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39bcee635e0ee8bc5da6798318fdcd4602c4baa6
rdkit/Code/GraphMol
History
Ric 39bcee635e Mem checkup (#3083) 
* clean up in testDatastructs

* avoid jump on unassigned mem in rxns

* set valgrind error exit code

* update suppressions

* clean up RDValue in testDict

* don't leak mol if parsing Maestro file fails

* don't leak mol if parsing PDB block fails

* cleanup leftover rxns in testReaction

* cleanup mol if CX extensions cannot be parsed

* cleanup leftover mols in smiTest1

* cleanup leftover mols in moldraw2DTest1

* cleanup leftover mols in testSubstructMatch

* make testEnumeration go easier on valgrind

* reduce R counts
2020-04-17 17:48:58 +02:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Mem checkup (#3083)
2020-04-17 17:48:58 +02:00
ChemTransforms
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Depictor
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
Descriptors
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
DistGeomHelpers
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
FileParsers
Mem checkup (#3083)
2020-04-17 17:48:58 +02:00
FilterCatalog
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Fingerprints
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
FMCS
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ForceFieldHelpers
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
FragCatalog
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
MolAlign
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolCatalog
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
MolChemicalFeatures
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolDraw2D
Mem checkup (#3083)
2020-04-17 17:48:58 +02:00
MolHash
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
MolInterchange
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
MolStandardize
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolTransforms
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
PartialCharges
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ReducedGraphs
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
RGroupDecomposition
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ScaffoldNetwork
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ShapeHelpers
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
SLNParse
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
SmilesParse
Mem checkup (#3083)
2020-04-17 17:48:58 +02:00
StructChecker
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Subgraphs
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Substruct
Mem checkup (#3083)
2020-04-17 17:48:58 +02:00
SubstructLibrary
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
test_data
fix start/end atoms when wedging bonds (#2861)
2019-12-27 07:21:49 -05:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Wrap
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
AddHs.cpp
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
AdjustQuery.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
Aromaticity.cpp
Fixes #2895 (#2906)
2020-01-26 07:41:51 -05:00
Atom.cpp
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
Atom.h
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
atomic_data.cpp
Fixes #2784 (#2787)
2019-11-15 07:53:42 -05:00
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
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Bond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Bond.h
Fixes #2450 (#2457)
2019-05-22 09:23:44 -04:00
BondIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
BondIterators.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
bulktest.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
Canon.cpp
adds a one-liner for getting a vector of random smiles for a molecule (#3002)
2020-03-12 13:10:29 -04:00
Canon.h
Use the same criteria to flip chiral atoms in SMILES parsing/writing (Fixes #1028) (#2600)
2019-08-15 07:47:27 +02:00
catch_graphmol.cpp
Correct TEST_CASE tags for Catch2 (#3069)
2020-04-08 15:43:38 +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
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
Chirality.cpp
Address issue #2890 (#3015)
2020-03-21 14:01:54 +01:00
Chirality.h
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
CMakeLists.txt
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)
2020-04-01 14:30:07 +02:00
ConjugHybrid.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +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
Address build warnings (#3082)
2020-04-17 14:40:15 +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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
itertest.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
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
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolDiscriminators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.h
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
molopstest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolPickler.cpp
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolPickler.h
Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)
2020-04-01 14:30:07 +02:00
MonomerInfo.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
new_canon.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
new_canon.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
PeriodicTable.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryBond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryBond.h
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryOps.cpp
Enable larger ring matches in SMARTS expressions (#2981)
2020-03-07 15:09:38 +01:00
QueryOps.h
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +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
- fixes GitHub #3048 (#3081)
2020-04-17 14:19:53 +02:00
Resonance.cpp
- fixes GitHub #3048 (#3081)
2020-04-17 14:19:53 +02:00
Resonance.h
- fixes #3041 (#3045)
2020-04-01 10:00:22 +02:00
RingInfo.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
RingInfo.h
Use query molecule rather than ambiguous SMARTS for MCS matching (#2759)
2019-12-16 04:57:54 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
ROMol.h
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
RWMol.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
Do not catch exceptions by value
2019-10-10 20:22:17 +09:00
StereoGroup.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
StereoGroup.h
Python wrap enhanced stereo setters (#2509)
2019-07-03 10:24:26 +02:00
SubstanceGroup.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
SubstanceGroup.h
[WIP] Make StructureGroups editable from Python (#2692)
2019-10-15 22:32:26 -04:00
test1.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testMolBundle.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
testPickler.cpp
Fixes #2510 (#2907)
2020-01-28 05:07:31 +01:00
testPicklerGlobalSettings.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
testSGroup.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00