Greg Landrum 32608ae0b4 Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318) ...

* refactor the code to determine whether or not an atom is in brackets

* move the definition of isMetal to QueryOps

* atoms bound to metals in SMILES should always be in square brackets

Implementation and some test updates

needs confirmation that all of tests run

* basic tests pass

* java tests pass

* update js tests

* doc updates

* Update Code/GraphMol/catch_graphmol.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* Update Code/GraphMol/SmilesParse/test.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* finish fixing tests

* bump yaehmop version to allow compilation to work

---------

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

2025-03-29 07:26:03 +01:00

..

AbbreviationsTests.java

Add support for abbreviations (#3406)

2020-09-28 17:09:46 -04:00

AlignTests.java

Branch/vf2 optimisations (#2500)

2019-06-30 04:49:24 +02:00

AromaticTests.java

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

AtomPairsTests.java

Get the wrappers working with SWIG 4.0 (#5795)

2022-12-10 07:13:55 +01:00

AvalonLibTests.java

add java tests

2015-01-19 23:17:32 +01:00

BasicMolecule2Tests.java

Allow identification of chemistry problems (#2587)

2019-08-28 14:15:55 -07:00

BasicMoleculeTests.java

- Restore mol writing functions in the RDKFuncs module (#7544)

2024-06-21 05:51:18 +02:00

BitOpsTests.java

expose FPS functions to java; add tests for that (#897)

2016-05-02 14:39:48 -04:00

ChemAtomTests.java

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

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

ChemBondTests.java

add test for bond iterators

2014-05-22 10:32:46 +02:00

ChemReactionTests.java

Stereochemistry-related SWIG updates (#6127)

2023-02-28 06:44:50 +01:00

ChemSmartsTests.java

add initial version of new swig wrappers

2011-04-07 05:22:00 +00:00

ChemTests.java

another clang-format run

2017-10-12 06:42:15 +02:00

ChemTransformsTests.java

update expected results in java

2015-04-10 09:29:26 +02:00

Chemv2Tests.java

Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)

2025-03-29 07:26:03 +01:00

ConformerTests.java

add initial version of new swig wrappers

2011-04-07 05:22:00 +00:00

DescriptorTests.java

small changes in java wrappers

2013-10-23 08:09:18 +02:00

DistanceGeometryTests.java

fixes #2727 (#2728)

2019-10-19 09:07:54 -04:00

DiversityPickerTests.java

Fixes #2245 (#2250)

2019-01-31 00:03:39 -05:00

ErrorHandlingTests.java

Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

2020-04-01 14:30:07 +02:00

FilterCatalogTests.java

Add threaded runner for the filter catalog (#2718)

2019-10-19 07:42:14 +02:00

FingerprintsTests.java

add support for generating pattern fps for MolBundles (#3665)

2020-12-29 07:33:09 +01:00

FMCSTests.java

Added AtomComparator.AtomCompareAnyHeavyAtom and test cases to FMCS code (#2656)

2019-10-03 17:19:22 +02:00

ForceFieldsTests.java

mmff into SWIG wrapper. first tests

2013-10-12 16:24:18 +02:00

GraphMolTest.java

add initial version of new swig wrappers

2011-04-07 05:22:00 +00:00

GraphMolTestSuite.java

Java wrappers for Trajectory/Snapshot objects (#977)

2016-07-20 22:51:01 -04:00

GzStreamTests.java

Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF (#4933)

2022-01-23 07:06:36 +01:00

HManipulationsTests.java

add initial version of new swig wrappers

2011-04-07 05:22:00 +00:00

InchiTests.java

Unset executable flag

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

LipinskiTests.java

Exposes NumRotatableBondsOptions to java, adds tests

2016-03-17 10:14:20 -04:00

MemoryTests.java

Fix leak with renumberAtoms() in the SWIG wrappers (#1064)

2016-09-13 12:24:08 -04:00

MolDraw2DCairoTests.java

Swig MolDraw2D cairo (#5128)

2022-03-24 05:54:12 +01:00

MolEnumeratorTests.java

support enumerating from lists of enumerators (#3664)

2020-12-25 05:14:46 +01:00

MolHashTest.java

Fixes #2677 (#2687)

2019-10-03 18:07:26 -04:00

MolQueryTests.java

Add hasQueryHs (#6702)

2023-09-15 08:59:56 +02:00

MolStandardizeTest.java

Fixes a regression introduced in #7582 which made all SWIG enums become type-unsafe (#7972)

2024-10-30 06:08:14 +01:00

PDBTests.java

first java wrappers of pdb stuff

2013-10-11 18:06:09 +02:00

PicklingTests.java

Expose the property pickle options to SWIG (#7448)

2024-05-24 07:37:06 +02:00

QueryAtomTest.java

Handle query atoms and bonds in SWIG wrappers (#7431)

2024-05-23 07:18:49 +02:00

RascalMCESTest.java

C sharp rascal mcs wrapper (#7390)

2024-05-05 05:52:24 +02:00

RGroupDecompositionTests.java

Allow Java to see RGroup labels in the std::map wrapper. (#2681)

2019-10-03 16:52:01 +02:00

ScaffoldNetworkTests.java

Add a scaffold network implementation (#2911)

2020-02-11 08:21:01 -05:00

SequenceTests.java

add support the new sequence readers to wrappers (#1181) (#1221)

2016-12-21 04:42:17 +01:00

SmilesCreationTests.java

add initial version of new swig wrappers

2011-04-07 05:22:00 +00:00

SmilesDetailsTests.java

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

SmilesTests.java

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

SubstanceGroupTests.java

Sgroup (#3390)

2020-09-09 04:59:08 +02:00

SubstructLibraryTests.java

support generalized substructure search in the SubstructLibrary (#6835)

2023-11-01 14:55:28 -04:00

SuppliersTests.java

Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF (#4933)

2022-01-23 07:06:36 +01:00

TautomerQueryTests.java

Sgroup (#3390)

2020-09-09 04:59:08 +02:00

TrajectoryTests.java

Fix Java Trajectory Test

2016-11-15 14:51:05 +00:00

WrapperTests.java

Fixes #6479 (#6482)

2023-07-13 19:29:06 +02:00