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9ca7a2e00d518c11dc157c4aba4efe1cd5e031ce
rdkit/Code/GraphMol
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MarioAndWario 9ca7a2e00d Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842) 
* Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6370)

* static_cast<int> for integer comparison

* Add unittests for 0 explicit hydrogens

* Fix unittests of radical count in fileParsersTest1

* Fix testMolWriter

* Fix testMrvToMol

* Address Greg's comments
2024-01-23 06:21:26 +01:00
..
Abbreviations
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
add a test for Github #6492 (#7045)
2024-01-18 05:03:10 +01:00
ChemTransforms
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CIPLabeler
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
Depictor
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Deprotect
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
Descriptors
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
DetermineBonds
Fixes #6961 (#6971)
2023-12-09 06:17:53 +01:00
DistGeomHelpers
Update distance bounds calculation for conjugated double bonds in macrocycles (#7032)
2024-01-17 08:42:09 +01:00
FileParsers
Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842)
2024-01-23 06:21:26 +01:00
FilterCatalog
fix check of python version when updating Filters.cpp (#7035)
2024-01-18 13:35:22 +01:00
Fingerprints
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
FMCS
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
ForceFieldHelpers
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
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
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842)
2024-01-23 06:21:26 +01:00
MMPA
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
MolDraw2D
Fixes 7036 - middle line of triple bond meeting wedge (#7046)
2024-01-16 06:27:50 +01:00
MolEnumerator
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolHash
Fixes #6472 - remove aromatic bond flags in Molhash anonymous graph (#7027)
2024-01-09 06:12:03 +01:00
MolInterchange
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
MolStandardize
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Extra rascal option (#7073)
2024-01-23 06:05:58 +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
[v2 API] SMILES/SMARTS parsers (#6203)
2024-01-19 17:17:51 +01:00
StructChecker
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
SubstructLibrary
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
TautomerQuery
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
test_data
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-01-18 05:06:57 +01:00
AddHs.cpp
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
AdjustQuery.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Aromaticity.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Atom.cpp
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-01-18 05:06:57 +01:00
Atom.h
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-01-18 05:06:57 +01:00
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
Atropisomers.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Atropisomers.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Bond.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Bond.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
catch_graphmol.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
catch_molbundle.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
Chirality.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Chirality.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CMakeLists.txt
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
FindStereo.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842)
2024-01-23 06:21:26 +01:00
MolOps.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
molopstest.cpp
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
MolPickler.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
MolPickler.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
RingInfo.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
ROMol.h
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
RWMol.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
StereoGroup.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
SubstanceGroup.cpp
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
SubstanceGroup.h
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
test1.cpp
Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842)
2024-01-23 06:21:26 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00