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31de6b09fba6cb62f51c6c1253b6744c8a42a2dd
rdkit/Code/GraphMol
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Gareth Jones 31de6b09fb Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991) 
* Added fingerprints to GeneralizedSubstruct search

* Small change to fire tests

* Edits from code review

* Updated swig - newobject not required for GeneralizedSubstruct fingerprint methods

* GeneralizedSubstruct only supports unique_ptr in SWIG4.1
2023-12-19 04:44:06 +01:00
..
Abbreviations
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-13 04:49:34 +01:00
ChemTransforms
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
CIPLabeler
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Depictor
Update molecular templates headers and drop bond-length tests (#6960)
2023-12-09 05:47:44 +01:00
Deprotect
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
Descriptors
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
DetermineBonds
Fixes #6961 (#6971)
2023-12-09 06:17:53 +01:00
DistGeomHelpers
Change the defaults for the conformer generation to be ETKDGv3 (#6985)
2023-12-19 04:25:55 +01:00
FileParsers
Fixes #6973 (#6974)
2023-12-10 06:03:08 +01:00
FilterCatalog
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-13 04:49:34 +01:00
Fingerprints
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-13 04:49:34 +01:00
FMCS
Update CI, remove some warnings (#6882)
2023-11-09 13:14:00 -05:00
ForceFieldHelpers
fixes #6728 (#6755)
2023-09-27 17:01:53 +02:00
FragCatalog
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
GeneralizedSubstruct
Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)
2023-12-19 04:44:06 +01:00
GenericGroups
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Fixes #5819 (#6897)
2023-11-22 17:35:58 +01:00
MMPA
Removing stereoatoms requires removing CIS/Trans stereo flags (#6901)
2023-11-21 08:01:37 +01:00
MolAlign
Add multithreading to getBestRMS and new getAllConformerBestRMS (#6896)
2023-11-22 17:35:06 +01:00
MolCatalog
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolChemicalFeatures
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolDraw2D
Github6968 (#6979)
2023-12-18 06:25:23 +01:00
MolEnumerator
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolHash
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
MolInterchange
Segfault in JSONToMols when "commonchem" is an int #6890 (#6940)
2023-11-24 05:29:55 +01:00
MolStandardize
Add in place and multithread support for more of the MolStandardize code (#6970)
2023-12-12 17:21:18 +01:00
MolTransforms
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RascalMCES
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
ScaffoldNetwork
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
ShapeHelpers
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
SLNParse
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
SmilesParse
Fixes #6981 (#6982)
2023-12-16 08:01:33 +01:00
StructChecker
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
Fixes #6983 (#6984)
2023-12-16 08:06:11 +01:00
SubstructLibrary
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-13 04:49:34 +01:00
TautomerQuery
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
test_data
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Wrap
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-13 04:49:34 +01:00
AddHs.cpp
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
AdjustQuery.cpp
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
Aromaticity.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Atom.cpp
Some small cleanups from the UGM Hackathon (#6744)
2023-10-05 06:13:18 +02:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
Fixes #6961 (#6971)
2023-12-09 06:17:53 +01:00
atomic_data.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
AtomIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Bond.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Bond.h
add #include <utility> (#5060)
2022-03-17 04:56:34 +01:00
BondIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
BondIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Fixes #6975 (#6972)
2023-12-11 17:40:30 +01:00
Canon.h
Add a "rootedAtAtom" to MolToSmarts (#6581)
2023-08-19 19:17:45 +02:00
catch_adjustquery.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_canon.cpp
Fixes #6975 (#6972)
2023-12-11 17:40:30 +01:00
catch_chirality.cpp
Fixes #6981 (#6982)
2023-12-16 08:01:33 +01:00
catch_graphmol.cpp
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
catch_molbundle.cpp
Fix minimal build, allow building without boost::serialization (#6932)
2023-11-23 05:57:05 +01:00
catch_moliterators.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_organometallics.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_pickles.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Chirality.cpp
Fixes #6981 (#6982)
2023-12-16 08:01:33 +01:00
Chirality.h
Set squiggle bonds to STEREOANY with stereo atoms (#6877)
2023-11-29 04:52:39 +01:00
CMakeLists.txt
cmake cleanup (#6814)
2023-11-10 15:32:54 +01:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Allow some tolerance in flatness determination (#6696)
2023-09-07 16:50:56 +02:00
ConjugHybrid.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
cptest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Do not include dative bonds in ring finding by default (#6231)
2023-03-30 18:09:24 +02:00
FindStereo.cpp
Fixes #6975 (#6972)
2023-12-11 17:40:30 +01:00
GraphMol.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Fixes #5505: problems when kekulizing molecules with query bonds (#5550)
2022-09-13 14:49:45 +02:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolBundle.h
Fix minimal build, allow building without boost::serialization (#6932)
2023-11-23 05:57:05 +01:00
MolOps.cpp
Fixes for canonicalization, and stereochemistry (#6743)
2023-11-06 07:40:23 +01:00
MolOps.h
Fixes #6816 (#6827)
2023-11-10 20:23:15 +01:00
molopstest.cpp
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
MolPickler.cpp
make sure bond attachpt info is pickled (#6698)
2023-09-07 12:21:36 +02:00
MolPickler.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
new_canon.cpp
Fixes #6975 (#6972)
2023-12-11 17:40:30 +01:00
new_canon.h
Fixes #6975 (#6972)
2023-12-11 17:40:30 +01:00
NontetrahedralStereo.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Enable optional visualization of complex query atoms in a more compact form (#6056)
2023-02-16 12:34:05 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
QueryOps.cpp
Support additional generic groups (#6570)
2023-08-10 06:36:38 +02:00
QueryOps.h
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
querytest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RDKitBase.h
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
RDKitQueries.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
regress.txt
Unset executable flag
2019-10-10 20:18:43 +09:00
Renumber.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
resMolSupplierTest.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Resonance.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
- Changed all unsigned to unsigned int for clarity (#6646)
2023-08-25 06:09:19 +02:00
RingInfo.h
- Changed all unsigned to unsigned int for clarity (#6646)
2023-08-25 06:09:19 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Some small cleanups from the UGM Hackathon (#6744)
2023-10-05 06:13:18 +02:00
ROMol.h
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
RWMol.cpp
Removing stereoatoms requires removing CIS/Trans stereo flags (#6901)
2023-11-21 08:01:37 +01:00
RWMol.h
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
SanitException.h
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
StereoGroup.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
SubstanceGroup.cpp
Some small cleanups from the UGM Hackathon (#6744)
2023-10-05 06:13:18 +02:00
SubstanceGroup.h
Some small cleanups from the UGM Hackathon (#6744)
2023-10-05 06:13:18 +02:00
test1.cpp
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
test_fixtures.h
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Update CI, remove some warnings (#6882)
2023-11-09 13:14:00 -05:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Allow removal of non-special H atoms in SGroups (#5399)
2022-07-07 11:05:18 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Fixes #6816 (#6827)
2023-11-10 20:23:15 +01:00