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02d76edc09aadb6366e62b168686fdc2ef4e58ff
rdkit/Code/GraphMol
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Greg Landrum 02d76edc09 more bug fixes and cleanups from fuzz testing (#3339) 
* ossfuzz #22301

* ossfuzz 22307

* memory leak when failing cxsmiles

* MolPickler things found by ossfuzz

* changes in response to review
2020-08-17 06:51:24 +02:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Expanded support for CXSMILES features (#3292)
2020-07-25 05:06:08 +02:00
ChemTransforms
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
CIPLabeler
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
Depictor
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
Descriptors
Get PPC builds working (#3285)
2020-07-25 05:05:22 +02:00
DistGeomHelpers
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
FileParsers
more bug fixes and cleanups from fuzz testing (#3339)
2020-08-17 06:51:24 +02:00
FilterCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Fingerprints
Fixes for aromatic bond fuzzy queries (#3328)
2020-08-10 05:00:19 +02:00
FMCS
Use operator() and __call__() consistently across RDKit (#3295)
2020-07-23 14:15:58 +02:00
ForceFieldHelpers
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
FragCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolAlign
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
MolCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolChemicalFeatures
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolDraw2D
Embed default truetype font (#3288)
2020-07-15 08:03:58 +02:00
MolEnumerator
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolHash
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
MolInterchange
bonds with "either' stereo cannot be read from JSON (#3290)
2020-07-14 10:06:12 -04:00
MolStandardize
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
MolTransforms
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
PartialCharges
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ReducedGraphs
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
RGroupDecomposition
rgroup speedup (#3279)
2020-07-12 06:56:15 +02:00
ScaffoldNetwork
ScaffoldNetwork: add feature to count the number of molecules a scaffold originates from (#3275)
2020-07-15 06:59:51 +02:00
ShapeHelpers
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
SLNParse
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
SmilesParse
more bug fixes and cleanups from fuzz testing (#3339)
2020-08-17 06:51:24 +02:00
StructChecker
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Subgraphs
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Substruct
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
SubstructLibrary
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
TautomerQuery
Fixes for aromatic bond fuzzy queries (#3328)
2020-08-10 05:00:19 +02:00
test_data
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
Wrap
Fix #3312 (#3313)
2020-08-01 04:36:34 +02:00
AddHs.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
AdjustQuery.cpp
Fixes for aromatic bond fuzzy queries (#3328)
2020-08-10 05:00:19 +02:00
Aromaticity.cpp
Improve performance of aromaticity detection for large molecules (#3253)
2020-08-13 05:57:16 +02:00
Atom.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
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
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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 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
add test for #3325 (#3331)
2020-08-10 13:17:41 -04:00
catch_graphmol.cpp
Improve performance of aromaticity detection for large molecules (#3253)
2020-08-13 05:57:16 +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
Fix #3312 (#3313)
2020-08-01 04:36:34 +02:00
Chirality.cpp
Fixes #3314 (#3318)
2020-08-10 13:12:01 -04:00
Chirality.h
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
CMakeLists.txt
Fix #3312 (#3313)
2020-08-01 04:36:34 +02:00
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
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
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.h
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
molopstest.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolPickler.cpp
more bug fixes and cleanups from fuzz testing (#3339)
2020-08-17 06:51:24 +02:00
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
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
new_canon.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
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
Expanded support for CXSMILES features (#3292)
2020-07-25 05:06:08 +02:00
QueryOps.h
Expanded support for CXSMILES features (#3292)
2020-07-25 05:06:08 +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
Fixes #1735 (#1743)
2018-02-15 05:39:02 +01:00
resMolSupplierTest.cpp
Fixes #2597 (#3213)
2020-07-13 15:15:24 +02:00
Resonance.cpp
Fixes #2597 (#3213)
2020-07-13 15:15:24 +02:00
Resonance.h
Fixes #2597 (#3213)
2020-07-13 15:15:24 +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
Small bug fixes and cleanups from fuzz testing (#3299)
2020-07-22 16:57:31 +02:00
ROMol.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +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
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
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
Fixes #3314 (#3318)
2020-08-10 13:12:01 -04:00
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