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9214d4becb4bbeeeb6e19a49a00fc9aca0e2bf2c
rdkit/Code/GraphMol
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Greg Landrum 9214d4becb Support Python 3.11 (#5994) 
* remove some more deprecated numpy stuff

* workaround for changes to random.shuffle in python 3.11

* fix pickling of rdkit mols in python 3.11

* add py311 build to CI

* update py311 CI

* remove qt for py311 for the moment

* only use the new code with pyversion >=3.11

* use the new logic for all pickle_suites

* need to work with older py too
2023-02-23 05:01:12 +01:00
..
Abbreviations
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
ChemTransforms
cdxml parser (#5273)
2022-09-28 05:49:27 +02:00
CIPLabeler
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Depictor
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
Deprotect
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Descriptors
Fixes #5941 (#5942)
2023-01-16 04:45:40 +01:00
DetermineBonds
fixes #5902 (#5926)
2023-01-16 04:45:16 +01:00
DistGeomHelpers
Fix a problem when generating conformers for molecules with larger heteroatoms in conjugated 5-rings (#5586)
2022-10-03 10:26:33 +02:00
FileParsers
Allow unrecognized atom types when strictParsing=False (#5891)
2023-02-06 17:01:10 +01:00
FilterCatalog
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
Fingerprints
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
FMCS
fix potential bug (#5205)
2022-04-17 05:22:50 +02:00
ForceFieldHelpers
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
FragCatalog
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
GenericGroups
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
windows.h header should be lowercase to avoid issues when (#5712)
2022-11-23 06:24:01 +01:00
MolAlign
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
MolCatalog
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
MolChemicalFeatures
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolDraw2D
adjust test results for newer freetype versions (#5979)
2023-02-23 04:58:12 +01:00
MolEnumerator
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
MolHash
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
MolInterchange
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
MolStandardize
Fix disconnection of magnesium acetate in covalent form. (#5998)
2023-02-23 05:00:51 +01:00
MolTransforms
Fix Flake8 erorrs (#4252)
2022-03-10 06:55:18 +01:00
PartialCharges
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ReducedGraphs
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RGroupDecomposition
clear MDL Rgroup labels from core atoms when we aren't using them (#5904)
2023-02-06 16:57:54 +01:00
ScaffoldNetwork
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
ShapeHelpers
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
SLNParse
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
SmilesParse
fix a build failure
2022-11-23 09:21:00 +01:00
StructChecker
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Subgraphs
[ENH]: Support greater use of findAtomEnvironmentOfRadiusN() (#4970)
2022-03-09 14:01:24 +01:00
Substruct
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
SubstructLibrary
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
TautomerQuery
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
test_data
Add wavy stereo bond support to cdxml (#5755)
2022-11-23 06:40:11 +01:00
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
Support Python 3.11 (#5994)
2023-02-23 05:01:12 +01:00
AddHs.cpp
By default mergeQueryHs now will not remove isotopes (#5563)
2022-09-16 17:29:32 +02:00
AdjustQuery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
Aromaticity.cpp
Update warning message about aromaticity detection (#5696)
2022-11-23 06:22:39 +01:00
Atom.cpp
Fixes #5849 (#5861)
2023-01-16 04:28:35 +01:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
extend the allowed valences of the alkali earths (#5786)
2022-12-08 06:10:04 +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
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
Canon.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_canon.cpp
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
catch_chirality.cpp
we want to use _putenv_s also in MinGW builds (#5711)
2022-11-23 06:23:32 +01:00
catch_graphmol.cpp
Fixes #5849 (#5861)
2023-01-16 04:28:35 +01:00
catch_moliterators.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
Chirality.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
CMakeLists.txt
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
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
Speed up ring detection by reducing count() calls (#5663)
2022-10-18 15:13:46 +02:00
FindStereo.cpp
Support stereo for double bonds in rings from CXSMILES (#5636)
2022-10-20 07:44:11 +02:00
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
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
MolOps.cpp
Fixes #5849 (#5861)
2023-01-16 04:28:35 +01:00
MolOps.h
Fixes #5849 (#5861)
2023-01-16 04:28:35 +01:00
molopstest.cpp
fix + test (#5100)
2022-03-17 04:53:17 +01:00
MolPickler.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
MolPickler.h
Fixes https://github.com/rdkit/rdkit/issues/4621 (#5623)
2022-10-06 16:45:14 +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
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
new_canon.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
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
add #include <utility> (#5060)
2022-03-17 04:56:34 +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
Fixes #5930 (#5931)
2023-01-16 04:36:50 +01:00
QueryOps.h
Fixes #5210 (#5408)
2022-07-11 11:20:03 +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
Fix #4071 (#4080)
2021-04-23 16:45:54 -04:00
resMolSupplierTest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Resonance.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
Fixes #4721 (#4722)
2022-01-28 16:38:46 +01:00
RingInfo.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
ROMol.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
RWMol.cpp
Fix memory safety issues found by OSS-Fuzz (#4983)
2022-02-06 05:06:38 +01:00
RWMol.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +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
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
StereoGroup.h
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
SubstanceGroup.cpp
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
SubstanceGroup.h
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
test1.cpp
Fixes a couple of query-related bugs (#3398)
2020-09-17 08:16:43 +02:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
add boost::serialization support to ROMol (#5249)
2022-05-07 11:11:53 +02:00
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
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00