Greg Landrum
01829cc4e7
add support the new sequence readers to wrappers ( #1181 ) ( #1221 )
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* Fixes #1181
needs more testing
* improved docs and a couple tests
* add the new sequence support to the java wrappers too
2016-12-21 04:54:00 +01:00
Greg Landrum
275d2145a7
Merge pull request #1172 from mcs07/traj
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Fix Trajectory GetSnapshot behaviour after Clear
2016-11-23 04:31:58 +01:00
Steve Roughley
3680644ebf
Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper ( #1155 )
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* Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper
* Added missing argument
Added missing argument to call to getAlignmentTransform causing build failure
* Added test case for getAlignmentTransform
* Update AlignTests.java
* Update AlignTests.java
* Update AlignTests.java
2016-11-10 21:44:03 +01:00
Greg Landrum
051a4deb12
add tests for the new param objects from java
2016-11-05 20:03:25 +01:00
Greg Landrum
4315388f77
Add a parameters structure for controlling the embedding options. ( #1121 )
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* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
2016-11-01 11:39:03 +01:00
Brian Kelley
13c3eef7c4
Dev/expose filtermatch to swig ( #1117 )
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* Exposes FilterMatch and getFilterMatches to java
* Updates java test
* Fixes typo in test
2016-10-21 20:43:00 -04:00
Greg Landrum
74635c5fe1
Fix leak with renumberAtoms() in the SWIG wrappers ( #1064 )
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* fix a leak with renumberAtoms() in Java
* add a test to show that leak
2016-09-13 12:24:08 -04:00
Greg Landrum
cb710340a1
Support ETKDG from within the SWIG wrappers ( #1010 )
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* add test files
* add seed to the mol name so that it is obvious
* add support (and tests) for ETKDG to Java
2016-08-08 11:08:55 +02:00
Paolo Tosco
a286112cbe
Java wrappers for Trajectory/Snapshot objects ( #977 )
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* - started SWIG wrapping of Trajectory code
* - work in progress
* - wip
* - wip
* - WIP on TrajectoryTests.java
* - WIP
* - WIP
* - TrajectoryTests.java completed
* - reverted file modified my accident
2016-07-20 22:51:01 -04:00
Greg Landrum
db0db2e4e4
expose FPS functions to java; add tests for that ( #897 )
2016-05-02 14:39:48 -04:00
Brian Kelley
f26b53067e
Exposes NumRotatableBondsOptions to java, adds tests
2016-03-17 10:14:20 -04:00
Brian Kelley
f1ca9e6115
Merge pull request #791 from greglandrum/feat/lazy_picker_for_java
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Add a bit more control over the lazy MaxMin picker to the java layer
2016-03-01 23:47:40 -05:00
Brian Kelley
a779d5bcfd
Add test for addDummyAtoms==false flag
2016-02-27 13:26:35 -05:00
Brian Kelley
8c2aca2dcd
Exposes reduceProductToSideChains to Java
2016-02-27 09:53:56 -05:00
Greg Landrum
6002415bd2
add the useCache option to the java wrappers;
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add tests for the MaxMin picker to the java wrappers
2016-02-26 08:07:03 +01:00
Greg Landrum
1c730b489e
fix a typo, cleanup some (but not all) whitespace
2016-02-17 18:09:59 +01:00
Greg Landrum
27a267bd6c
Fixes #781
2016-02-17 16:19:01 +01:00
Greg Landrum
3db6d874ba
fix SWIG wrappers for the resonance mol suppliers
2015-11-04 05:29:50 +01:00
Paolo Tosco
ffa524c87b
- added SWIG Java wrappers for ResonanceMolSupplier and
...
getResonanceSubstructMatches()
- added a few tests
2015-11-02 22:45:41 +00:00
Brian Kelley
2d9a1c6791
Use class based Deserialize method
2015-09-10 08:18:24 -04:00
Brian Kelley
d16df573a8
Fix Serialize/Deserialze
2015-09-10 08:01:37 -04:00
Brian Kelley
5f62a5f62f
Properly use shared_ptrs
2015-09-09 16:49:08 -04:00
Brian Kelley
d03656c56e
Add getMatches interface
2015-09-09 10:54:03 -04:00
Brian Kelley
8ccb583dc0
Add serialization check
2015-09-04 09:11:19 +02:00
Brian Kelley
84c8e7df32
Add initial version of swig wrapper
2015-09-03 16:35:23 +02:00
Greg Landrum
96e86036fe
add basic java tests
2015-08-23 06:57:43 +02:00
Greg Landrum
d778060bcf
Merge branch 'master' into mol_hash_and_fmcs_Feb2015
2015-04-11 06:44:22 +02:00
Alexander Savelyev
b0177a4ea1
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
Greg Landrum
2cad2e05aa
update expected results in java
2015-04-10 09:29:26 +02:00
Greg Landrum
c3751181b1
add a couple SVG tests to the java wrappers
2015-02-06 03:21:04 +01:00
Greg Landrum
9e8c4b24ba
Merge pull request #412 from rdkit/new_drawing_Jan2015
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New C++ drawing code
2015-01-20 02:37:03 -05:00
Greg Landrum
99a0a6dc79
add java tests
2015-01-19 23:17:32 +01:00
Greg Landrum
cddaf519cd
switch to using MolDraw2D in the java wrapper
2015-01-13 07:20:13 +01:00
Greg Landrum
7cb35fd5a4
Fixes #397
2014-12-09 06:39:33 +01:00
Greg Landrum
23c56924fc
Merge branch 'master' into fmcs_port_21Feb2014
2014-08-24 06:27:59 +02:00
Schneider
8aac978f1b
ChemReactions: Extented functionality of chemical reactions
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- Module to generate reaction fingerprints: structural FP for screening,
difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
2014-08-19 13:08:11 +02:00
Greg Landrum
55ad544dde
first pass at FMCS in the java wrappers, including a basic test. this is nowhere near done
2014-08-10 08:00:37 +02:00
Greg Landrum
3216435d73
Fixes #270
2014-05-24 06:16:52 +02:00
Greg Landrum
12fd90c3c5
add test for bond iterators
2014-05-22 10:32:46 +02:00
Greg Landrum
3d6d1e6bb8
add a leak test for the reaction swig wrapper; it is disabled by default
2014-05-03 07:55:39 +02:00
Greg Landrum
296bbfb65b
Fixes #228
2014-03-05 05:48:17 +01:00
Greg Landrum
e82d0b5b00
Finish #173
2013-12-06 03:43:13 +01:00
Greg Landrum
7c4ead6d10
small changes in java wrappers
2013-10-23 08:09:18 +02:00
Greg Landrum
cdd096a616
fix a bad test filename
2013-10-18 01:31:46 -07:00
Greg Landrum
0639f0c3d4
Merge branch 'PDB_29September2013'
2013-10-16 05:35:12 +02:00
Greg Landrum
d5fac5501b
add basic support for O3A to Java wrapper
2013-10-12 16:54:49 +02:00
Greg Landrum
40908a43da
mmff into SWIG wrapper. first tests
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note: these changes remove some direct ff-manipulation functionality that was
present previously
2013-10-12 16:24:18 +02:00
Greg Landrum
21393521a3
first java wrappers of pdb stuff
2013-10-11 18:06:09 +02:00
Greg Landrum
0b83ef0097
get java tests working
2013-09-24 07:55:11 -04:00
Greg Landrum
88a4b03b20
get swig wrapper building again
2013-09-19 02:01:29 +02:00
