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c9199cf1dafd95fdecaaacc44d64abc10d47bced
rdkit/Code/GraphMol
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Ric c9199cf1da Address #2753 (#3750) 
* add test export heder to gitignore

* define export macros in separate file

* install new header

* patch GA with the new macros

* fix struct declarations

* fix conformerparser exports

* fix MolSGroupParsing ParseV3000Array export

* fix java wrappers

* export exceptions

* remove duplicated exports

* Build RDGeneral exceptions into lib

* export queries, only for *nix

* fix RingDecomposerLib header manipulation

* fix CIP labeler test issues
2021-02-15 14:29:04 +01:00
..
Abbreviations
Address #2753 (#3750)
2021-02-15 14:29:04 +01:00
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Addresses #3078 (second try) (#3729)
2021-02-04 17:54:13 +01:00
ChemTransforms
First pass at MolZip (now with bond stereo!) (#3644)
2020-12-25 05:15:12 +01:00
CIPLabeler
Address #2753 (#3750)
2021-02-15 14:29:04 +01:00
Depictor
Fixes #3648 (#3654)
2020-12-17 09:29:59 -05:00
Deprotect
[WIP] Deprotection Library (#3294)
2020-09-11 05:35:36 +02:00
Descriptors
Fixes issue 1761 (#3679)
2021-01-15 05:11:51 +01:00
DistGeomHelpers
Embedder callback (#3668)
2020-12-29 07:38:11 +01:00
FileParsers
Address #2753 (#3750)
2021-02-15 14:29:04 +01:00
FilterCatalog
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
Fingerprints
Address Issue 3723 (#3724)
2021-01-15 16:17:44 +01:00
FMCS
Include Winsock2.h instead of Windows.h in DebugTrace.h (#3756)
2021-01-26 05:35:43 +01:00
ForceFieldHelpers
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
FragCatalog
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
MolAlign
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
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
Fixes #3216 (#3772)
2021-01-29 13:31:01 -05:00
MolEnumerator
support enumerating from lists of enumerators (#3664)
2020-12-25 05:14:46 +01:00
MolHash
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
MolInterchange
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
MolStandardize
Fixes #3755 (#3758)
2021-01-27 08:20:25 +01:00
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
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
RGroupDecomposition
Add some more comprehensive R-Group Decomposition tests (#3778)
2021-02-05 10:35:32 +01:00
ScaffoldNetwork
- add #ifdef to enable building ScaffoldNetwork with no Boost serialization support (#3538)
2020-11-08 12:42:03 +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
Merge branch 'feat/bond_query_drawing' of https://github.com/greglandrum/rdkit into greglandrum-feat/bond_query_drawing
2020-12-17 06:43:49 +01:00
StructChecker
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
Subgraphs
switch to using target_compile_definitions instead of add_definitions (#3350)
2020-08-21 04:49:07 +02:00
Substruct
Fixes #3403 (#3405)
2020-09-10 08:11:47 +02:00
SubstructLibrary
Fixes crashes when using bad smiles in the cached smiles holders (#3798)
2021-02-15 10:49:19 +01:00
TautomerQuery
Some work on TautomerEnumerator (#3327)
2020-09-24 17:00:03 -04:00
test_data
Minor tweaks to SubstructLibrary (#3564)
2020-12-09 19:42:38 -05:00
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 Github issue 1631 (#3782)
2021-02-09 13:44:08 +01:00
AddHs.cpp
Fixes a number of issues flagged by clang (#3498)
2020-10-15 15:03:34 +02:00
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
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +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
Speed up GraphMol/Chirality.cpp/iterateCIPRanks (#3482)
2020-12-10 05:36:51 +01:00
Bond.h
Speed up GraphMol/Chirality.cpp/iterateCIPRanks (#3482)
2020-12-10 05:36:51 +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
Fix #3631 (#3632)
2020-12-12 05:50:29 +01:00
catch_graphmol.cpp
Mem checkup & fixes (#3510)
2020-11-09 12:08:36 -05:00
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
Fix #3631 (#3632)
2020-12-12 05:50:29 +01:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +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
Fix undefined behavior in testCoordGen test (#3495)
2020-10-17 04:26:13 +02:00
MolOps.h
Fix comment to match the code in RemoveHsParameters (#3747)
2021-01-20 16:53:29 +01:00
molopstest.cpp
Fix #3631 (#3632)
2020-12-12 05:50:29 +01:00
MolPickler.cpp
backup
2020-12-08 15:39:45 +01:00
MolPickler.h
more bug fixes and cleanups from fuzz testing (#3339)
2020-08-17 06:51:24 +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
Fixes some problems with findPotentialStereo() (#3499)
2020-10-17 04:35:58 +02:00
new_canon.h
Fixes some problems with findPotentialStereo() (#3499)
2020-10-17 04:35:58 +02:00
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
Fixes #3388 (#3389)
2020-09-04 12:38:25 -04:00
QueryBond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryBond.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
QueryOps.cpp
all tests now passing
2020-12-08 15:39:45 +01:00
QueryOps.h
backup
2020-12-08 15:39:45 +01:00
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
Fixes #1735 (#1743)
2018-02-15 05:39:02 +01:00
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
Make better use of strictParsing for SGroups (#3705)
2021-01-14 10:29:41 +01:00
ROMol.h
ROMol: add inline impl for common getNumAtoms call (#3469)
2020-10-11 08:02:58 +02:00
RWMol.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
RWMol.h
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
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
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +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