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7153918af4dff37c768577441c5286b425e6bf3d
rdkit/Code/GraphMol
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Greg Landrum 7153918af4 Fixes #4642 (#6115) 
* Fixes #4642

We should consider whether or not it's right to remove stereo from atoms which were in stereo groups but are not any longer.

* split stereogroups across fragments

* cleanup

* Changes in response to review
2023-03-02 19:01:45 +01:00
..
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
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
ChemTransforms
Fixes #6034 (#6035)
2023-02-02 05:00:47 +01:00
CIPLabeler
Add a timeout protection for CIP calculations (#5772)
2022-12-09 05:28:38 +01:00
Depictor
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
Deprotect
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Descriptors
Fixes #6049 (#6061)
2023-02-09 08:31:39 +01:00
DetermineBonds
fixes #5902 (#5926)
2023-01-11 09:43:05 +01:00
DistGeomHelpers
cleanup a compiler warning (#6016)
2023-02-01 04:31:45 +01:00
FileParsers
Start a Maestro file (.mae) writer. (#6069)
2023-02-17 11:53:17 +01:00
FilterCatalog
The new Filters should have a FilterSet property (#6129)
2023-02-27 07:41:04 +01:00
Fingerprints
Add option to only include shortest paths for topological torsion fingerprints (#6090)
2023-02-20 11:13:53 +01:00
FMCS
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
ForceFieldHelpers
Create getExperimentalTorsions() function (#5969)
2023-01-25 12:15:04 +01:00
FragCatalog
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +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
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
MolChemicalFeatures
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
MolDraw2D
Github6112 (#6113)
2023-03-01 04:52:34 +01:00
MolEnumerator
Propagate query features from reacting molecules to products (#6021)
2023-01-28 04:47:46 +01:00
MolHash
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
MolInterchange
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
MolStandardize
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +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
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
ScaffoldNetwork
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +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
Enable "smilesSymbol" substitution in SMARTS (#6096)
2023-02-20 11:12:26 +01:00
StructChecker
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Subgraphs
Add option to only include shortest paths for topological torsion fingerprints (#6090)
2023-02-20 11:13:53 +01:00
Substruct
Remove check for ring information from Atom::Match (#6063)
2023-02-08 04:30:05 +01:00
SubstructLibrary
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
TautomerQuery
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
test_data
Fix a problem with pickling molecules with more than 255 rings (#5992)
2023-01-30 23:24:00 -05:00
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 option to only include shortest paths for topological torsion fingerprints (#6090)
2023-02-20 11:13:53 +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
Remove check for ring information from Atom::Match (#6063)
2023-02-08 04:30:05 +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)
2022-11-25 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
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
Canon.h
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_canon.cpp
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
catch_chirality.cpp
Fixes #6049 (#6061)
2023-02-09 08:31:39 +01:00
catch_graphmol.cpp
Fixes #4642 (#6115)
2023-03-02 19:01:45 +01:00
catch_moliterators.cpp
- added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms (#5995)
2023-01-20 15:00:32 +01:00
catch_queries.cpp
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
Remove spurious full stops from warnings. (#6124)
2023-02-24 05:07:09 +01:00
Chirality.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
CMakeLists.txt
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
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
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
FindStereo.cpp
Fix #6011 and #6012 (#6013)
2023-01-26 19:26:19 +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
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
MolOps.cpp
Fixes #4642 (#6115)
2023-03-02 19:01:45 +01:00
MolOps.h
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
molopstest.cpp
fix + test (#5100)
2022-03-17 04:53:17 +01:00
MolPickler.cpp
Fix a problem with pickling molecules with more than 255 rings (#5992)
2023-01-30 23:24:00 -05:00
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
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +01:00
new_canon.h
Add canonicalization of stereo groups (enhanced stereo) (#6051)
2023-02-08 04:21:51 +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
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
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
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
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
Fix some minor leaks (#6029)
2023-01-31 17:30:34 +01:00
ROMol.h
- added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms (#5995)
2023-01-20 15:00:32 +01:00
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
Properly check for boost::any in rdvalue_is (#6086)
2023-02-16 13:03:52 +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
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00