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553424d6b69ff053ca92446f8dbe02ef3fb9b973
rdkit/Code/GraphMol
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Brian Kelley 553424d6b6 Revert "Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) (#8743)" (#8814) 
This reverts commit 040bdb61c7.

During testing of using this as a replacement for portions of
getTheFrags in getMolFrags, several issues came up regarding
how copies should actually work in practice.  These are being
corrected in a new pr:  https://github.com/rdkit/rdkit/pull/8811

Co-authored-by: Brian Kelley <bkelley@glysade.com>
2025-09-25 10:54:36 +02:00
..
Abbreviations
Improve doc string for ParseAbbreviations in python wrapper. (#8049)
2024-11-28 13:54:04 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
ChemTransforms
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
CIPLabeler
Make assignCIPLabels Ctrl+c interruptable (#8589)
2025-06-27 08:27:44 +02:00
Depictor
Add the useRingTemplates option to generateDepictionMatching2DStructure (#8688)
2025-08-25 19:39:57 +02:00
Deprotect
Fixes #7989 Incorrect benzyl deprotection reaction (#7990)
2024-11-07 18:34:59 +01:00
Descriptors
Fixes #7264 (#8696)
2025-08-12 16:27:18 +02:00
DetermineBonds
Some cleanup of the xyz2mol code (#8567)
2025-06-05 08:43:22 -04:00
DistGeomHelpers
Fix grad scaling (#8791)
2025-09-21 18:19:50 +02:00
EnumerateStereoisomers
Mem fixes (#8640)
2025-07-21 05:57:50 +02:00
FileParsers
support bond property lists in SDF (#8778)
2025-09-17 16:17:12 +02:00
FilterCatalog
Check for PAINS_C file existence in update_pains.py script (#8431)
2025-04-11 11:16:25 +02:00
Fingerprints
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
FMCS
style: apply modernize-use-override (#8137)
2025-04-25 12:24:58 +02:00
ForceFieldHelpers
update default ET version to 2 in getExperimentalTorsions (#8798)
2025-09-24 05:56:35 +02:00
FragCatalog
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
GeneralizedSubstruct
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
GenericGroups
Modernization of some substructure code (#8450)
2025-05-12 06:33:25 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
MMPA
Fixes #8569 (#8588)
2025-07-21 23:45:09 -04:00
MolAlign
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolCatalog
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolChemicalFeatures
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
MolDraw2D
- move MolDrawOptions JSON parsing code to a separate compilation unit (#8783)
2025-09-23 09:27:13 +02:00
MolEnumerator
Implements #8222 adds react_idx (index of reactant) to product atoms (#8231)
2025-02-06 17:07:55 +01:00
MolHash
Fixes #8654 (#8657)
2025-07-30 05:56:52 +02:00
MolInteractionFields
style: apply modernize-use-override (#8137)
2025-04-25 12:24:58 +02:00
MolInterchange
Fixes #8460 (#8468)
2025-04-28 07:38:50 +02:00
MolProcessing
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-10 16:08:50 +02:00
MolStandardize
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
MolTransforms
CanonicalizeConformer inverts structure (#8734)
2025-08-27 17:12:08 +02:00
PartialCharges
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +01:00
RascalMCES
Fix Rascal out of memory bug. (#8648)
2025-07-24 16:43:09 +02:00
ReducedGraphs
Fix off-by-one error in Reduced Graph fingerprint bitstring. (#8385)
2025-04-07 13:20:19 +02:00
RGroupDecomposition
fix a mistake caused by a dumb suggestion (#8792)
2025-09-19 09:33:32 +02:00
ScaffoldNetwork
Allow inclusion of molecule names in ScaffoldNetwork (#7956)
2024-10-30 06:11:30 +01:00
ShapeHelpers
Fix inversion of stereo with canonicalizeConformer (#7878)
2024-10-10 09:57:39 -04:00
SLNParse
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
SmilesParse
Avoid code duplication through a templated function and improve JSON parsing of Boolean flags (#8773)
2025-09-16 16:29:04 +02:00
StructChecker
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
Subgraphs
Revert "Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) (#8743)" (#8814)
2025-09-25 10:54:36 +02:00
Substruct
Modernization of some substructure code (#8450)
2025-05-12 06:33:25 +02:00
SubstructLibrary
remove no-op macros and dead code (pt 1) (#8012)
2024-11-19 04:31:56 +01:00
SynthonSpaceSearch
Fixes Github8650 - spaces in columns in tab-separated synthon space files (#8652)
2025-07-25 06:35:35 +02:00
TautomerQuery
Modernization of some substructure code (#8450)
2025-05-12 06:33:25 +02:00
test_data
Fixes #8689 (#8738)
2025-09-03 12:15:09 +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
support bond property lists in SDF (#8778)
2025-09-17 16:17:12 +02:00
AddHs.cpp
fix a logic error in needsHs (#8442)
2025-04-16 14:36:45 +02:00
AdjustQuery.cpp
apply query adjustments when makeAtomsGeneric is enabled (#8315)
2025-03-04 13:50:24 +01:00
Aromaticity.cpp
fixes #5078 (#8795)
2025-09-22 11:06:42 +02:00
Atom.cpp
add clearPropertyCache() (#8533)
2025-05-18 08:14:05 +02:00
Atom.h
add clearPropertyCache() (#8533)
2025-05-18 08:14:05 +02:00
atomic_data.cpp
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
atomic_data.h
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
AtomIterators.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Atropisomers.cpp
Fix for Issue 8602 (#8668)
2025-08-20 10:10:47 +02:00
Atropisomers.h
Fixes #7983 (#8342)
2025-03-20 07:40:33 +01:00
Bond.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
Bond.h
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
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
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
Canon.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
Canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
catch_adjustquery.cpp
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
catch_canon.cpp
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
catch_chirality.cpp
Fixes #8712 (#8736)
2025-09-11 05:01:08 +02:00
catch_graphmol.cpp
fixes #5078 (#8795)
2025-09-22 11:06:42 +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_molops.cpp
Fix the way carbon is handed in cleanupOrganometallics() (#8301)
2025-03-03 17:30:41 +01:00
catch_organometallics.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_periodictable.cpp
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
catch_pickles.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Chirality.cpp
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
Chirality.h
style: apply modernize-use-override (#8137)
2025-04-25 12:24:58 +02:00
CMakeLists.txt
Cpp enumerate stereoisomers (#8563)
2025-06-05 08:29:54 +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
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
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
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
FindStereo.cpp
Fixes #8712 (#8736)
2025-09-11 05:01:08 +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 across everything (#7849)
2024-09-26 13:39:02 +02:00
itertest.cpp
remove no-op macros and dead code (pt 2) (#8035)
2025-01-11 14:10:00 +01:00
Kekulize.cpp
Synthon space bad chiral count (#8550)
2025-06-03 13:09:09 +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 problem with stereogroups involving bonds and getMolFrags() (#8558)
2025-05-27 16:43:20 +02:00
MolOps.h
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
molopstest.cpp
fixes #5078 (#8795)
2025-09-22 11:06:42 +02:00
MolPickler.cpp
GitHub 7865 haspropwithvaluequery leaks (#7872)
2024-10-30 06:12:40 +01:00
MolPickler.h
Expose propertyFlags to CFFI and MinimalLib (#7960)
2024-11-07 06:08:27 +01:00
MolProps.cpp
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
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
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
new_canon.h
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
NontetrahedralStereo.cpp
fix: apply modernize-use-nullptr (#8134)
2025-01-09 07:56:10 +01:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
QueryAtom.cpp
Github8353 (#8354)
2025-03-17 19:54:15 +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
Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)
2025-03-29 07:26:03 +01:00
QueryOps.h
Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)
2025-03-29 07:26:03 +01:00
querytest.cpp
A few mem fixes in tests (#8521)
2025-05-13 12:17:52 +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 canonicalization of stereogroups (#7041)
2024-10-11 17:09:18 +02:00
resMolSupplierTest.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Resonance.cpp
Fix #8638 (#8639)
2025-07-25 14:33:32 +02:00
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
add clearPropertyCache() (#8533)
2025-05-18 08:14:05 +02:00
ROMol.h
add clearPropertyCache() (#8533)
2025-05-18 08:14:05 +02:00
RWMol.cpp
fix a problem with stereogroups involving bonds and getMolFrags() (#8558)
2025-05-27 16:43:20 +02:00
RWMol.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +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
fix a problem with stereogroups involving bonds and getMolFrags() (#8558)
2025-05-27 16:43:20 +02:00
StereoGroup.h
fix a problem with stereogroups involving bonds and getMolFrags() (#8558)
2025-05-27 16:43:20 +02:00
SubstanceGroup.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
SubstanceGroup.h
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
test1.cpp
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
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
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-15 14:00:32 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
A couple optimizations to when the ring finding code is called (#8482)
2025-04-30 16:21:49 +02:00