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2b99ee477c19cb7bf4e826b386ab465cbc21bb2f
rdkit/Code/GraphMol
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Brian Kelley 2b99ee477c Allow fragments to be grouped in cdxml (#7529) 
* Allow fragments to be groups in CDXML

* Add support for grouped reactants

* run clang-format

* Change github issue to 7528

* Add documents to the code

* response to review, check grouped reactants in cdxml against rxn file

* Remove unused code

* Add missing file

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
2024-06-23 07:02:19 +02:00
..
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
Allow fragments to be grouped in cdxml (#7529)
2024-06-23 07:02:19 +02:00
ChemTransforms
Fix performance issue in PR 7327 (#7391)
2024-04-28 06:16:20 +02:00
CIPLabeler
Ring stereo atropisomers (#7486)
2024-06-13 08:35:42 +02:00
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
Numpy 2 Support (#7531)
2024-06-19 07:54:50 +02:00
DetermineBonds
Fixes github 7331 (#7352)
2024-04-19 10:17:02 +02:00
DistGeomHelpers
add option to symmetrize conjugated terminal groups when RMS pruning conformers (#7270)
2024-03-19 04:38:29 +01:00
FileParsers
Allow fragments to be grouped in cdxml (#7529)
2024-06-23 07:02:19 +02:00
FilterCatalog
Remove unnecessary wrapped pointers (#7465)
2024-05-30 14:12:33 +02:00
Fingerprints
Fixes github #7533 (#7539)
2024-06-20 09:27:27 +02:00
FMCS
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
ForceFieldHelpers
Allow creation of an empty forcefield (#7494)
2024-06-08 05:18:22 +02:00
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
Prefer wedging ring bonds around atropisomers (#7373)
2024-05-08 06:04:23 +02:00
MMPA
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
MolAlign
add option to symmetrize conjugated terminal groups when RMS pruning conformers (#7270)
2024-03-19 04:38:29 +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
Fix issues arising from useMolBlockWedging and the new atropisomer kekulization code (#7540)
2024-06-20 19:32:41 +02:00
MolEnumerator
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolHash
Shrink the tautomeric zone for the v2 hash of things like imines (#7502)
2024-06-07 05:09:57 +02:00
MolInterchange
- patch RapidJSON 1.1.0 release backporting a fix from the master branch to avoid a compilation error on newer compilers (fix #7485) (#7550)
2024-06-23 06:59:52 +02:00
MolStandardize
Optionally limit the MolStandardize::Uncharger to only alter the protonation state (#7458)
2024-06-13 08:37:24 +02:00
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
Add option for RASCAL to restrict atom matching to atoms of same degree (#7344)
2024-04-11 16:20:38 +02:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
remove some warnings with -Wextra (#7339)
2024-04-11 11:01:59 +02:00
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
Favor nonwedged bonds in kekulization (#7456)
2024-06-05 13:56:00 +02:00
StructChecker
fix location of MolFileSterechem.h (#7420)
2024-05-07 06:26:42 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-01-23 17:13:53 +01:00
SubstructLibrary
Allow the substruct library to be deleted when refcount goes to 0 (#7462)
2024-05-28 04:39:54 +02:00
TautomerQuery
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
test_data
Allow fragments to be grouped in cdxml (#7529)
2024-06-23 07:02:19 +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
add MolToV2KMolBlock() (#7511)
2024-06-13 09:43:59 +02:00
AddHs.cpp
Postpone clearing computed properties until after all Hs removed (#7241)
2024-03-16 06:14:24 +01:00
AdjustQuery.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Aromaticity.cpp
Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)
2024-01-23 17:13:53 +01:00
Atom.cpp
Fixes #7318 (#7319)
2024-04-03 15:34:37 +02:00
Atom.h
Fixes #7318 (#7319)
2024-04-03 15:34:37 +02:00
atomic_data.cpp
Fix #7311: problem with InChI for phosphinic acid (#7419)
2024-05-03 21:23:37 +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
Atropisomers.cpp
Fixes #7367 (#7426)
2024-05-16 09:24:55 +02:00
Atropisomers.h
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +01:00
Bond.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +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
Fixes #7023 (#7136)
2024-02-06 15:57:21 +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 #7023 (#7136)
2024-02-06 15:57:21 +01:00
catch_chirality.cpp
Fixes #7509 (#7513)
2024-06-14 05:39:48 +02:00
catch_graphmol.cpp
Favor nonwedged bonds in kekulization (#7456)
2024-06-05 13:56:00 +02:00
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_periodictable.cpp
Fixes #7162 (#7220)
2024-03-09 15:40:51 -05:00
catch_pickles.cpp
fix a problem with reading older pickles (#7180)
2024-02-22 14:03:45 +01:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
Fixes #7246 (#7247)
2024-03-16 07:37:16 +01:00
Chirality.cpp
Fixes #7509 (#7513)
2024-06-14 05:39:48 +02:00
Chirality.h
Fixes #7438 (#7474)
2024-05-31 14:41:22 +02:00
CMakeLists.txt
install atrop header (#7487)
2024-06-04 16:15:21 +02:00
Conformer.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
Conformer.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ConjugHybrid.cpp
Fixes #7318 (#7319)
2024-04-03 15:34:37 +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
Ring stereo atropisomers (#7486)
2024-06-13 08:35:42 +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
Fix a pathological slow case with the new getMolFrags() (#7121)
2024-02-06 04:23:48 +01:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Favor nonwedged bonds in kekulization (#7456)
2024-06-05 13:56:00 +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
Include macrocycles in atropisomer calculation by not sanitizing them away (#7291)
2024-04-09 06:05:25 +02:00
MolOps.h
Expose a couple of additional functions to Python (#7444)
2024-05-17 04:47:30 +02:00
molopstest.cpp
make sure outdated ring fusion information is recomputed before attempting to use it (#7274)
2024-03-20 09:37:10 +01:00
MolPickler.cpp
fix a problem with reading older pickles (#7180)
2024-02-22 14:03:45 +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
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
new_canon.cpp
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +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
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryOps.cpp
fixing issue 5890 (#7152)
2024-02-09 13:24:59 +01:00
QueryOps.h
Expose replaceAtomWithQueryAtom to Python (#7380)
2024-05-07 06:50:59 +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
make sure outdated ring fusion information is recomputed before attempting to use it (#7274)
2024-03-20 09:37:10 +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
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ROMol.h
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
RWMol.cpp
Fix performance issue in PR 7327 (#7391)
2024-04-28 06:16:20 +02:00
RWMol.h
Postpone clearing computed properties until after all Hs removed (#7241)
2024-03-16 06:14:24 +01:00
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)
2024-02-25 17:46:21 +01:00
StereoGroup.h
fragmentation of mol loses any sgroups (#7056)
2024-01-25 13:32:55 +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
switch to range-based for loops (#7278)
2024-04-08 14:16:27 +02:00
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
Fixes #7064 (#7141)
2024-02-22 06:46:39 +01:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
No coords atropisomers - fix smiles output of atrop wedges after reordering (#7418)
2024-05-07 17:06:33 +02:00