James Thompson 63123278ca Vulnerability fixes

2024-12-17 15:26:41 +00:00

..

sgroup_test_data

basic handling of XBCORR and XBHEAD (#3242)

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

test_data

Fix for kekuleAtrop wedge error (#7992)

2024-11-15 04:39:38 +01:00

testExecs

Unset executable flag

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

cdxml_parser_catch.cpp

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

CDXMLParser.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

CDXMLParser.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

CMakeLists.txt

Add callbacks to the multithreaded mol suppliers (#7763)

2024-08-29 15:53:47 +02:00

CMLWriter.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

connectTheDots_catch.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

file_parsers_catch.cpp

fixes #8060 (#8087)

2024-12-12 18:13:29 +01:00

FileParsers.h

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

FileParserUtils.h

Fixes #7306 (#7510)

2024-07-01 05:00:24 +02:00

FileWriters.h

add MolToV2KMolBlock() (#7511)

2024-06-13 09:43:59 +02:00

ForwardSDMolSupplier.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

GeneralFileReader.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MaeMolSupplier.cpp

MaeWriter: handle the R group label property and update the Maestro property prefixing (#7454)

2024-05-30 14:11:19 +02:00

MaestroProperties.h

MaeWriter: handle the R group label property and update the Maestro property prefixing (#7454)

2024-05-30 14:11:19 +02:00

MaeWriter.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

mol1.cdxml

Unset executable flag

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

Mol2FileParser.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

mol.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

molfile_stereo_catch.cpp

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

MolFileParser.cpp

Vulnerability fixes

2024-12-17 15:26:41 +00:00

MolFileStereochem.cpp

No coords atropisomers - fix smiles output of atrop wedges after reordering (#7418)

2024-05-07 17:06:33 +02:00

MolFileStereochem.h

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

MolFileWriter.cpp

Fixes #8023 (#8024)

2024-11-21 14:28:19 +01:00

MolSGroupParsing.cpp

Vulnerability fixes

2024-12-17 15:26:41 +00:00

MolSGroupParsing.h

Fix some problems turned up by ossfuzz (#4927)

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

MolSGroupWriting.cpp

remove a bunch of std::endls (#7233)

2024-03-17 06:03:37 +01:00

MolSGroupWriting.h

cleanup a bunch of compiler warnings (#3849)

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

MolSupplier.h

add mol processing API (#7773)

2024-09-19 18:42:25 +02:00

MolSupplier.v1API.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolWriters.h

Fix some build warnings (#6618)

2023-08-11 06:04:55 +02:00

multithreaded_supplier_catch.cpp

Catch exceptions in MultithreadedMolSupplier callbacks (#7810)

2024-11-19 17:22:25 +01:00

MultithreadedMolSupplier.cpp

Catch exceptions in MultithreadedMolSupplier callbacks (#7810)

2024-11-19 17:22:25 +01:00

MultithreadedMolSupplier.h

Add callbacks to the multithreaded mol suppliers (#7763)

2024-08-29 15:53:47 +02:00

MultithreadedSDMolSupplier.cpp

Add callbacks to the multithreaded mol suppliers (#7763)

2024-08-29 15:53:47 +02:00

MultithreadedSDMolSupplier.h

Fix aliasing bug in MultithreadedSDMolSupplier and move GeneralFileReader to v2 API (#7761)

2024-08-29 15:53:28 +02:00

MultithreadedSmilesMolSupplier.cpp

Add callbacks to the multithreaded mol suppliers (#7763)

2024-08-29 15:53:47 +02:00

MultithreadedSmilesMolSupplier.h

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

PDBParser.cpp

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

PDBWriter.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

PNGParser.cpp

drop zlib include (#6966)

2023-12-08 10:00:22 +01:00

PNGParser.h

fix doxygen comments (#5254)

2022-07-11 13:55:35 +02:00

ProximityBonds.cpp

Fixes #6756 (#6780)

2023-10-05 20:55:52 +02:00

ProximityBonds.h

clang-tidy-7 pass (#2408)

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

SDMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

SDWriter.cpp

switch from boost::any to std::any (#6662)

2023-08-25 17:55:33 +02:00

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

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

SmilesWriter.cpp

Start a Maestro file (.mae) writer. (#6069)

2023-02-17 11:53:17 +01:00

SVGParser.cpp

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

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

TDTMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

2024-02-29 06:46:56 +01:00

TDTWriter.cpp

Start a Maestro file (.mae) writer. (#6069)

2023-02-17 11:53:17 +01:00

test1.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

testAtropisomers.cpp

Fix for kekuleAtrop wedge error (#7992)

2024-11-15 04:39:38 +01:00

testExtendedStereoParsing.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

testGeneralFileReader.cpp

Fix aliasing bug in MultithreadedSDMolSupplier and move GeneralFileReader to v2 API (#7761)

2024-08-29 15:53:28 +02:00

testMol2ToMol.cpp

Add v2 API to FileParsers (#7077)

2024-01-28 05:11:54 +01:00

testMolSupplier.cpp

Fixes for canonicalization, and stereochemistry (#6743)

2023-11-06 07:40:23 +01:00

testMolWriter.cpp

remove no-op macros and dead code (pt 1) (#8012)

2024-11-19 04:31:56 +01:00

testMultithreadedMolSupplier.cpp

run clang_format (#5676)

2022-11-01 04:14:26 +01:00

testPropertyLists.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

testSequence.cpp

Modernize deprecated header inclusion (#3137)

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

testSquiggleDoubleBonds.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +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

Add v2 API to FileParsers (#7077)

2024-01-28 05:11:54 +01:00

TplFileWriter.cpp

remove a bunch of std::endls (#7233)

2024-03-17 06:03:37 +01:00

v2_file_parsers_catch.cpp

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

v2_suppliers_catch.cpp

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

XYZFileParser.cpp

Add v2 API to FileParsers (#7077)

2024-01-28 05:11:54 +01:00

XYZFileParserCatchTest.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

XYZFileWriter.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00