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0fb492dfb464f0b0abffd58967e867c224f9c607
rdkit/Code/GraphMol/FileParsers
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Brian Kelley e904452400 Fixes #8284 (#8556) 
* Adds a df_forceStop to stop readers and writers, clears out queues on destructor

* Propery implement close function, requires protected closeStreams

* changes from greg's version

* close() needs to be called in the derived destructors

* Close the writers before the reader to avoid deadlock

* Don't process trailing new lines

* Don't accept pushes if the queue is done

* Add mutex protecting d_threadCounter, remove unneeded forceStop checks

* Update Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Add comment for the d_threadCounterMutex unlock

---------

Co-authored-by: = <=>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2025-06-30 08:51:03 +02:00
..
sgroup_test_data
basic handling of XBCORR and XBHEAD (#3242)
2020-06-22 16:54:57 +02:00
test_data
allow nested parentheses in tokens (#8553)
2025-06-30 08:49:38 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
atropisomers_catch.cpp
Fixes #7983 (#8342)
2025-03-20 07:40:33 +01:00
cdxml_parser_catch.cpp
Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)
2025-03-29 07:26:03 +01:00
CDXMLParser.cpp
switch to C++20 (#8039)
2025-04-26 06:36:57 +02:00
CDXMLParser.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
CMakeLists.txt
rdkit-targets.cmake now uses cmake package names for external libraries instead of absolute paths (#8552)
2025-05-27 05:23:18 +02:00
CMLWriter.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
connectTheDots_catch.cpp
support forming H2 with connectTheDots (#8452)
2025-04-26 06:47:42 +02:00
file_parsers_catch.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
FileParsers.h
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
FileParserUtils.h
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
FileWriters.h
Make MaeWriter to throw on errors. (#8297)
2025-02-25 16:59:40 +01:00
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
macromols_catch.cpp
allow nested parentheses in tokens (#8553)
2025-06-30 08:49:38 +02:00
MaeMolSupplier.cpp
Ignore invalid chirality labels when reading MAE inputs (#8347)
2025-03-22 05:12:14 +01:00
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
Make MaeWriter to throw on errors. (#8297)
2025-02-25 16:59:40 +01:00
mol1.cdxml
Unset executable flag
2019-10-10 20:18:43 +09:00
Mol2FileParser.cpp
Fix the way carbon is handed in cleanupOrganometallics() (#8301)
2025-03-03 17:30:41 +01:00
mol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
molfile_stereo_catch.cpp
remove no-op macros and dead code (pt 2) (#8035)
2025-01-11 14:10:00 +01:00
MolFileParser.cpp
allow nested parentheses in tokens (#8553)
2025-06-30 08:49:38 +02:00
MolFileStereochem.cpp
Move creation of 2D coords to before markUnspecifiedStereoAsUnknown. (#8179)
2025-01-23 06:03:20 +01:00
MolFileStereochem.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
MolFileWriter.cpp
Throw error when V2000 coords are out of range (#8269)
2025-02-20 07:50:40 +01:00
MolSGroupParsing.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
MolSGroupParsing.h
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
MolSGroupWriting.cpp
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +01:00
MolSGroupWriting.h
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +01:00
MolSupplier.h
add mol processing API (#7773)
2024-09-19 18:42:25 +02:00
MolSupplier.v1API.h
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
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
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
MultithreadedMolSupplier.h
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
MultithreadedSDMolSupplier.cpp
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
MultithreadedSDMolSupplier.h
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
MultithreadedSmilesMolSupplier.cpp
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
MultithreadedSmilesMolSupplier.h
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
PDBParser.cpp
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
PDBWriter.cpp
Make MaeWriter to throw on errors. (#8297)
2025-02-25 16:59:40 +01:00
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
support forming H2 with connectTheDots (#8452)
2025-04-26 06:47:42 +02:00
ProximityBonds.h
support forming H2 with connectTheDots (#8452)
2025-04-26 06:47:42 +02:00
SCSRMolFileParser.cpp
Add SCSR parsing to RDKit (#8147)
2025-05-27 05:21:04 +02:00
SDMolSupplier.cpp
V2 API for the MolSuppliers (#7168)
2024-02-29 06:46:56 +01:00
SDWriter.cpp
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +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
remove no-op macros and dead code (pt 4) (#8037)
2025-01-26 07:49:50 +01:00
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
Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)
2025-01-28 21:09:03 +01:00
TDTMolSupplier.cpp
V2 API for the MolSuppliers (#7168)
2024-02-29 06:46:56 +01:00
TDTWriter.cpp
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +01:00
test1.cpp
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-26 06:42:48 +02:00
testAtropisomers.cpp
Fix for removing bad stereo indications from Atropisomer parsing (#7984)
2024-12-22 04:47:18 +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
Moving towards getting all tests to pass when using the new stereo code (#8409)
2025-04-26 06:42:48 +02:00
testMolSupplier.cpp
A few mem fixes in tests (#8521)
2025-05-27 05:20:22 +02:00
testMolWriter.cpp
A few mem fixes in tests (#8521)
2025-05-27 05:20:22 +02:00
testMultithreadedMolSupplier.cpp
Fixes #8284 (#8556)
2025-06-30 08:51:03 +02:00
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
A few mem fixes in tests (#8521)
2025-05-27 05:20:22 +02:00
XYZFileParser.cpp
Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)
2025-03-29 20:04:58 +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