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09aa009f197fb006e105f4dbd1339a2bf7ed55ac
rdkit/Code/GraphMol
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Greg Landrum 09aa009f19 [v2 API] reaction parsers (#7138) 
* basic approach to v2api

* does not work, backup commit

* well, that now compiles

* cleaner

* more cleanup and testing

* get the SWIG wrappers to build

* swig wrappers now build

* switch back to using references to default values

* adjust to new catch version

* move the implementation to v2 and call it from v1

* update the parameter object too

* move debugParse down

* a couple of review changes

* make v2 naming consistent with Python

* first pass at v2 for the ctab parsers

* move a the writing functionality to a different header

this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code

* do v2 of the tpl parser

* fix missing dependency

* Mol2 parser

* move over the XYZ parser

* switch over the PDB parsers too

* get mac and java builds working (hopefully)

* add v2 API for the reaction parsers

Fixes #7075

* v2 of the fileparser API about done

This cannot be completed until the CDXML changes are merged
2024-02-07 17:41:01 +01:00
..
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
[v2 API] reaction parsers (#7138)
2024-02-07 17:41:01 +01:00
ChemTransforms
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CIPLabeler
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
DetermineBonds
Fixes #6961 (#6971)
2023-12-09 06:17:53 +01:00
DistGeomHelpers
fix a memory overwrite (#7147)
2024-02-07 17:40:41 +01:00
FileParsers
restore the header installation (#7143)
2024-02-07 06:47:57 +01:00
FilterCatalog
fix several warnings originating from the swig wrappers (#7063)
2024-01-30 04:44:43 +01:00
Fingerprints
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
FMCS
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
ForceFieldHelpers
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
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
[v2 API] MRV parsers (#7110)
2024-02-02 18:48:30 +01:00
MMPA
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
MolAlign
Add multithreading to getBestRMS and new getAllConformerBestRMS (#6896)
2023-11-22 17:35:06 +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
Fixes #7122 (#7126)
2024-02-03 06:47:28 +01:00
MolEnumerator
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolHash
Fixes #6472 - remove aromatic bond flags in Molhash anonymous graph (#7027)
2024-01-09 06:12:03 +01:00
MolInterchange
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
MolStandardize
Add a 'force' option to MolStandardizer::Uncharger (#7088)
2024-02-06 15:34:28 +01:00
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
Extra rascal option (#7073)
2024-01-23 06:05:58 +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)
2024-01-23 17:13:53 +01:00
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
Fixes #5499 (#7118)
2024-02-01 17:20:21 +01:00
StructChecker
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
TautomerQuery
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
test_data
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Add v2 API to FileParsers (#7077)
2024-01-28 05:11:54 +01:00
AddHs.cpp
Fixes #7123 (#7124)
2024-02-02 05:27:47 +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
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-01-18 05:06:57 +01:00
Atom.h
Add Atom::hasValenceViolation (Take 2) (#7030)
2024-01-18 05:06:57 +01:00
atomic_data.cpp
Fixes #6961 (#6971)
2023-12-09 06:17:53 +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
Atropisomers.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Atropisomers.h
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +01:00
Bond.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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 #7076 (#7092)
2024-01-25 19:31:18 +01:00
catch_graphmol.cpp
Fixes #7131 (#7132)
2024-02-06 15:55:42 +01:00
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_pickles.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
Chirality.cpp
Fixes #7131 (#7132)
2024-02-06 15:55:42 +01:00
Chirality.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CMakeLists.txt
Add v2 API to FileParsers (#7077)
2024-01-28 05:11:54 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
FindStereo.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
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
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)
2023-11-23 05:57:05 +01:00
MolOps.cpp
Fix a pathological slow case with the new getMolFrags() (#7121)
2024-02-06 04:23:48 +01:00
MolOps.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
molopstest.cpp
Fixes #7123 (#7124)
2024-02-02 05:27:47 +01:00
MolPickler.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
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
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
Support additional generic groups (#6570)
2023-08-10 06:36:38 +02:00
QueryOps.h
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
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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
ROMol.h
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
RWMol.cpp
Fixes #7128 (#7129)
2024-02-04 06:40:31 +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
fragmentation of mol loses any sgroups (#7056)
2024-01-25 13:32:55 +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
Fixes #7115 (#7117)
2024-02-01 05:02:46 +01:00
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
Allow removal of non-special H atoms in SGroups (#5399)
2022-07-07 11:05:18 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00