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293328845bbbd985575702077448e19ba4d9e8be
rdkit/Code/GraphMol
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David Cosgrove 293328845b Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823) 
* Add overloads of getMolFrags and getMolFragsWithQuery that fill in using std::unique_ptr rather than boost::shared_ptr.

* Response to review - do things in unique_ptrs from the outset rather than raw pointers.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
2024-09-20 09:48:08 +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
consolidate numeric vectors (#7792)
2024-09-18 07:43:17 +02:00
ChemTransforms
Fix performance issue in PR 7327 (#7391)
2024-04-28 06:16:20 +02:00
CIPLabeler
Fix some missing headers when doing "make install" (#7667)
2024-07-25 11:07:03 -04:00
Depictor
reject template if it doesn't match bond stereo (#7567)
2024-09-17 06:00:01 +02:00
Deprotect
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
Descriptors
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
DetermineBonds
Removes call to debugMol that logs to std::err (#7690)
2024-08-06 15:41:56 +02:00
DistGeomHelpers
Ensure 13 bounds constraints are added to angles that are part of an improper torsion (#7729)
2024-08-21 16:06:29 +02:00
FileParsers
add mol processing API (#7773)
2024-09-19 18:42:25 +02:00
FilterCatalog
consolidate numeric vectors (#7792)
2024-09-18 07:43:17 +02:00
Fingerprints
fix typo (Fingeprint -> Fingerprint) (#7801)
2024-09-16 06:18:43 +02:00
FMCS
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
ForceFieldHelpers
Expose MMFF aromaticity model for SetAromaticity (#7765)
2024-09-18 05:59:02 +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
Fix some missing headers when doing "make install" (#7667)
2024-07-25 11:07:03 -04:00
MMPA
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
MolAlign
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
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
add mol processing API (#7773)
2024-09-19 18:42:25 +02:00
MolEnumerator
Add Python modules to generate stubs and automatically patch docstrings (#6919)
2023-11-30 04:54:18 +01:00
MolHash
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +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
MolProcessing
add mol processing API (#7773)
2024-09-19 18:42:25 +02:00
MolStandardize
refactor MolStandardize::PipelineOptions::allowEmptyMolecules (#7699)
2024-08-13 15:33:13 +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
Rascal match exact atom type (#7673)
2024-09-16 04:45:18 +02:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
Enable RGD highlights as in blog post (#7322)
2024-09-16 16:14:13 +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
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
SmilesParse
Fixes #7725 (#7728)
2024-08-26 08:56:51 +02:00
StructChecker
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
SubstructLibrary
add mol processing API (#7773)
2024-09-19 18:42:25 +02:00
TautomerQuery
consolidate numeric vectors (#7792)
2024-09-18 07:43:17 +02:00
test_data
Fixes #7501 dative bonds in cdxml (#7757)
2024-08-28 05:59:43 +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
Expose MMFF aromaticity model for SetAromaticity (#7765)
2024-09-18 05:59:02 +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
Expose MMFF aromaticity model for SetAromaticity (#7765)
2024-09-18 05:59:02 +02:00
Atom.cpp
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
Atom.h
Fixes #7318 (#7319)
2024-04-03 15:34:37 +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 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
A collection of small improvements from Roger S (#7566)
2024-06-26 08:29:57 +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
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
add findMesoCenters (#7574)
2024-06-28 04:55:49 +02:00
catch_chirality.cpp
Fixes #7598 (#7604)
2024-07-15 14:15:32 -04:00
catch_graphmol.cpp
add findMesoCenters (#7574)
2024-06-28 04:55:49 +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
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
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
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
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 #6757 (#7664)
2024-07-25 15:26:22 +02:00
Chirality.h
add findMesoCenters (#7574)
2024-06-28 04:55:49 +02:00
CMakeLists.txt
add mol processing API (#7773)
2024-09-19 18:42:25 +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 #7556 (#7646)
2024-07-22 16:34:08 +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
Fixes #7598 (#7604)
2024-07-15 14:15:32 -04:00
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
Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)
2024-09-20 09:48:08 +02:00
MolOps.h
Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)
2024-09-20 09:48:08 +02:00
molopstest.cpp
Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)
2024-09-20 09:48:08 +02:00
MolPickler.cpp
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
MolPickler.h
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
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
add findMesoCenters (#7574)
2024-06-28 04:55:49 +02:00
new_canon.h
add findMesoCenters (#7574)
2024-06-28 04:55:49 +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
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +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
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
QueryOps.h
give a HasPropWithValueQueryBase a virtual destructor (#7786)
2024-09-09 13:06:44 +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
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +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
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +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