Brian Kelley 2b99ee477c Allow fragments to be grouped in cdxml (#7529) ...

* Allow fragments to be groups in CDXML

* Add support for grouped reactants

* run clang-format

* Change github issue to 7528

* Add documents to the code

* response to review, check grouped reactants in cdxml against rxn file

* Remove unused code

* Add missing file

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>

2024-06-23 07:02:19 +02:00

..

sgroup_test_data

basic handling of XBCORR and XBHEAD (#3242)

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

test_data

Prefer wedging ring bonds around atropisomers (#7373)

2024-05-08 06:04:23 +02:00

testExecs

Unset executable flag

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

cdxml_parser_catch.cpp

Allow fragments to be grouped in cdxml (#7529)

2024-06-23 07:02:19 +02:00

CDXMLParser.cpp

Allow fragments to be grouped in cdxml (#7529)

2024-06-23 07:02:19 +02:00

CDXMLParser.h

v2 API for the molecule CDXML parser (#7113)

2024-02-02 18:05:55 +01:00

CMakeLists.txt

deprecations for the 2024.09 release (#7398)

2024-05-05 07:30:00 -04:00

CMLWriter.cpp

atropisomer handling added (#6903)

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

connectTheDots_catch.cpp

switch to catch2 v3 (#6898)

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

file_parsers_catch.cpp

add MolToV2KMolBlock() (#7511)

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

FileParsers.h

V2 API for the MolSuppliers (#7168)

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

FileParserUtils.h

Custom decimal precision (#7229)

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

FileWriters.h

add MolToV2KMolBlock() (#7511)

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

ForwardSDMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

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

GeneralFileReader.h

Fixes #6818 (#6820)

2023-10-22 05:23:05 +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

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

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

mol1.cdxml

Unset executable flag

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

Mol2FileParser.cpp

Add v2 API to FileParsers (#7077)

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

mol.py

Reformat Python code for 2023.03 release (#6294)

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

molfile_stereo_catch.cpp

allow perception of stereo from T-shaped structures (#7183)

2024-03-05 15:59:11 +01:00

MolFileParser.cpp

Support zero order bonds in V3K CTABs (#7269)

2024-03-18 18:45:08 +01:00

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

add MolToV2KMolBlock() (#7511)

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

MolSGroupParsing.cpp

Fixes #7246 (#7247)

2024-03-16 07:37:16 +01:00

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

deprecations for the 2024.09 release (#7398)

2024-05-05 07:30:00 -04:00

MolSupplier.v1API.h

deprecations for the 2024.09 release (#7398)

2024-05-05 07:30:00 -04:00

MolWriters.h

Fix some build warnings (#6618)

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

MultithreadedMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

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

MultithreadedMolSupplier.h

V2 API for the MolSuppliers (#7168)

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

MultithreadedSDMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

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

MultithreadedSDMolSupplier.h

V2 API for the MolSuppliers (#7168)

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

MultithreadedSmilesMolSupplier.cpp

V2 API for the MolSuppliers (#7168)

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

MultithreadedSmilesMolSupplier.h

V2 API for the MolSuppliers (#7168)

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

PDBParser.cpp

Add v2 API to FileParsers (#7077)

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

PDBWriter.cpp

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

2023-02-17 11:53:17 +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

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

Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)

2024-01-23 17:13:53 +01:00

testAtropisomers.cpp

Include macrocycles in atropisomer calculation by not sanitizing them away (#7291)

2024-04-09 06:05:25 +02:00

testExtendedStereoParsing.cpp

atropisomer handling added (#6903)

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

testGeneralFileReader.cpp

Fixes #6818 (#6820)

2023-10-22 05:23:05 +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

- avoid inconsistency between V2K and V3K MDL output wrt isotopic labelling of R groups (neither should be isotopically labelled) (#7504)

2024-06-09 07:32:16 +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

testSquiggleDoubleBonds.cpp

atropisomer handling added (#6903)

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

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

V2 API for the MolSuppliers (#7168)

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

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

Custom decimal precision (#7229)

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