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facb15f703bd9e2dfc363d078a577e3aeb5dd577
rdkit/Code/GraphMol/FileParsers
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Greg Landrum 286cb21302 Allow unrecognized atom types when strictParsing=False (#5891) 
We should just read them in as dummies instead of throwing an exception.
A bit of light refactoring to accompany that
2022-12-28 08:25:34 -05:00
..
sgroup_test_data
basic handling of XBCORR and XBHEAD (#3242)
2020-06-22 16:54:57 +02:00
test_data
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
cdxml_parser_catch.cpp
Add wavy stereo bond support to cdxml (#5755)
2022-11-17 04:58:46 +01:00
CDXMLParser.cpp
Add wavy stereo bond support to cdxml (#5755)
2022-11-17 04:58:46 +01:00
CDXMLParser.h
cdxml parser (#5273)
2022-09-28 05:49:27 +02:00
CMakeLists.txt
Fixes #5863 (#5870)
2022-12-16 05:39:38 +01:00
CMLWriter.cpp
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
file_parsers_catch.cpp
Allow unrecognized atom types when strictParsing=False (#5891)
2022-12-28 08:25:34 -05:00
FileParsers.h
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
FileParserUtils.h
Start using string_views in the file parsers (#5301)
2022-06-14 17:18:40 -04:00
ForwardSDMolSupplier.cpp
Start using string_views in the file parsers (#5301)
2022-06-14 17:18:40 -04:00
GeneralFileReader.h
Fixes #5210 (#5408)
2022-07-11 11:20:03 +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
molfile_stereo_catch.cpp
Fixes #5863 (#5870)
2022-12-16 05:39:38 +01:00
MolFileParser.cpp
Allow unrecognized atom types when strictParsing=False (#5891)
2022-12-28 08:25:34 -05:00
MolFileStereochem.cpp
Fixes #5863 (#5870)
2022-12-16 05:39:38 +01:00
MolFileStereochem.h
Add CXSMILES support for bond wedging and wiggly bonds (#5575)
2022-09-24 05:44:01 +02:00
MolFileWriter.cpp
Fixes #5785 (#5871)
2022-12-16 16:00:30 +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
Fixes #5692 (#5706)
2022-11-02 09:32:54 -04:00
MolWriters.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
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
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
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
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
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
ProximityBonds.cpp
fix warnings (#5561)
2022-09-14 06:36:42 +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
fixes #5827 (#5873)
2022-12-16 06:36:28 +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
Fixes #5692 (#5706)
2022-11-02 09:32:54 -04:00
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
[WIP] Fixes #5327 and #5328 (#5330)
2022-06-01 04:45:14 +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
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
testMolWriter.cpp
Remove boost::foreach from public headers (#3820)
2021-02-17 14:15:48 +01:00
testMultithreadedMolSupplier.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
testPropertyLists.cpp
Refactor mol draw2 d (#4948)
2022-02-18 16:30:21 +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
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
XYZFileWriter.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00