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85608555fe5a122d28b60b6279440b35e482a534
rdkit/Code/GraphMol
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Greg Landrum 85608555fe add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573) 
* add ROMol::atomBonds() and ROMol::atomNeighbors() methods

* remove some warnings

* start using the new code

* add default for those template params

* some more applications

* get the SWIG builds working

* get rid of extraneous ref

* remove extraneous comments
2021-10-02 07:28:24 +02:00
..
Abbreviations
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
ChemTransforms
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
CIPLabeler
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Depictor
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Deprotect
Allow applying single-reactant/single-product reactions in place (#4511)
2021-09-26 14:35:23 -04:00
Descriptors
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
DistGeomHelpers
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
FileParsers
Fixes #4561 (#4562)
2021-09-27 04:48:59 +02:00
FilterCatalog
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
Fingerprints
Fixes #4273 (#4523)
2021-09-28 04:18:18 +02:00
FMCS
cleanup some compiler warnings (#4521)
2021-09-16 04:34:40 +02:00
ForceFieldHelpers
fix a thread-safety bug in the UFF parameter acquisition (#4553)
2021-09-29 09:31:36 +02:00
FragCatalog
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
cleanup some compiler warnings (#4521)
2021-09-16 04:34:40 +02:00
MolAlign
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +02:00
MolCatalog
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
MolChemicalFeatures
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
MolDraw2D
Fixes #4538 (#4539)
2021-09-21 18:16:25 +02:00
MolEnumerator
Add support for SRUs to MolEnumerator (#4563)
2021-09-28 16:37:39 +02:00
MolHash
- removed spurious dllexport on enums (#4353)
2021-07-27 18:06:51 +02:00
MolInterchange
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
MolStandardize
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
MolTransforms
cleanup some compiler warnings (#4521)
2021-09-16 04:34:40 +02:00
PartialCharges
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
ReducedGraphs
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +02:00
RGroupDecomposition
Major speed-up of RGD scoring (#4544)
2021-09-30 09:31:49 -04:00
ScaffoldNetwork
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
ShapeHelpers
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +02:00
SLNParse
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
SmilesParse
Fixes #4503 (#4507)
2021-09-15 18:00:18 +02:00
StructChecker
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
Subgraphs
cleanup a bunch of compiler warnings (#3849)
2021-02-26 05:10:02 +01:00
Substruct
save one search (#4566)
2021-09-28 04:37:24 +02:00
SubstructLibrary
cleanup some compiler warnings (#4521)
2021-09-16 04:34:40 +02:00
TautomerQuery
save one search (#4566)
2021-09-28 04:37:24 +02:00
test_data
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Run clang-tidy (modernize-pass-by-value) (#4224)
2021-06-14 06:57:08 +02:00
Wrap
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
AddHs.cpp
Make sure that added R-groups have non-zero coordinates (#3877)
2021-03-19 08:17:56 +01:00
AdjustQuery.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Aromaticity.cpp
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
Atom.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Atom.h
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +02:00
atomic_data.cpp
Fixes #3531 (#3545)
2020-11-08 07:17:37 +01:00
atomic_data.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
AtomIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
BondIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Canon.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
catch_adjustquery.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
catch_chirality.cpp
fixes (#4569)
2021-09-28 04:42:39 +02:00
catch_graphmol.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
catch_main.cpp
Fixes #4508 (#4512)
2021-09-15 16:06:36 +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 ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Chirality.h
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
CMakeLists.txt
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
ConjugHybrid.cpp
Stop trying to assign hybridization to actinides (#3281)
2020-07-25 05:04:54 +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
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
FindStereo.cpp
Fix some problems with perception of ring chirality in spiro-linked systems (#4280)
2021-07-02 14:14:02 -04:00
GraphMol.cpp
first pass, using google style
2015-11-14 14:58:11 +01:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
Fixes some problems with findPotentialStereo() (#3499)
2020-10-17 04:35:58 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Allow applying single-reactant/single-product reactions in place (#4511)
2021-09-26 14:35:23 -04:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
MolBundle.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
MolDiscriminators.cpp
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
MolOps.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
MolOps.h
Allow applying single-reactant/single-product reactions in place (#4511)
2021-09-26 14:35:23 -04:00
molopstest.cpp
fixes (#4569)
2021-09-28 04:42:39 +02:00
MolPickler.cpp
Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
2021-08-24 17:19:46 -04:00
MolPickler.h
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +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
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
new_canon.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
PeriodicTable.cpp
Fixes #3646 (#3653)
2020-12-17 08:34:15 -05:00
PeriodicTable.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryOps.cpp
Fixes #4496 (#4497)
2021-09-13 04:54:26 +02:00
QueryOps.h
fix warning (#4555)
2021-09-25 15:46:48 +02:00
querytest.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +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-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
Resonance.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
RingInfo.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
ROMol.h
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
RWMol.cpp
Fixes #4468 and #4476 (#4482)
2021-09-05 05:43:13 +02:00
RWMol.h
Fixes #4468 and #4476 (#4482)
2021-09-05 05:43:13 +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
lambda cleanup (#4432)
2021-08-24 10:29:31 -04:00
StereoGroup.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
SubstanceGroup.cpp
lambda cleanup (#4432)
2021-08-24 10:29:31 -04:00
SubstanceGroup.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +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
Fixes #4494 (#4495)
2021-09-13 04:39:55 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPicklerGlobalSettings.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
testSGroup.cpp
Fixes #4468 and #4476 (#4482)
2021-09-05 05:43:13 +02:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00