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104 Commits

Author SHA1 Message Date
Greg Landrum
4315388f77 Add a parameters structure for controlling the embedding options. (#1121) 
* 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) 
* Exposes FilterMatch and getFilterMatches to java

* Updates java test

* Fixes typo in test
 2016-10-21 20:43:00 -04:00
Brian Kelley
092ab6ff12 Fixes csharp build for 64 bit systems (#1098) 
* Fixes csharp build for 64 bit systems

* Need to support make and make install stages

* switch to an alternate strategy and get it working for the java wrappers too
this now builds for me on 64bit win10 with MSVC14

* add missing files from that last commit

* Hopefully fixes unix and osx builds while maintaining msvc builds

* Fixes mono builds, removes python check
 2016-10-14 15:40:05 +02:00
Greg Landrum
74635c5fe1 Fix leak with renumberAtoms() in the SWIG wrappers (#1064) 
* 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) 
* 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
Greg Landrum
df0036cb12 try and resolve intermittent travis build problems 
There seems to be a problem in some travis builds where some java wrapper files aren't finished writing before the next step of the build happens. This is an attempt to resolve that.
 2016-08-02 17:19:03 +02:00
Paolo Tosco
a286112cbe Java wrappers for Trajectory/Snapshot objects (#977) 
* - 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
Brian Kelley
2debdfde0d Adds RDAny (smaller generic holder) Updates all used dictionaries (#896) 
* Adds RDAny (smaller generic holder) Updates all used dictionaries

This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.

* Removes code duplication

* Converts CHECK_INVARIANT to TEST_ASSERT

* Fixes DoubleTag issue

* Adds Bool to DoubleMagic implementation

* Removes reference to property pickler
 2016-05-29 17:04:21 +01:00
Greg Landrum
db0db2e4e4 expose FPS functions to java; add tests for that (#897) 2016-05-02 14:39:48 -04:00
Paolo Tosco
15f358bb56 - fixed a build failure on CentOS 7 (which has Java 8, but whose javadoc does not seem to support the -Xdoclint:none flag 
while the Java documentation builds fine in its absence)
 2016-04-21 22:30:03 +01:00
Greg Landrum
76a338c1be Fixes #859 - add automatic downloads of the junit.jar code too 
* download junit.jar automatically when it is needed

* do not need to download junit anymore

* doc update

* try a different maven url to see if that solves the MD5 problems
 2016-04-13 09:54:03 -04:00
Brian Kelley
e647af599d Updates NumRotatableBondsOptions to be an enum 2016-03-21 20:37:52 -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 
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; 
add tests for the MaxMin picker to the java wrappers
 2016-02-26 08:07:03 +01:00
Greg Landrum
a2278045da Gets Java wrappers building with modern C++ compilers and recent versions of boost 2016-02-18 06:24:42 +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
Josep Arús
54cca7dad1 removed doclint fix on java archive command 2016-02-11 12:11:13 +01:00
Greg Landrum
2fef24656f try to get this working with multiple java versions 2015-11-19 14:32:05 +01:00
Greg Landrum
678e771a71 this works for java8, but not java6. Need java version detection 2015-11-19 08:34:33 +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
Greg Landrum
1aec53181d add Int_List to SWIG wrappers 2015-10-12 07:34:57 +02:00
Greg Landrum
2cb414e639 Merge pull request #612 from bp-kelley/dev/filter-catalog-java-wrapper 
Dev/filter catalog java wrapper
 2015-09-26 05:38:49 -04:00
Brian Kelley
fe3bbb8944 Merge branch 'dev/filter-catalog-java-wrapper' of https://github.com/bp-kelley/rdkit into dev/filter-catalog-java-wrapper 2015-09-24 11:11:25 -04:00
Brian Kelley
73e1790383 Add boost root for running java tests 2015-09-24 11:10:46 -04:00
Brian Kelley
0d75ecf847 Fix Boost_Serialization dependencies ordering - link as late as possible. 
Uses Greg's patch.

Issue: this links boost_serialization dynamically.  This may make
  it harder to distribute Knime nodes since we will now have
  to distribute boost_serialization.so/.dylib.
 2015-09-11 14:01:12 +00:00
Brian Kelley
8a66860d74 Updated docs 2015-09-10 11:34:41 -04:00
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
Greg Landrum
f844c7348a SWIG wrappers now require cmake 2.8 instead of 2.6 2015-09-04 10:35:27 +02:00
Gianluca Sforna
0edca4dac8 use system's junit when available 2015-09-04 10:17:21 +02:00
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
Brian Kelley
7240f92ab5 Add First pass at Java FilterCatalog wrapper 2015-09-03 14:55:06 +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
a5548e6e26 initial support for an explicit MolDraw2DSVG object; bring the csharp wrappers somewhat up-to-date 2015-02-04 07:16:30 +01:00
Greg Landrum
9e8c4b24ba Merge pull request #412 from rdkit/new_drawing_Jan2015 
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