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fd44d72fb75d9c1353494c4fc2429b9eadbccccb
rdkit/Code/GraphMol
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Greg Landrum fd44d72fb7 Fixes #5849 (#5861) 
* Fixes #5849
This may not be the best fix since it adds another step to canonicalization

* more test cases

* update docs
2022-12-28 20:10:13 +00:00
..
Abbreviations
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Fixes #5785 (#5871)
2022-12-16 16:00:30 +01:00
ChemTransforms
Bug/github5613 (#5735)
2022-12-16 05:36:49 +01:00
CIPLabeler
Add a timeout protection for CIP calculations (#5772)
2022-12-09 05:28:38 +01:00
Depictor
Add a Python Context Manager for SetPreferCoordGen (#5693)
2022-10-31 04:35:49 +01:00
Deprotect
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Descriptors
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
DetermineBonds
Fixes #5894 (#5898)
2022-12-25 17:44:05 +00:00
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)
2022-12-28 08:25:34 -05:00
FilterCatalog
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Fingerprints
FingerprintGenerator refactoring (#5748)
2022-12-28 17:40:13 +00:00
FMCS
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
ForceFieldHelpers
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
FragCatalog
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +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)
2022-10-31 06:43:57 +01:00
MolAlign
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
MolCatalog
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
MolChemicalFeatures
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
MolDraw2D
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +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
Fixes #5784 (#5817)
2022-12-01 17:11:50 +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)
2022-12-28 08:25:08 -05:00
ScaffoldNetwork
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
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 #5683 (#5773)
2022-11-18 16:23:35 +01:00
StructChecker
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Subgraphs
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Substruct
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
SubstructLibrary
Fix documentation example for KeyFromPropHolder (#5886)
2022-12-20 07:06:29 +01:00
TautomerQuery
fix warnings (#5561)
2022-09-14 06:36:42 +02:00
test_data
Add wavy stereo bond support to cdxml (#5755)
2022-11-17 04:58:46 +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
Do deprecations for the 2023.03 release (#5675)
2022-11-01 13:29:58 +01:00
AddHs.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
AdjustQuery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
Aromaticity.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Atom.cpp
Fixes #5849 (#5861)
2022-12-28 20:10:13 +00:00
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)
2022-11-25 04:50:36 +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
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Canon.h
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
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
Do deprecations for the 2023.03 release (#5675)
2022-11-01 13:29:58 +01:00
catch_graphmol.cpp
Fixes #5849 (#5861)
2022-12-28 20:10:13 +00:00
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
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
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)
2022-12-28 20:10:13 +00:00
MolOps.h
Fixes #5849 (#5861)
2022-12-28 20:10:13 +00:00
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 #5152 (#5153)
2022-04-04 06:07:57 +02:00
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
Fix a hang in ResonanceMolSupplier when the computed ceMap is empty (#5701)
2022-10-28 19:47:06 +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
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