Raul Sofia 372fbad131 Extended fix for #9101 (#9255) ...

* fix extended boundary issue (3 mols)

* clang pass

* no change. retrigger CI for failed java test

there's a failing java test that seems to be failing by chance rather than by changes, as it depends on rng. this is just to retrigger the CI pipeline to confirm this

* no change. retrigger the CI (yet again)

* raw strings and removed garbage collector

2026-05-06 06:10:37 +02:00

..

sgroup_test_data

basic handling of XBCORR and XBHEAD (#3242)

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

test_data

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +02:00

testExecs

Unset executable flag

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

atropisomers_catch.cpp

Fix for Issue 8602 (#8668)

2025-08-20 10:10:47 +02:00

cdxml_parser_catch.cpp

style: apply readability-braces-around-statements (#8136)

2026-02-09 12:10:50 +01:00

CDXMLParser.cpp

Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)

2025-08-29 04:39:22 +02:00

CDXMLParser.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

CMakeLists.txt

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +02:00

CMLWriter.cpp

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

connectTheDots_catch.cpp

support forming H2 with connectTheDots (#8452)

2025-04-25 07:19:16 -04:00

file_parsers_catch.cpp

Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)

2026-04-29 16:54:00 +02:00

FileParsers.h

Fix deprecated literal operators and macro redefinition warnings for modern compilers (#9055)

2026-01-19 08:14:52 +01:00

fileParsersIterTest.cpp

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +02:00

FileParserUtils.h

Check for correctly sized propertylists to avoid dropping molecules (#8921)

2026-01-08 06:08:54 +01:00

FileWriters.h

Make MaeWriter to throw on errors. (#8297)

2025-02-25 16:59:40 +01:00

ForwardSDMolSupplier.cpp

Read SD property names till the last '>' (#9047)

2026-01-09 05:23:26 +01:00

GeneralFileReader.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

macromols_catch.cpp

Handle chiral atoms with 2 hydrogens in SCSR parser (#8939)

2026-01-29 08:08:14 +01:00

MaeMolSupplier.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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

Hide data representation inside RDKit::Dict (#9113)

2026-03-20 06:58:36 +01:00

mol1.cdxml

Unset executable flag

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

Mol2FileParser.cpp

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

mol.py

Reformat Python code for 2023.03 release (#6294)

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

molfile_stereo_catch.cpp

Fixes #9020 (#9025)

2026-01-03 06:42:09 +01:00

MolFileParser.cpp

Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)

2026-04-29 16:54:00 +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

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

MolSGroupParsing.cpp

Fixes #9068: raise a ValueError when trying to set properties with empty names (#9085)

2026-02-09 05:58:25 +01:00

MolSGroupParsing.h

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +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

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

multithreaded_supplier_catch.cpp

Catch exceptions in MultithreadedMolSupplier callbacks (#7810)

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

MultithreadedMolSupplier.cpp

Revert "Fixes #8644 (#8768)" (#8787)

2025-09-16 16:28:01 +02:00

MultithreadedMolSupplier.h

Revert "Fixes #8644 (#8768)" (#8787)

2025-09-16 16:28:01 +02:00

MultithreadedSDMolSupplier.cpp

style: apply readability-braces-around-statements (#8136)

2026-02-09 12:10:50 +01:00

MultithreadedSDMolSupplier.h

Fixes #8284 (#8556)

2025-06-06 14:09:57 +02:00

MultithreadedSmilesMolSupplier.cpp

Fixes #8284 (#8556)

2025-06-06 14:09:57 +02:00

MultithreadedSmilesMolSupplier.h

Fixes #8284 (#8556)

2025-06-06 14:09:57 +02:00

PDBParser.cpp

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

PDBWriter.cpp

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

PNGParser.cpp

Expose reading/writing PNG metadata to CFFI and MinimalLib (#8381)

2025-07-23 17:10:38 +02:00

PNGParser.h

Expose reading/writing PNG metadata to CFFI and MinimalLib (#8381)

2025-07-23 17:10:38 +02:00

ProximityBonds.cpp

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

ProximityBonds.h

support forming H2 with connectTheDots (#8452)

2025-04-25 07:19:16 -04:00

SCSRMolFileParser.cpp

Allow spaces and special chars in SCSR fullname attrs (#8982)

2025-12-29 17:54:56 +01:00

SDMolSupplier.cpp

Extended fix for #9101 (#9255)

2026-05-06 06:10:37 +02:00

SDWriter.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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

Cleanup/get atoms and bonds (#9243)

2026-04-18 05:22:09 +02:00

SequenceWriters.h

clang-tidy-7 pass (#2408)

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

SmilesMolSupplier.cpp

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +02:00

SmilesWriter.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SVGParser.cpp

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

TDTMolSupplier.cpp

Support using iterators with MolSuppliers (#9230)

2026-05-05 13:36:15 +02:00

TDTWriter.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

test1.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

testAtropisomers.cpp

Deterministic kekulize, independent of atom and bond order (#9125)

2026-03-19 08:43:13 +01:00

testExtendedStereoParsing.cpp

atropisomer handling added (#6903)

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

testGeneralFileReader.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

testMol2ToMol.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

testMolSupplier.cpp

Extended fix for #9101 (#9255)

2026-05-06 06:10:37 +02:00

testMolWriter.cpp

Deterministic kekulize, independent of atom and bond order (#9125)

2026-03-19 08:43:13 +01:00

testMultithreadedMolSupplier.cpp

Fixes #8284 (#8556)

2025-06-06 14:09:57 +02:00

testPropertyLists.cpp

Check for correctly sized propertylists to avoid dropping molecules (#8921)

2026-01-08 06:08:54 +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 #9068: raise a ValueError when trying to set properties with empty names (#9085)

2026-02-09 05:58:25 +01:00

v2_suppliers_catch.cpp

A few mem fixes in tests (#8521)

2025-05-13 12:17:52 +02:00

XYZFileParser.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

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