Greg Landrum fc374a9622 Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646) ...

* Fixes a molblock writing problem
with undervalent atoms from the organic subset

* Fixes #2649

Also ensures that allenes are not written as crossed bonds
(which does not make sense at the moment anyway)

* clang-format run

2019-09-20 09:13:19 -04:00

..

sgroup_test_data

Add a read-only Python wrapper for SGroups (#2343)

2019-03-15 08:50:32 -04:00

test_data

Keep PDB info from Maestro files if available (#2619)

2019-08-23 14:00:52 -07:00

testExecs

initial import

2006-05-06 22:20:08 +00:00

catch_tests.cpp

Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646)

2019-09-20 09:13:19 -04:00

CMakeLists.txt

Support XYZ format for output (#2498)

2019-07-12 05:26:42 +02:00

FileParsers.h

Support XYZ format for output (#2498)

2019-07-12 05:26:42 +02:00

FileParserUtils.h

Add RDKIT_FILEPARSERS_EXPORT to finishMolProcessing (#2551)

2019-07-28 06:26:25 +02:00

ForwardSDMolSupplier.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

MaeMolSupplier.cpp

Keep PDB info from Maestro files if available (#2619)

2019-08-23 14:00:52 -07:00

mol1.cdxml

initial import

2006-05-06 22:20:08 +00:00

Mol2FileParser.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

mol.py

Remove a bunch of Python2-related warts (#2315)

2019-03-06 20:43:49 -05:00

MolFileParser.cpp

make "R" in CTABs an AtomNull query (#2528)

2019-07-15 19:53:53 -04:00

MolFileStereochem.cpp

#2329 wrap detect atom stereochemistry (#2351)

2019-03-19 10:54:28 +01:00

MolFileStereochem.cpp.hold

Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)

2018-01-07 14:19:47 -05:00

MolFileStereochem.h

clang-tidy-7 pass (#2408)

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

MolFileWriter.cpp

Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646)

2019-09-20 09:13:19 -04:00

MolSGroupParsing.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

MolSGroupParsing.h

rename SGroup -> SubstanceGroup (#2375)

2019-03-30 14:53:24 -04:00

MolSGroupWriting.cpp

rename SGroup -> SubstanceGroup (#2375)

2019-03-30 14:53:24 -04:00

MolSGroupWriting.h

rename SGroup -> SubstanceGroup (#2375)

2019-03-30 14:53:24 -04:00

MolSupplier.h

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

MolWriters.h

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

PDBParser.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

PDBSupplier.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

PDBWriter.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

ProximityBonds.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

ProximityBonds.h

clang-tidy-7 pass (#2408)

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

SDMolSupplier.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

SDWriter.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

SequenceParsers.cpp

- enable building DLLs on Windows (#1861)

2018-05-16 08:42:41 +02:00

SequenceParsers.h

clang-tidy-7 pass (#2408)

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

SequenceWriters.cpp

- enable building DLLs on Windows (#1861)

2018-05-16 08:42:41 +02:00

SequenceWriters.h

clang-tidy-7 pass (#2408)

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

SmilesMolSupplier.cpp

Fixes #2479 (#2482)

2019-06-07 12:44:51 -04:00

SmilesWriter.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

SVGParser.cpp

add export flags for the MolStandardize library (#2072)

2018-09-29 07:43:07 +02:00

TDTMolSupplier.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

TDTWriter.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

test1.cpp

Build warnings revisited (#2318)

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

test_list.py

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00

testExtendedStereoParsing.cpp

Enhanced stereo read/write support in SDF files. (#2022)

2018-09-26 15:44:23 +02:00

testMol2ToMol.cpp

Build warnings revisited (#2318)

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

testMolSupplier.cpp

Keep PDB info from Maestro files if available (#2619)

2019-08-23 14:00:52 -07:00

testMolWriter.cpp

Fixes #2229 (#2235)

2019-01-22 10:53:48 -05:00

testPropertyLists.cpp

support reading/writing atom props from SD files (#2297)

2019-03-03 13:17:13 -05:00

testSequence.cpp

moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)

2018-10-11 17:35:23 -04:00

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

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

TplFileWriter.cpp

Code cleanups from PVS/Studio (#2531)

2019-07-13 07:25:37 +02:00

XYZFileWriter.cpp

Support XYZ format for output (#2498)

2019-07-12 05:26:42 +02:00