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rdkit/Code/GraphMol
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Greg Landrum ad2cae35a7 Improve output of debugMol (#7172) 
* better bond output with debugMol

* update atom output

* fix typo in the StereoGroup output
2024-03-05 04:28:02 +01:00
..
Abbreviations
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Adding missing headers in ReactionParser.h (#7163)
2024-03-05 04:27:42 +01:00
ChemTransforms
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
CIPLabeler
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
Depictor
Update molecular templates headers and drop bond-length tests (#6960)
2023-12-27 07:13:46 +01:00
Deprotect
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
Descriptors
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
DetermineBonds
Fixes #6961 (#6971)
2023-12-27 07:14:03 +01:00
DistGeomHelpers
expose EmbedParameters::coordMap to Python (#7086)
2024-02-08 06:48:46 +01:00
FileParsers
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-02-02 15:33:31 +01:00
FilterCatalog
fix several warnings originating from the swig wrappers (#7063)
2024-02-02 15:39:40 +01:00
Fingerprints
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-02-02 15:21:30 +01:00
FMCS
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-02-02 15:21:30 +01:00
ForceFieldHelpers
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-02-02 15:21:30 +01:00
FragCatalog
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
GeneralizedSubstruct
Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)
2023-12-27 07:40:35 +01:00
GenericGroups
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Fixes for canonicalization, and stereochemistry (#6743)
2023-12-02 15:01:03 +01:00
MMPA
Removing stereoatoms requires removing CIS/Trans stereo flags (#6901)
2023-12-02 14:57:40 +01:00
MolAlign
Add multithreading to getBestRMS and new getAllConformerBestRMS (#6896)
2023-12-02 14:58:32 +01:00
MolCatalog
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
MolChemicalFeatures
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-02-02 15:21:30 +01:00
MolDraw2D
Fixes #7140 (#7150)
2024-03-05 04:23:17 +01:00
MolEnumerator
Used const reference to prevent copying in PositionVariationOp::getVariationCounts() (#6906) (#6907)
2024-02-02 15:21:56 +01:00
MolHash
Fixes #6472 - remove aromatic bond flags in Molhash anonymous graph (#7027)
2024-02-02 15:21:09 +01:00
MolInterchange
Fixes #5923 (#7039)
2024-02-02 15:29:38 +01:00
MolStandardize
Add a 'force' option to MolStandardizer::Uncharger (#7088)
2024-02-07 04:42:21 +01:00
MolTransforms
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RascalMCES
Extra rascal option (#7073)
2024-02-02 15:32:37 +01:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-02-02 15:33:31 +01:00
ScaffoldNetwork
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
ShapeHelpers
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +01:00
SLNParse
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
SmilesParse
fix leaks and add a test (#7178)
2024-03-05 04:26:18 +01:00
StructChecker
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
Substruct
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-02-02 15:33:31 +01:00
SubstructLibrary
- enable building stubs in both in-tree and out-of-tree builds (#6980)
2023-12-27 07:21:25 +01:00
TautomerQuery
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-12-08 04:57:19 +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
Fix #7157 (#7166)
2024-03-05 04:24:38 +01:00
AddHs.cpp
Fixes #6944 (#6950)
2023-12-02 15:11:06 +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
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-02-02 15:33:31 +01:00
Atom.cpp
Improve output of debugMol (#7172)
2024-03-05 04:28:02 +01:00
Atom.h
Improve output of debugMol (#7172)
2024-03-05 04:28:02 +01:00
atomic_data.cpp
Fixes #6961 (#6971)
2023-12-27 07:14:03 +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 output of debugMol (#7172)
2024-03-05 04:28:02 +01:00
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 #7023 (#7136)
2024-02-07 04:42:55 +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)
2023-12-02 14:56:21 +01:00
catch_canon.cpp
remove SMILES comparison in test for 7023
2024-02-08 06:34:42 +01:00
catch_chirality.cpp
Fixes #7140 (#7150)
2024-03-05 04:23:17 +01:00
catch_graphmol.cpp
Improve output of debugMol (#7172)
2024-03-05 04:28:02 +01:00
catch_molbundle.cpp
Fix minimal build, allow building without boost::serialization (#6932)
2023-12-02 14:59:03 +01:00
catch_moliterators.cpp
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
catch_organometallics.cpp
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
catch_pickles.cpp
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-12-02 14:56:21 +01:00
catch_sgroups.cpp
Fixes #5923 (#7039)
2024-02-02 15:29:38 +01:00
Chirality.cpp
Fixes #7140 (#7150)
2024-03-05 04:23:17 +01:00
Chirality.h
Fixes #7140 (#7150)
2024-03-05 04:23:17 +01:00
CMakeLists.txt
Fixes #7140 (#7150)
2024-03-05 04:23:17 +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)
2023-12-27 07:20:07 +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)
2023-12-02 14:59:03 +01:00
MolOps.cpp
Fixes for canonicalization, and stereochemistry (#6743)
2023-12-02 15:01:03 +01:00
MolOps.h
Fix #7157 (#7166)
2024-03-05 04:24:38 +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)
2023-12-27 07:20:07 +01:00
new_canon.h
Fixes #6975 (#6972)
2023-12-27 07:20:07 +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
fixing issue 5890 (#7152)
2024-03-05 04:21:02 +01:00
QueryOps.h
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-02-02 15:33:31 +01:00
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
Fixes #7064 (#7141)
2024-03-05 04:24:11 +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
Improve output of debugMol (#7172)
2024-03-05 04:28:02 +01:00
StereoGroup.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
SubstanceGroup.cpp
Fixes #5923 (#7039)
2024-02-02 15:29:38 +01:00
SubstanceGroup.h
Fixes #5923 (#7039)
2024-02-02 15:29:38 +01:00
test1.cpp
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-02-02 15:29:06 +01:00
test_fixtures.h
Fixes #6944 (#6950)
2023-12-02 15:11:06 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Fixes #7115 (#7117)
2024-02-02 15:40:55 +01:00
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 19:18:20 +01:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Fixes #7064 (#7141)
2024-03-05 04:24:11 +01:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Fixes #6816 (#6827)
2023-12-02 08:02:11 +01:00