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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

Release_2011_03_1beta1

Release_2011_03_2

Release_2011_06_1

Release_2011_06_1beta1

Release_2011_09_1

Release_2011_09_1beta1

Release_2011_12_1

Release_2011_12_1beta1

Release_2012_03_1

Release_2012_03_1beta1

Release_2012_06_1

Release_2012_06_1beta1

Release_2012_09_1

Release_2012_09_1beta1

Release_2012_09_1beta2

Release_2012_09_2

Release_2012_09_beta2

Release_2012_12_1

Release_2012_12_1beta1

Release_2013_01_1beta1

Release_2013_03_1

Release_2013_03_1beta1

Release_2013_03_2

Release_2013_06_1

Release_2013_06_1beta1

Release_2013_09_1

Release_2013_09_1beta

Release_2013_09_1beta1

Release_2013_09_1pre

Release_2013_09_2

Release_2014_03_1

Release_2014_03_1beta1

Release_2014_09_1

Release_2014_09_2

Release_2015_03_1

Release_2015_03_1beta1

Release_2015_09_1

Release_2015_09_1beta1

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Release_2016_03_1b1

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Release_2016_09_1

Release_2016_09_1a1

Release_2016_09_1b1

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Release_2017_03_1

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Release_2017_09_1

Release_2017_09_1b1

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Release_2017_09_3

Release_2018_03_1

Release_2018_03_1b1

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Release_2018_03_4

Release_2018_09_1

Release_2018_09_1b1

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Release_2019_03_1

Release_2019_03_1b1

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Release_2019_03_4

Release_2019_09_1

Release_2019_09_1b1

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Release_2019_09_3

Release_2020_03_1

Release_2020_03_1b1

Release_2020_03_2

Release_2020_03_3

Release_2020_03_4

Release_2020_03_5

Release_2020_03_6

Release_2020_09_1

Release_2020_09_1b1

Release_2020_09_2

Release_2020_09_3

Release_2020_09_4

Release_2020_09_5

Release_2021_03_1

Release_2021_03_1b1

Release_2021_03_2

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Release_2021_03_5

Release_2021_09_1

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Release_2023_09_1b1

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Release_2023_09_6

Release_2024_03_1

Release_2024_03_1b1

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Release_2024_09_1b1

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Release_Aug2007_1

Release_Jan2007_1

Release_Jan2008_1

Release_Jan2008_1RC1

Release_Jan2008_1beta1

Release_Jan2008_1beta2

Release_Jan2008_1beta3

Release_May2008_1

Release_May2008_1RC1

Release_May2008_1RC2

Release_Oct20006_1

Release_Oct2006_1

Release_Q12009_1

Release_Q12009_1beta3

Release_Q12009_1beta4

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Release_Q42008_1

Release_Q42008_1RC1

Release_Q42009_1

Release_Q42009_1beta1

Release_test_for_zenodo

inactive/premodern_master

Mono Color

• 0de215a1f8 Fix canonicalization of stereogroups (#7041) tadhurst-cdd 2024-10-11 10:09:18 -05:00
• 4bffa95db2 Optimize Butina Clustering for Performance and Expand API (#7892) EvaSnow 2024-10-10 21:44:03 -07:00
• 0909d753b8 Fixes #7873 (#7885) Brian Kelley 2024-10-11 00:42:52 -04:00
• a7404cdd91 Do the announced deprecations (#7910) Greg Landrum 2024-10-11 06:42:18 +02:00
• 875596eb12 [IterateCIPRanks] Precompute neighbor indices and counts, sort them together for each atom (#7889) Kevin Boyd 2024-10-10 07:27:33 -07:00
• bd79893dd3 Additional compatibility updates for commutator/negator settings for operator @= (#7834) esiaero 2024-10-10 07:12:27 -07:00
• 0164ac7fae Fix some more mem errors in 2024.09.1 (#7899) Ricardo Rodriguez 2024-10-10 10:08:50 -04:00
• 315939f7ae Fix inversion of stereo with canonicalizeConformer (#7878) Greg Landrum 2024-10-10 15:57:39 +02:00
• e66f3f35fa Prevent SIGSEGV in SplitMolByPDBResidues (#7880) Timothy Palpant 2024-10-10 14:31:31 +02:00
• 39fbc8bfa1 expose preset color palettes to MinimalLib through JSON (#7853) Paolo Tosco 2024-10-10 14:30:42 +02:00
• 070f07c974 Update PUBCHEMSHAPE_URL and remove patch code (#7900) UENO, M. 2024-10-07 23:17:58 +09:00
• 4140f95a79 Restore "oops, exponential is a pain" code snippet in the RGD algorithm (#7898) Paolo Tosco 2024-10-07 15:08:50 +02:00
• c1de3aefb5 Another performance improvement in CIP labelling (#7854) Dan Nealschneider 2024-10-05 20:25:14 -07:00
• 07bcf45126 Use smart pointer for bits. (#7884) David Cosgrove 2024-10-05 06:30:55 +01:00
• 0345c2e70a Improve Morgan Fingerprint Performance (#7862) Kevin Boyd 2024-10-04 21:46:46 -07:00
• 23aaf51862 expose three ROMol methods which were not previously exposed to SWIG wrappers (#7895) Paolo Tosco 2024-10-05 06:38:33 +02:00
• ea7f51f3b1 Fix some mem errors in 2024.09.1 (#7867) Ricardo Rodriguez 2024-10-03 10:05:43 -04:00
• 42008ded5f Use smart pointer for buffer. (#7883) David Cosgrove 2024-10-03 05:55:45 +01:00
• 7aca92b914 fix #7782 (#7783) Paolo Tosco 2024-10-03 06:52:34 +02:00
• bc0020fb51 [CI]: temporarily be explicit about using the macos-12 image (#7882) Greg Landrum 2024-10-03 06:44:07 +02:00
• a4fe959523 Simple speed up for CIPLabeler (#7826) Dan Nealschneider 2024-09-30 19:11:03 -07:00
• 1f3c092f01 Gitignore fix (#7861) PatrickPenner 2024-10-01 02:10:24 +00:00
• d9254aed90 Fix RDKit Year (#7863) Ricardo Rodriguez 2024-09-30 22:08:52 -04:00
• a44cbe8699 Fixes #7685 (#7864) Ricardo Rodriguez 2024-09-28 23:23:24 -04:00
• fcf8b8eb16 ready next release cycle (#7858) Greg Landrum 2024-09-27 14:02:43 +02:00
• 9b9392266a update README and tag release (#7855) Release_2024_09_1 Greg Landrum 2024-09-27 13:52:16 +02:00
• 7d2598267a Fixes #7689 (#7851) Greg Landrum 2024-09-26 19:22:26 +02:00
• da6cd73168 Run clang-format across everything (#7849) Greg Landrum 2024-09-26 13:39:02 +02:00
• f1606cb940 massive simplification of README.md (#7831) Greg Landrum 2024-09-25 11:53:27 +02:00
• 746435527a Allow subsets of ring systems to match templates (#7468) Nic Zonta 2024-09-25 08:57:29 +02:00
• b5d6a3dba7 beta release prep (#7836) Release_2024_09_1b1 Greg Landrum 2024-09-20 17:20:05 +02:00
• 5b584a9d88 Rename MolProcessing header (#7835) Paolo Tosco 2024-09-20 13:32:57 +02:00
• 293328845b Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823) David Cosgrove 2024-09-20 08:48:08 +01:00
• 165525b3ba Fixes #7731 (#7833) Greg Landrum 2024-09-19 18:42:42 +02:00
• bb066c43f4 add mol processing API (#7773) Greg Landrum 2024-09-19 18:42:25 +02:00
• c8cd4e7c20 consolidate numeric vectors (#7792) Brian Kelley 2024-09-18 01:43:17 -04:00
• 9824a9d964 Expose MMFF aromaticity model for SetAromaticity (#7765) Juuso Lehtivarjo 2024-09-18 06:59:02 +03:00
• 75771be090 Update SA score to use FingerprintGenerators (#7795) François Bérenger 2024-09-17 19:19:23 +09:00
• aeb70c4dfc Drop mol_hash for legacy databases to enable upgrade to recent versions (#7804) Maciej Wójcikowski 2024-09-17 06:09:53 +02:00
• 9fc2c47817 reject template if it doesn't match bond stereo (#7567) Nic Zonta 2024-09-17 06:00:01 +02:00
• c0145ab063 - Allow overriding the default image size through individual image options in the InteractiveRenderer (#7805) Paolo Tosco 2024-09-16 18:17:01 +02:00
• 765eb042c1 Fixes #7526 (#7800) Paolo Tosco 2024-09-16 16:18:07 +02:00
• 53c917f676 Fixes #7401 (#7799) Paolo Tosco 2024-09-16 16:16:36 +02:00
• 786393beb1 Enable RGD highlights as in blog post (#7322) Paolo Tosco 2024-09-16 16:14:13 +02:00
• 5484738f3e Highlighted hetero atoms disappear (#7672) David Cosgrove 2024-09-16 14:14:14 +01:00
• dd6100d836 Remove Documentation Status link (#7809) Chris Von Bargen 2024-09-16 00:24:14 -04:00
• 62b9f7a019 fix typo (Fingeprint -> Fingerprint) (#7801) Paolo Tosco 2024-09-16 06:18:43 +02:00
• 4cc3d759ce avoid pubchem-align3d build failure on g++ >=13 (#7817) Paolo Tosco 2024-09-16 06:14:35 +02:00
• d44758ee5e Rascal match exact atom type (#7673) David Cosgrove 2024-09-16 04:45:18 +02:00
• ae27738964 Torsion energy calculations are sometimes nan (#7814) Rachel Walker 2024-09-14 06:38:05 +02:00
• 095e287996 [bot] Update molecular templates header (#7808) github-actions[bot] 2024-09-14 06:33:44 +02:00
• da2a9242bf Provide an RDKit wrapper around pubchem-align3d (#7798) Greg Landrum 2024-09-14 06:08:24 +02:00
• 4c37b03071 give a HasPropWithValueQueryBase a virtual destructor (#7786) Ricardo Rodriguez 2024-09-09 07:06:44 -04:00
• 41f5c82ccf Use Boost_INCLUDE_DIRS instead of Boost_INCLUDE_DIR (#7793) Andrew Kane 2024-09-07 22:26:58 -07:00
• e4f4644a89 - Expose multicolor highlights to MinimalLib (#7787) Paolo Tosco 2024-09-03 21:03:40 +02:00
• d8e3eab165 Speed up boost vector iterators (#7719) Brian Kelley 2024-09-03 14:55:24 -04:00
• cf5b56784d use make_unique (#7771) Greg Landrum 2024-09-03 16:08:21 +02:00
• b72c4945c7 update cmake syntax (#7778) Ricardo Rodriguez 2024-08-30 22:32:14 -04:00
• 0be09f8e70 Fix typo in 4.5.0--4.6.0 sql upgrade script (#7775) esiaero 2024-08-29 23:53:44 -07:00
• 9dc263b7b4 Add callbacks to the multithreaded mol suppliers (#7763) Greg Landrum 2024-08-29 15:53:47 +02:00
• 90c5334848 Fix aliasing bug in MultithreadedSDMolSupplier and move GeneralFileReader to v2 API (#7761) Greg Landrum 2024-08-29 15:53:28 +02:00
• 8bd74d9111 update release notes; bump version Release_2024_03_6 Release_2024_03 greg landrum 2024-08-29 09:44:49 +02:00
• b43bb39197 Fixes #7501 dative bonds in cdxml (#7757) Brian Kelley 2024-08-27 23:59:43 -04:00
• 18079741a3 Fix drawing of 2 colour wedges. (#7760) David Cosgrove 2024-08-28 04:58:18 +01:00
• 9b29fe8a64 fix vectToString such that it outputs valid JSON (#7749) Paolo Tosco 2024-08-26 16:27:03 +02:00
• 7d684ce48d Fixes #7725 (#7728) Greg Landrum 2024-08-26 08:56:51 +02:00
• 12bdbf5b68 add useChirality flag to SaltRemover (#7758) JuniorSen 2024-08-25 06:05:47 +01:00
• 5ce0cf3c7f Allow atom map numbers to be ignored when generating canonical SMILES (#7732) David Cosgrove 2024-08-23 16:15:31 +01:00
• 170eb77d1e Don't do the fancy merging of solid wedges and bond lines for triple … (#7738) David Cosgrove 2024-08-23 16:14:15 +01:00
• f74502c8ac JSMol, where the underlying RWMol is stored as a unique_ptr, is now complemented by JSMolShared, where the underlying RWMol is stored as ROMOL_SPTR; both classes inherit from JSMolBase (#7744) Paolo Tosco 2024-08-23 13:49:00 +02:00
• 70c3353ac5 Code cleanup, minor refactoring and typos (#7742) Paolo Tosco 2024-08-23 12:48:50 +02:00
• 6537e564ca restore the ability to build RDKit_minimal.js after #7700 (#7734) Paolo Tosco 2024-08-21 04:52:44 +02:00
• 6f2e586e8a expose two additional boolean flags for mol creation to MinimalLib (CFFI, JS), assignChiralTypesFromMolParity and makeDummiesQueries, both defaulting to false (#7743) Paolo Tosco 2024-08-23 05:13:34 +02:00
• 1341b4ade5 Reduce code duplication in ff (#7715) nmaeder 2024-08-22 05:54:35 +02:00
• 4f8e646d5f Ensure 13 bounds constraints are added to angles that are part of an improper torsion (#7729) nmaeder 2024-08-21 16:06:29 +02:00
• a310a69983 New contribs for DG (#7711) nmaeder 2024-08-21 06:06:58 +02:00
• 37b9d1f466 Fixes #7625 (#7641) Greg Landrum 2024-07-23 06:00:29 +02:00
• 28184c9b39 Some cmake cleanup work (#7720) Greg Landrum 2024-08-16 17:11:31 +02:00
• a31bfe1f2e Fix some missing headers when doing "make install" (#7667) Greg Landrum 2024-07-25 17:07:03 +02:00
• 1df17c1770 doc: fix -Wdocumentation-html (#7721) Eisuke Kawashima 2024-08-16 15:12:42 +09:00
• e00178beb4 Remove Descriptors as a dependency of many other RDKit libraries (#7700) Greg Landrum 2024-08-13 13:22:43 +02:00
• 3b4d98a97a only test InChI functionality if it was built into JS MinimalLib (#7706) Paolo Tosco 2024-08-13 06:02:49 +02:00
• e91c145f94 Add support for building the CFFI lib without InChI (#7698) Andrew Kane 2024-08-10 12:16:58 -07:00
• e58b0dc73b Make sure angleconstraints only take angles between 0 and 180 degrees. (#7688) nmaeder 2024-08-10 06:32:25 +02:00
• 2209aea10d Removes call to debugMol that logs to std::err (#7690) Brian Kelley 2024-08-06 09:41:56 -04:00
• 244efe7068 Refactor distgeom minimizations (#7652) nmaeder 2024-07-25 06:14:12 +02:00
• 9f03aa832c Fixes #7674 (#7681) Greg Landrum 2024-08-01 17:19:58 +02:00
• 19e7661aa2 Fixes #6757 (#7664) Greg Landrum 2024-07-25 15:26:22 +02:00
• ae915d97cd Fix parsing RBCNT from mol files, and add exporting it (#7638) Ricardo Rodriguez 2024-07-24 22:54:46 -04:00
• 07bfa8235e Fixes #7642 (#7643) Greg Landrum 2024-07-25 04:48:00 +02:00
• 54f6879bf9 fix(rdmolfiles): fix parameters and docstrings (#7648) Eisuke Kawashima 2024-07-23 12:59:59 +09:00
• 4be548ff68 Fixes #7608 (#7633) Greg Landrum 2024-07-24 18:57:45 +02:00
• f20f3c0be9 Fixes #7364 (#7657) Greg Landrum 2024-07-24 18:51:57 +02:00
• 93557931c1 fixes #7583 (#7644) Greg Landrum 2024-07-24 14:35:46 +02:00
• f17fa04afb - fix misformatted molblock and make sure unit test is actually executed (#7647) Paolo Tosco 2024-07-23 08:37:44 +02:00
• acd9c2088e Rascal atom and bond equivalences (#7612) David Cosgrove 2024-07-23 05:02:33 +01:00
• 2f8710a05c Update commutator/negator settings for operator @= (#7596) Riccardo Vianello 2024-07-23 06:01:56 +02:00
• ea99cd695f Fixes #7556 (#7646) Greg Landrum 2024-07-22 16:34:08 +02:00
• b1b7fb1892 Fixes #7501 dative bonds in cdxml (#7757) Brian Kelley 2024-08-27 23:59:43 -04:00
• 9aa77acd1f Fix drawing of 2 colour wedges. (#7760) David Cosgrove 2024-08-28 04:58:18 +01:00