Greg Landrum a102eaf932 Add options for substructure searching (#2254) ...

* first pass at adding a SubstructMatchParameter struct

* start moving the rest of the backend to use the parameters

* backend at least mostly moved over

* add aromaticMatchesConjugated
add tests

* switch over the MolBundle too
Add templates to reduce duplicated code

* support older compilers

let's see if it works...

* add SubstructMatchParameters to Python wrapper

* remove some deprecations and warnings

* damn compilers

* parameter support for bundles in python wrapper

* add the parameters to the java wrappers

* response to review

2019-02-08 09:10:10 -05:00

..

AlignTests.java

Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper (#1155)

2016-11-10 21:44:03 +01:00

AromaticTests.java

Fixes #72

2013-08-25 06:36:10 +02:00

AtomPairsTests.java

add initial version of new swig wrappers

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

AvalonLibTests.java

add java tests

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

BasicMolecule2Tests.java

fix SWIG wrappers for the resonance mol suppliers

2015-11-04 05:29:50 +01:00

BasicMoleculeTests.java

Add options for substructure searching (#2254)

2019-02-08 09:10:10 -05:00

BitOpsTests.java

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

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

ChemAtomTests.java

add initial version of new swig wrappers

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

ChemBondTests.java

add test for bond iterators

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

ChemReactionTests.java

Add test for addDummyAtoms==false flag

2016-02-27 13:26:35 -05:00

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

Make svg xmlns prefix use more consistent (#1866)

2018-05-14 17:07:55 +02:00

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

make sure that the global EmbedParameter objects are not writeable from Java (#1824)

2018-04-17 13:37:04 +02:00

DiversityPickerTests.java

Fixes #2245 (#2250)

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

ErrorHandlingTests.java

add initial version of new swig wrappers

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

FilterCatalogTests.java

Dev/expose filtermatch to swig (#1117)

2016-10-21 20:43:00 -04:00

FingerprintsTests.java

Fixes #1776 (#1780)

2018-03-20 10:10:40 -04:00

FMCSTests.java

restore java and python wrappers. New parameter (matchChiralTag) was added. New function findFMCS_P() receives json parameters

2015-04-10 16:24:58 +03:00

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

HManipulationsTests.java

add initial version of new swig wrappers

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

InchiTests.java

initial addition of avalontoolkit support

2011-12-23 06:17:39 +00:00

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

MolQueryTests.java

add basic java tests

2015-08-23 06:57:43 +02:00

MolStandardizeTest.java

Dev/GSOC2018_MolVS_Integration (#2002)

2018-09-28 11:24:25 +02:00

PDBTests.java

first java wrappers of pdb stuff

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

PicklingTests.java

add initial version of new swig wrappers

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

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

refactoring the SMILES parser to make it more efficient

2012-08-28 04:01:49 +00:00

SmilesTests.java

add support for replacements in smiles and smarts.

2011-07-07 05:45:31 +00:00

SuppliersTests.java

Fixes #270

2014-05-24 06:16:52 +02:00

TrajectoryTests.java

Fix Java Trajectory Test

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

WrapperTests.java

- added SWIG Java wrappers for ResonanceMolSupplier and

2015-11-02 22:45:41 +00:00