg Landrum 2024-05-17 04:47:30 +02:00
• eab8dd68f6 Fixes #7153 (#7441) Ricardo Rodriguez 2024-05-16 13:42:46 -04:00
• 0dd83300a4 Fixes #7434 greg landrum 2024-05-16 09:03:59 +02:00
• c5085d3db3 Fixes #7367 (#7426) Ricardo Rodriguez 2024-05-16 03:24:55 -04:00
• abf17b320f Fixes #7375 (#7381) Ricardo Rodriguez 2024-05-16 03:13:32 -04:00
• f57e7afd86 Cleanup: Force field (#7406) Anna Brünisholz 2024-05-10 13:22:15 +02:00
• 0484b24615 Make CXSMILES writer use the default conformer ID (#7415) Greg Landrum 2024-05-09 14:43:49 +02:00
• dd23d62ecb allow static builds to work with clang and no coordgen (#7416) Greg Landrum 2024-05-09 04:26:38 +02:00
• 13c597ad3d fix a lifetime bug Andrew Dalke identified (#7408) Greg Landrum 2024-05-09 04:25:43 +02:00
• c4fa266f7c Prefer wedging ring bonds around atropisomers (#7373) Greg Landrum 2024-05-08 06:04:23 +02:00
• 6af7b53f33 Expose replaceAtomWithQueryAtom to Python (#7380) David Cosgrove 2024-05-07 05:50:59 +01:00
• c8649ba838 fix location of MolFileSterechem.h (#7420) tadhurst-cdd 2024-05-06 23:26:42 -05:00
• 7ab15fdec6 C sharp rascal mcs wrapper (#7390) Gareth Jones 2024-05-04 21:52:24 -06:00
• 3c4f4945cd Fix #7311: problem with InChI for phosphinic acid (#7419) Greg Landrum 2024-05-03 21:23:37 +02:00
• 6c523ea0bd Fixes #7300 (#7413) Greg Landrum 2024-05-02 17:32:05 +02:00
• 3a4a744611 Allow the substruct library to be deleted when refcount goes to 0 (#7462) Brian Kelley 2024-05-27 22:39:54 -04:00
• 2bc3a2d3e2 Allow disabling output of dative bonds to SMILES (#7384) Greg Landrum 2024-05-25 06:48:55 +02:00
• 18eb648d56 Expose the property pickle options to SWIG (#7448) Greg Landrum 2024-05-24 07:37:06 +02:00
• b5041c3c51 Fix a python 3.12 compatibility issue (#7450) Riccardo Vianello 2024-05-24 07:32:50 +02:00
• 930c7d6345 Handle query atoms and bonds in SWIG wrappers (#7431) Gareth Jones 2024-05-22 23:18:49 -06:00
• db952786b6 Expose a couple of additional functions to Python (#7444) Greg Landrum 2024-05-17 04:47:30 +02:00
• a9b7881b8b Fixes #7153 (#7441) Ricardo Rodriguez 2024-05-16 13:42:46 -04:00
• 748f36f7d8 Fixes #7434 (#7446) Greg Landrum 2024-05-16 14:32:38 +02:00
• bedd58e10c Fixes #7367 (#7426) Ricardo Rodriguez 2024-05-16 03:24:55 -04:00
• d71e82179d Fixes #7375 (#7381) Ricardo Rodriguez 2024-05-16 03:13:32 -04:00
• 3457c1eb60 a couple of additional cleanups (#7432) Greg Landrum 2024-05-13 06:07:45 +02:00
• d315e246e1 Cleanup: Force field (#7406) Anna Brünisholz 2024-05-10 13:22:15 +02:00
• c2369f9041 Update MinimalLib for Function Exposure: runReactants (#7210) Syed Zayyan Masud 2024-05-09 18:30:49 +01:00
• 6bc3aa4b47 Make CXSMILES writer use the default conformer ID (#7415) Greg Landrum 2024-05-09 14:43:49 +02:00
• 4e0c7d4f67 allow static builds to work with clang and no coordgen (#7416) Greg Landrum 2024-05-09 04:26:38 +02:00
• a64ab4ef5f fix a lifetime bug Andrew Dalke identified (#7408) Greg Landrum 2024-05-09 04:25:43 +02:00
• 18d1ff5f8f Prefer wedging ring bonds around atropisomers (#7373) Greg Landrum 2024-05-08 06:04:23 +02:00
• a2b149a806 No coords atropisomers - fix smiles output of atrop wedges after reordering (#7418) tadhurst-cdd 2024-05-07 10:06:33 -05:00
• f48c87444d Expose replaceAtomWithQueryAtom to Python (#7380) David Cosgrove 2024-05-07 05:50:59 +01:00
• 9386481b19 fix location of MolFileSterechem.h (#7420) tadhurst-cdd 2024-05-06 23:26:42 -05:00
• 34e5569866 deprecations for the 2024.09 release (#7398) Greg Landrum 2024-05-05 13:30:00 +02:00
• 7ec4661f84 C sharp rascal mcs wrapper (#7390) Gareth Jones 2024-05-04 21:52:24 -06:00
• 31f11952e0 Fix #7311: problem with InChI for phosphinic acid (#7419) Greg Landrum 2024-05-03 21:23:37 +02:00
• 757d3ed2bc Wedge bond from atrop error (#7355) tadhurst-cdd 2024-05-03 10:01:18 -05:00
• a7ac25cbe8 Fixes #7300 (#7413) Greg Landrum 2024-05-02 17:32:05 +02:00
• 3654e143fe patch release prep Release_2024_03_2 greg landrum 2024-05-02 08:37:48 +02:00
• 53e279ce4f Prevent the normalization of conjugated cations from applying to the oxime oxygen (#7403) Riccardo Vianello 2024-04-30 17:06:07 +02:00
• 5f4c94a948 Allow any bond (smiles ~) recognition in CDXML (#7363) Brian Kelley 2024-04-29 10:20:23 -04:00
• 330b65c18f extend mol_to_smiles mol_to_cxsmiles to support optional non-isomeric output (#7395) Riccardo Vianello 2024-04-29 09:24:43 +02:00
• 94f2a959fb Fix performance issue in PR 7327 (#7391) Ricardo Rodriguez 2024-04-28 00:16:20 -04:00
• fc99d18953 Fixes #7378, raw docstring to escape null chars (#7379) Yakov Pechersky 2024-04-28 00:23:06 -04:00
• 0bebf4f152 Revert "fix #7221 (#7230)" (#7387) Paolo Tosco 2024-04-28 06:21:31 +02:00
• 7eb1fbfc81 Include header for boost::numeric_cast (#7389) Michael Cho 2024-04-28 00:19:42 -04:00
• 85a5d3e17d Code/PgSQL: Fix Pointer vs Datum (#6733) Christoph Berg 2024-04-28 06:17:55 +02:00
• 688701000e fixes typo in minilib: MolToCXSmiles should have read MolToSmiles (#7388) Paolo Tosco 2024-04-27 08:20:19 +02:00
• 138f44ed79 Allow reapplyMolBlockWedging() to restore the original wedging regardless the bond type (#7386) Riccardo Vianello 2024-04-27 06:40:36 +02:00
• ca7af57c58 Restore mono build (#7377) Gareth Jones 2024-04-24 05:01:08 -06:00
• 45234ac81c Fix the Uncharger 'force' option w/ non-neutralizable negatively charged sites (#7382) Riccardo Vianello 2024-04-24 09:19:27 +02:00
• 903bdbf759 fixes bug with overly large count_bounds (#7368) Greg Landrum 2024-04-23 07:34:04 +02:00
• c5993f8c05 Cleanup of Code/DataStructs (#7365) Anna Brünisholz 2024-04-21 06:41:52 +02:00
• 410e7284b6 C# Build Net6 library and tests using cmake (#7326) Gareth Jones 2024-04-08 15:15:05 +03:00
• 9090978f2c Fixes github 7331 (#7352) Greg Landrum 2024-04-19 10:17:02 +02:00
• 64b77f5130 Added JSON parameters to MinimalLib get_(cx)?sm(ile|art)s() functions (#7194) Paolo Tosco 2024-04-18 06:28:36 +02:00