Greg Landrum db15b372a1 Fix some problems turned up by ossfuzz (#4927) ...

* resolves oss-fuzz #24399

* clean up some undefined behavior

* fix some UB in mergeQueryHs

* be more defensive

* defensive programming

* fix a _cxsmilesBondIdx bug

* more defensive programming

2022-01-22 04:30:06 +01:00

..

sgroup_test_data

basic handling of XBCORR and XBHEAD (#3242)

2020-06-22 16:54:57 +02:00

test_data

Addresses issue #3815 (#3816)

2021-02-16 08:04:37 +01:00

testExecs

Unset executable flag

2019-10-10 20:18:43 +09:00

catch_main.cpp

Fixes #4468 and #4476 (#4482)

2021-09-05 05:43:13 +02:00

CMakeLists.txt

Add support for Beilstein generics when doing substructure queries (#4673)

2021-12-01 06:01:53 +01:00

CMLWriter.cpp

Fixes #4127 (#4129)

2021-05-18 15:39:15 +02:00

file_parsers_catch.cpp

Fix some problems turned up by ossfuzz (#4927)

2022-01-22 04:30:06 +01:00

FileParsers.h

miscellaneous updates (#4284)

2021-07-13 06:57:29 +02:00

FileParserUtils.h

more bug fixes and cleanups from fuzz testing (#3339)

2020-08-17 06:51:24 +02:00

ForwardSDMolSupplier.cpp

Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

2020-04-01 14:30:07 +02:00

GeneralFileReader.h

- fixes MinGW build (#4347)

2021-07-22 06:26:20 +02:00

MaeMolSupplier.cpp

Addresses issue #3815 (#3816)

2021-02-16 08:04:37 +01:00

mol1.cdxml

Unset executable flag

2019-10-10 20:18:43 +09:00

Mol2FileParser.cpp

Swap from RDUNUSED_PARAM to unnamed parameters (#4433)

2021-08-24 17:19:46 -04:00

mol.py

Remove a bunch of Python2-related warts (#2315)

2019-03-06 20:43:49 -05:00

MolFileParser.cpp

Fixes #4785: aromatic bonds no longer set aromatic flags on atoms (#4806)

2021-12-17 10:26:59 +01:00

MolFileStereochem.cpp

Fixes #4238 (#4255)

2021-06-22 10:51:09 +02:00

MolFileStereochem.h

a few doxygen comment fixes (#4368)

2021-08-09 04:58:01 +02:00

MolFileWriter.cpp

Add support for Beilstein generics when doing substructure queries (#4673)

2021-12-01 06:01:53 +01:00

MolSGroupParsing.cpp

Fix some problems turned up by ossfuzz (#4927)

2022-01-22 04:30:06 +01:00

MolSGroupParsing.h

Fix some problems turned up by ossfuzz (#4927)

2022-01-22 04:30:06 +01:00

MolSGroupWriting.cpp

fix + test (#4478)

2021-09-04 14:01:56 +02:00

MolSGroupWriting.h

cleanup a bunch of compiler warnings (#3849)

2021-02-26 05:10:02 +01:00

MolSupplier.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

MolWriters.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

MultithreadedMolSupplier.cpp

[GSoC-2020] Generalized and Multithreaded File Reader (#3363)

2020-10-09 04:31:05 +02:00

MultithreadedMolSupplier.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

MultithreadedSDMolSupplier.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

MultithreadedSDMolSupplier.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

MultithreadedSmilesMolSupplier.cpp

[GSoC-2020] Generalized and Multithreaded File Reader (#3363)

2020-10-09 04:31:05 +02:00

MultithreadedSmilesMolSupplier.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

PDBParser.cpp

Avoid C preprocessor macros (#3138)

2020-05-05 08:08:20 +02:00

PDBSupplier.cpp

Fix a hang when trying to read mols from a directory not a file on linux (#2983)

2020-03-09 15:27:58 +01:00

PDBWriter.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

PNGParser.cpp

Fixes #3543 (#3615)

2020-12-08 08:45:46 -05:00

PNGParser.h

Molecule metadata in PNGs (#3316)

2020-08-25 07:51:18 +02:00

ProximityBonds.cpp

Avoid C preprocessor macros (#3138)

2020-05-05 08:08:20 +02:00

ProximityBonds.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

SDMolSupplier.cpp

Fixes #3517 (#3523)

2020-11-04 12:54:47 +01:00

SDWriter.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

SequenceParsers.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

SequenceParsers.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

SequenceWriters.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

SequenceWriters.h

clang-tidy-7 pass (#2408)

2019-04-16 12:05:47 -04:00

SmilesMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

SmilesWriter.cpp

Swap from RDUNUSED_PARAM to unnamed parameters (#4433)

2021-08-24 17:19:46 -04:00

SVGParser.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

TDTMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

TDTWriter.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

test1.cpp

Improve test coverage and some bug fixes (#4536)

2021-09-26 07:45:06 +02:00

testExtendedStereoParsing.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

testGeneralFileReader.cpp

Fix clang warning -Wabsolute-value (#4616)

2021-10-17 07:44:34 +02:00

testMol2ToMol.cpp

Build warnings revisited (#2318)

2019-03-08 16:42:54 +01:00

testMolSupplier.cpp

cleanup a bunch of compiler warnings (#3849)

2021-02-26 05:10:02 +01:00

testMolWriter.cpp

Remove boost::foreach from public headers (#3820)

2021-02-17 14:15:48 +01:00

testMultithreadedMolSupplier.cpp

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

testPropertyLists.cpp

Correct TEST_CASE tags for Catch2 (#3069)

2020-04-08 15:43:38 +02:00

testSequence.cpp

Modernize deprecated header inclusion (#3137)

2020-05-04 10:40:57 +02:00

testTpls.cpp

moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)

2018-10-11 17:35:23 -04:00

TplFileParser.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

TplFileWriter.cpp

Swap from RDUNUSED_PARAM to unnamed parameters (#4433)

2021-08-24 17:19:46 -04:00

XYZFileWriter.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00