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c2fb57c19f8bac4aac07f4d0915ece8d95f7c963
rdkit/Code/GraphMol
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Gareth Jones c2fb57c19f RGD - a fix for the cubane issue (single target atom matches 2 user R group attachments) (#4002) 
* Most tests working

* All tests working

* Fixed tests after merge with master

* Create header and implementations for RCore

* Updated comments

* Removed old code

* DLL export for MolMatchFinalCheckFunctor

* Information line for failing Mac test

* Log replace core behaviour

* Ordering fix for OSX

* Possible fuzzer fix

* Removed debug output

* Fix unmatched user R group bug

* Code review changes

* Bug fix and ChemTransforms test
2021-05-23 15:16:03 -04:00
..
Abbreviations
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
ChemTransforms
RGD - a fix for the cubane issue (single target atom matches 2 user R group attachments) (#4002)
2021-05-23 15:16:03 -04:00
CIPLabeler
Address #2753 (#3750)
2021-02-15 14:29:04 +01:00
Depictor
renames optional parameter that I forgot to rename previously (#3853)
2021-02-25 04:53:08 +01:00
Deprotect
[WIP] Deprotection Library (#3294)
2020-09-11 05:35:36 +02:00
Descriptors
MinimalLib: add CFFI interface (#4018)
2021-04-15 21:33:52 +02:00
DistGeomHelpers
Cleanup some problems found during an ASAN build (#4054)
2021-04-21 10:22:04 -04:00
FileParsers
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
FilterCatalog
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
Fingerprints
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
FMCS
avoid that lone atoms which are part of a ring in one of the molecules become part of the MCS (#4065)
2021-04-27 11:10:29 +02:00
ForceFieldHelpers
fixes #3824 (#3949)
2021-03-19 04:57:28 +01:00
FragCatalog
A collection of MolStandardize improvements (#4118)
2021-05-19 09:11:23 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
MolAlign
Enhanced generateDepictionMatching2DStructure functionality (#3811)
2021-02-24 05:37:31 +01:00
MolCatalog
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
MolChemicalFeatures
Fix for Github issue 2530 (#3657)
2020-12-19 05:49:11 +01:00
MolDraw2D
MolDraw2D: support changing annotation colours (#3919)
2021-03-17 15:20:20 +01:00
MolEnumerator
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
MolHash
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
MolInterchange
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
MolStandardize
A collection of MolStandardize improvements (#4118)
2021-05-19 09:11:23 +02:00
MolTransforms
Add rendering of SGroup brackets to MolDraw2D (#3586)
2020-11-28 08:03:20 +01:00
PartialCharges
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
ReducedGraphs
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
RGroupDecomposition
RGD - a fix for the cubane issue (single target atom matches 2 user R group attachments) (#4002)
2021-05-23 15:16:03 -04:00
ScaffoldNetwork
Allow batch editing of molecules: removal only (#3875)
2021-03-11 05:10:43 +01:00
ShapeHelpers
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
SLNParse
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
SmilesParse
make sure atom and bond bookmarks survive replaceAtom/Bond (#4033)
2021-04-16 04:54:09 +02:00
StructChecker
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
Subgraphs
cleanup a bunch of compiler warnings (#3849)
2021-02-26 05:10:02 +01:00
Substruct
RGD - a fix for the cubane issue (single target atom matches 2 user R group attachments) (#4002)
2021-05-23 15:16:03 -04:00
SubstructLibrary
Cleanup some problems found during an ASAN build (#4054)
2021-04-21 10:22:04 -04:00
TautomerQuery
A collection of MolStandardize improvements (#4118)
2021-05-19 09:11:23 +02:00
test_data
Allow partial deserialization of molecules (#4040)
2021-04-24 07:22:55 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
Wrap
Fixes #4138 (#4145)
2021-05-18 08:44:12 -04:00
AddHs.cpp
Make sure that added R-groups have non-zero coordinates (#3877)
2021-03-19 08:17:56 +01:00
AdjustQuery.cpp
all tests now passing
2020-12-08 15:39:45 +01:00
Aromaticity.cpp
Improve performance of aromaticity detection for large molecules (#3253)
2020-08-13 05:57:16 +02:00
Atom.cpp
fix problem with H+ caused by #3473 (#3503)
2020-10-19 12:45:00 -04:00
Atom.h
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
atomic_data.cpp
Fixes #3531 (#3545)
2020-11-08 07:17:37 +01:00
atomic_data.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
AtomIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
AtomIterators.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Bond.cpp
basic h bond support (#3871)
2021-03-06 09:39:13 -05:00
Bond.h
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
BondIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
BondIterators.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
Canon.h
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
catch_adjustquery.cpp
Fixes a number of issues flagged by clang (#3498)
2020-10-15 15:03:34 +02:00
catch_chirality.cpp
Fixes #4115 (#4117)
2021-05-07 10:21:48 -04:00
catch_graphmol.cpp
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
catch_main.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
catch_sgroups.cpp
add methods to allow the following properties from SubstanceGroups to be cleared: (#3547)
2020-11-03 12:02:25 -05:00
Chirality.cpp
Fixes #4115 (#4117)
2021-05-07 10:21:48 -04:00
Chirality.h
Fixes some problems with findPotentialStereo() (#3499)
2020-10-17 04:35:58 +02:00
CMakeLists.txt
Clean up CMake files (#3417)
2020-11-28 08:00:39 +01:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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
Sped up SSSR by not storing every path back to root (#3333)
2020-08-15 06:00:40 +02:00
FindStereo.cpp
Fixes some problems with findPotentialStereo() (#3499)
2020-10-17 04:35:58 +02:00
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
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
Matrices.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
memtest1.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
MolBundle.h
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolDiscriminators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.cpp
Fixes #3330 (#3869)
2021-03-05 19:59:37 -05:00
MolOps.h
Make sure that added R-groups have non-zero coordinates (#3877)
2021-03-19 08:17:56 +01:00
molopstest.cpp
Cleanup some problems found during an ASAN build (#4054)
2021-04-21 10:22:04 -04:00
MolPickler.cpp
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
MolPickler.h
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
MonomerInfo.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
new_canon.cpp
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
new_canon.h
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
PeriodicTable.cpp
Fixes #3646 (#3653)
2020-12-17 08:34:15 -05:00
PeriodicTable.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
QueryBond.cpp
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
QueryBond.h
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
QueryOps.cpp
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
QueryOps.h
Enable storing queries in JSON (#4003)
2021-05-04 06:37:24 +02:00
querytest.cpp
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
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
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
Resonance.cpp
Mem checkup & fixes (#3510)
2020-11-09 12:08:36 -05:00
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
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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
Allow partial deserialization of molecules (#4040)
2021-04-24 07:22:55 +02:00
RWMol.cpp
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
RWMol.h
fix a leak in RWMol (#3970)
2021-03-24 20:16:00 +01:00
SanitException.h
Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)
2020-04-01 14:30:07 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
StereoGroup.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
SubstanceGroup.cpp
Small bug fixes and cleanups from fuzz testing (#3299)
2020-07-22 16:57:31 +02:00
SubstanceGroup.h
Make better use of strictParsing for SGroups (#3705)
2021-01-14 10:29:41 +01:00
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
Updated code for chirality perception (#3324)
2020-09-02 15:00:29 +02:00
testMolBundle.cpp
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
testPickler.cpp
Allow partial deserialization of molecules (#4040)
2021-04-24 07:22:55 +02:00
testPicklerGlobalSettings.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
testSGroup.cpp
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00