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42eed2605dbd5fb6ce03bd72ab714c8a537dfea5
rdkit/Code/GraphMol
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Greg Landrum 42eed2605d Add CXSMILES support for bond wedging and wiggly bonds (#5575) 
* initial support for wiggly and wedged bonds in cxsmiles
add CX_ALL_BUT_COORDS convenience option to CXSMILES writer

* move ClearSingleBondDirFlags to MolOps

* do a better job of handling the wiggly bonds

* mark 3D conformers from CXSMILES

* remove some extraneous printing

* test wD as well

* remove non-applicable test

* basic tests (not passing) for parsing t/c/ctu

* remove test for unimplemented feature

* changes in response to review

* changes in response to review

check for attempt to set the wedging more than once
testing for invalid w blocks
fix a bad comment
2022-09-24 05:44:01 +02:00
..
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
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
ChemTransforms
Fixed R-group attachment positions in RGD (#5570)
2022-09-20 06:35:13 +02:00
CIPLabeler
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Depictor
Fixes #5156 (#5412)
2022-07-27 08:21:28 +02:00
Deprotect
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Descriptors
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
DistGeomHelpers
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
FileParsers
Add CXSMILES support for bond wedging and wiggly bonds (#5575)
2022-09-24 05:44:01 +02:00
FilterCatalog
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
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
Fix typo: quarternary --> quaternary (#5243)
2022-04-29 08:09:34 +02:00
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
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
MolAlign
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
MolCatalog
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
MolChemicalFeatures
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolDraw2D
fix warnings (#5561)
2022-09-14 06:36:42 +02:00
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 #5402 (#5542)
2022-09-09 05:06:42 +02:00
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
Fixed R-group attachment positions in RGD (#5570)
2022-09-20 06:35:13 +02:00
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
Add CXSMILES support for bond wedging and wiggly bonds (#5575)
2022-09-24 05:44:01 +02:00
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
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
TautomerQuery
fix warnings (#5561)
2022-09-14 06:36:42 +02:00
test_data
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +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
By default mergeQueryHs now will not remove isotopes (#5563)
2022-09-16 17:29:32 +02:00
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
Fix performance issue in RingUtils::checkFused that slowed down sanitization (#5410)
2022-07-08 05:19:22 +02:00
Atom.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
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
Fixes #2984 (#5560)
2022-09-15 04:55:31 +02:00
catch_graphmol.cpp
Fixes #5505: problems when kekulizing molecules with query bonds (#5550)
2022-09-13 14:49:45 +02:00
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
Add CXSMILES support for bond wedging and wiggly bonds (#5575)
2022-09-24 05:44:01 +02:00
Chirality.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
CMakeLists.txt
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +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
Move to C++17 (#5155)
2022-04-12 13:53:07 +02:00
FindStereo.cpp
Fixes #2984 (#5560)
2022-09-15 04:55:31 +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 #5462 (#5463)
2022-08-03 04:46:17 +02:00
MolOps.h
Add CXSMILES support for bond wedging and wiggly bonds (#5575)
2022-09-24 05:44:01 +02:00
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
fix doxygen comments (#5254)
2022-07-11 13:55:35 +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
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