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378 Commits

Author SHA1 Message Date
gedeck
e9af48ffd7 Issue1071/yapf (#1078) 
* Issue #1071: add yapf configuration file

* yapf formatting of Code directory

* yapf formatting of Contrib directory

* yapf formatting of Data directory

* yapf formatting of Docs directory

* yapf formatting of External directory

* yapf formatting of Projects directory

* yapf formatting of Regress directory

* yapf formatting of Scripts directory

* yapf formatting of Web directory

* yapf formatting of rdkit directory
 2016-09-23 04:58:46 +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
Brian Kelley
71a0ae32b2 Adds replaceCore function that takes a matchVect (#1013) 
* Adds replaceCore function that takes a matchVect

* Fixes error reporting, adds tests

* Switches PRECONDITION to ValueError exceptions

* Fixes MatchVectType annoyance in swig.  Don't know why this is necessary.

* Silences warnings

* Adds working doctests and better explanations.
 2016-08-17 04:40:59 +02:00
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
23b9b2ab66 Add newobject declarations 2016-02-27 13:16:53 -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
a321337f33 remove assignAtomCIPRanks() from the SWIG Wrappers 2015-12-25 06:42:28 +01:00
Greg Landrum
3b68cdd24d move the boost serialization configuration to the global cmakelists.txt 2015-12-04 06:13:17 +01:00
Brian Kelley
8bde707bef Add RDK_USE_BOOST_SERIALIZATION configure option (On by default) 2015-12-03 13:52:41 -05:00
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
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +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
12d562399a Merge branch 'master' into fix/const-string-ref 2015-10-13 07:08:00 -04:00
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
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -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
efc18e9aa5 So many languages, so many comment styles 2015-09-10 21:58:15 +00:00
Brian Kelley
a82cda21a9 Link boost statically 2015-09-10 16:01:18 -04:00
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
895668e610 changes to the SWIG wrappers to get them working on windows 2015-04-15 05:32:06 +01:00