Greg Landrum a2ecd6723c Fixes #5819 (#6897) ...

* Fixes #5819
still some things to think about there

* test parsing

* make sure the fix for 5819 also shows up in reactions

* patch some other holes

2023-11-22 17:35:58 +01:00

..

sgroup_test_data

basic handling of XBCORR and XBHEAD (#3242)

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

test_data

Add support for Marvin files (#6575)

2023-09-01 04:50:34 +02:00

testExecs

Unset executable flag

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

cdxml_parser_catch.cpp

switch to catch2 v3 (#6898)

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

CDXMLParser.cpp

Fixes #6887 - issue where stereogroups could overwrite each other (#6892)

2023-11-12 17:03:12 +01:00

CDXMLParser.h

Reformat C/C++ code ahead of 2023.03 release (#6295)

2023-04-28 04:42:35 +02:00

CMakeLists.txt

cmake cleanup (#6814)

2023-11-10 15:32:54 +01:00

CMLWriter.cpp

Fixes #4127 (#4129)

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

connectTheDots_catch.cpp

switch to catch2 v3 (#6898)

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

file_parsers_catch.cpp

Fixes #5819 (#6897)

2023-11-22 17:35:58 +01:00

FileParsers.h

Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)

2022-10-06 05:46:08 +02:00

FileParserUtils.h

Fixes #5819 (#6897)

2023-11-22 17:35:58 +01:00

ForwardSDMolSupplier.cpp

Start using string_views in the file parsers (#5301)

2022-06-14 17:18:40 -04:00

GeneralFileReader.h

Fixes #6818 (#6820)

2023-10-22 05:23:05 +02:00

MaeMolSupplier.cpp

Fixes #6664 (#6692)

2023-09-07 12:32:38 +02:00

MaeWriter.cpp

Add support for writing chirality and stereo in MaeWriter (#6810)

2023-11-09 06:36:11 +01:00

mol1.cdxml

Unset executable flag

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

Mol2FileParser.cpp

Fixes #6664 (#6692)

2023-09-07 12:32:38 +02:00

mol.py

Reformat Python code for 2023.03 release (#6294)

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

molfile_stereo_catch.cpp

switch to catch2 v3 (#6898)

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

MolFileParser.cpp

Fixes #5819 (#6897)

2023-11-22 17:35:58 +01:00

MolFileStereochem.cpp

Removed some code duplication between Depictor.cpp and common.h (#6799)

2023-10-18 04:04:45 +02:00

MolFileStereochem.h

Removed some code duplication between Depictor.cpp and common.h (#6799)

2023-10-18 04:04:45 +02:00

MolFileWriter.cpp

Fixes #5819 (#6897)

2023-11-22 17:35:58 +01:00

MolSGroupParsing.cpp

Fix memory safety issues found by OSS-Fuzz (#4983)

2022-02-06 05:06:38 +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

Improve MaeMolSupplier API (#6053)

2023-02-08 04:31:51 +01:00

MolWriters.h

Fix some build warnings (#6618)

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

MultithreadedMolSupplier.cpp

Fixes #5210 (#5408)

2022-07-11 11:20:03 +02:00

MultithreadedMolSupplier.h

fix doxygen comments (#5254)

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

MultithreadedSDMolSupplier.cpp

Fixes #5210 (#5408)

2022-07-11 11:20:03 +02:00

MultithreadedSDMolSupplier.h

fix doxygen comments (#5254)

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

MultithreadedSmilesMolSupplier.cpp

Update CI, remove some warnings (#6882)

2023-11-09 13:14:00 -05:00

MultithreadedSmilesMolSupplier.h

fix doxygen comments (#5254)

2022-07-11 13:55:35 +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

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

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

PNGParser.cpp

Fixes #3543 (#3615)

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

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

Start using string_views in the file parsers (#5301)

2022-06-14 17:18:40 -04:00

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

Update CI, remove some warnings (#6882)

2023-11-09 13:14:00 -05:00

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

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

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

TDTWriter.cpp

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

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

test1.cpp

Add support for dative bonds in MOL files (#6566)

2023-07-21 08:43:23 +02:00

testExtendedStereoParsing.cpp

Optionally forward Enhanced Stereo Group ids (#6560)

2023-07-27 18:53:40 +02:00

testGeneralFileReader.cpp

Fixes #6818 (#6820)

2023-10-22 05:23:05 +02:00

testMol2ToMol.cpp

Build warnings revisited (#2318)

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

testMolSupplier.cpp

Fixes for canonicalization, and stereochemistry (#6743)

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

testMolWriter.cpp

Fixes #6241 (#6257)

2023-04-13 15:38:29 +02:00

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

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

XYZFileParser.cpp

Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)

2022-10-06 05:46:08 +02:00

XYZFileParserCatchTest.cpp

switch to catch2 v3 (#6898)

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

XYZFileWriter.cpp

Run clang-format against cpp (#4358)

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