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dd21db1b06856721ca6208884b163ee16c2c80fe
rdkit/Code/JavaWrappers
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Greg Landrum dd21db1b06 Integrate Unique Ring Families from RingDecomposerLib (#2558) 
* add the ring decomposer lib (temporarily?)

* simplify makefile

* very basics work

* backup

* 	basics working

* builds and basic tests pass

* get this building again

* expose the ring families

* add tests on the python side

* make the pywrapper for this optional

* remove some extra bits

* cleanup

* switch to using RDL as an external project

* make sure this still works if we do not use the URF code

* remove BUILD_ALWAYS

* fix linkage of Java wrapper and cartridge (hopefully)

* fix cmake for wrappers (hopefully)

* forgot a semicolon

* try to force URF lib to build first

* improve memory management and interface

* fix dependency specifier

* make pointer initialization explicit

This may not be necessary, but it feels safer.

* not pleasing and needs to be cleaned up
but it builds

* not pleasing and needs to be cleaned up
but it builds

* cleanup in preparation for merging

* cleanup in preparation for merging

* switch to rareylab repo

* fix updated copyright date

* Fix updated copyright date

* switch to a specific library tag

Co-Authored-By: Florian Flachsenberg <flachsenberg@zbh.uni-hamburg.de>

* change in response to review
2019-07-30 06:41:55 -04:00
..
csharp_wrapper
Add java builds to azure devops (#2460)
2019-05-22 15:31:42 +02:00
gmwrapper
Fixes #2532 (#2533)
2019-07-08 15:13:41 -04:00
AddHs.i
add svn props
2011-07-01 04:43:39 +00:00
Atom_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Atom.i
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
AtomIterators.i
add svn props
2011-07-01 04:43:39 +00:00
AtomPairs.i
add svn props
2011-07-01 04:43:39 +00:00
AvalonLib.i
initial addition of avalontoolkit support
2011-12-23 06:17:39 +00:00
BitOps.i
expose FPS functions to java; add tests for that (#897)
2016-05-02 14:39:48 -04:00
Bond_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Bond.i
Added IsInRing methods to Bond in Java wrapper(addresses #1535) (#1536)
2017-08-18 12:01:15 -04:00
BondIterators_doc.i
add svn props
2011-07-01 04:43:39 +00:00
BondIterators.i
add svn props
2011-07-01 04:43:39 +00:00
boost_tuple.i
initial support for an explicit MolDraw2DSVG object; bring the csharp wrappers somewhat up-to-date
2015-02-04 07:16:30 +01:00
build_docs.sh
add
2011-04-08 02:48:25 +00:00
Canon.i
add svn props
2011-07-01 04:43:39 +00:00
ChemReactions_doc.i
add svn props
2011-07-01 04:43:39 +00:00
ChemReactions.i
Add newobject declarations
2016-02-27 13:16:53 -05:00
ChemTransforms.i
Adds replaceCore function that takes a matchVect (#1013)
2016-08-17 04:40:59 +02:00
CMakeLists.txt
Integrate Unique Ring Families from RingDecomposerLib (#2558)
2019-07-30 06:41:55 -04:00
Conformer_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Conformer.i
Add some 3D molecular descriptors (#1084)
2016-10-10 08:34:08 -04:00
Descriptors.i
remove USR references from SWIG wrappers
2013-10-08 05:48:40 +02:00
Dict.i
Dev/pickle properties (#1277)
2017-02-09 16:06:01 +01:00
DistGeom.i
make sure that the global EmbedParameter objects are not writeable from Java (#1824)
2018-04-17 13:37:04 +02:00
DiversityPick.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
DiversityPick.i
add support for a diversity picker to java wrapper
2011-10-08 12:59:40 +00:00
ErrorGenerator.i
add svn props
2011-07-01 04:43:39 +00:00
ExplicitBitVect_doc.i
add svn props
2011-07-01 04:43:39 +00:00
ExplicitBitVect.i
Cart fixes (#2462)
2019-05-27 14:29:09 +02:00
extend_std_vector.i
stop including our own std_vector.i, instead just extend the one provided with swig; duplicate the std_list file into the csharp wrapper in case it ends up needing to be different
2012-11-21 16:11:16 +00:00
FilterCatalog_doc.i
Updated docs
2015-09-10 11:34:41 -04:00
FilterCatalog.i
Dev/general csharp fixes (#2341)
2019-03-13 04:41:48 +01:00
FilterCatalogParams_doc.i
Updated docs
2015-09-10 11:34:41 -04:00
FilterCatalogs_doc.i
Updated docs
2015-09-10 11:34:41 -04:00
Fingerprints.i
GSoC 2018 - Fingerprints (#2005)
2018-10-07 05:02:12 +02:00
FMCS.i
changes to the SWIG wrappers to get them working on windows
2015-04-15 05:32:06 +01:00
ForceField.i
patch a leak
2013-12-06 03:39:00 +01:00
GenericRDKitException.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Inchi.i
add svn props
2011-07-01 04:43:39 +00:00
make_templates.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
MolDraw2D.i
Enable SimilarityMaps in C++ (#2562)
2019-07-28 08:59:06 -04:00
MolOps.i
Fix leak with renumberAtoms() in the SWIG wrappers (#1064)
2016-09-13 12:24:08 -04:00
MolStandardize.i
Dev/GSOC2018_MolVS_Integration (#2002)
2018-09-28 11:24:25 +02:00
MolSupplier.i
Adds gzstream stream, exposes to swig (#2314)
2019-03-18 05:32:42 +01:00
MolTransforms.i
add svn props
2011-07-01 04:43:39 +00:00
MolWriters.i
add svn props
2011-07-01 04:43:39 +00:00
MonomerInfo.i
first java wrappers of pdb stuff
2013-10-11 18:06:09 +02:00
MorganFingerprints.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MorganFingerprints.i
Cart fixes (#2462)
2019-05-27 14:29:09 +02:00
msvc_stdint.i
Fixes csharp build for 64 bit systems (#1098)
2016-10-14 15:40:05 +02:00
parse_doxy_html.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
PeriodicTable_doc.i
add svn props
2011-07-01 04:43:39 +00:00
PeriodicTable.i
add svn props
2011-07-01 04:43:39 +00:00
Point3D_doc.i
add svn props
2011-07-01 04:43:39 +00:00
point.i
add svn props
2011-07-01 04:43:39 +00:00
QueryAtom_doc.i
add svn props
2011-07-01 04:43:39 +00:00
QueryAtom.i
add svn props
2011-07-01 04:43:39 +00:00
QueryBond_doc.i
add svn props
2011-07-01 04:43:39 +00:00
QueryBond.i
add svn props
2011-07-01 04:43:39 +00:00
QueryOps.i
update the flex files; get the swig wrappers building on the mac
2012-10-08 12:08:24 +00:00
RDKFuncs_doc.i
Fixes Issue 1614 (#1781)
2018-04-01 17:48:36 +02:00
RDKitExceptions.i
Code/RDBoost/Exceptions.h moved to Code/RDGeneral
2015-03-16 23:06:50 +01:00
RDProps.i
Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)
2016-05-29 17:04:21 +01:00
ReactionFingerprints.i
Fixes #1776 (#1780)
2018-03-20 10:10:40 -04:00
RGroupDecomposition.i
Expose RGroupDecomposition to SWIG (#2345)
2019-03-13 08:23:23 -04:00
RingInfo_doc.i
add svn props
2011-07-01 04:43:39 +00:00
RingInfo.i
add svn props
2011-07-01 04:43:39 +00:00
Rings.i
add svn props
2011-07-01 04:43:39 +00:00
ROMol_doc.i
add svn props
2011-07-01 04:43:39 +00:00
ROMol.i
Support XYZ format for output (#2498)
2019-07-12 05:26:42 +02:00
RWMol_doc.i
add svn props
2011-07-01 04:43:39 +00:00
RWMol.i
allow the cleanup step of Mol2 parsing to be disabled (#1898)
2018-06-09 05:44:10 +02:00
SanitException.i
add svn props
2011-07-01 04:43:39 +00:00
SDMolSupplier_doc.i
add svn props
2011-07-01 04:43:39 +00:00
SmartsWrite.i
add svn props
2011-07-01 04:43:39 +00:00
SmilesMolSupplier_doc.i
add svn props
2011-07-01 04:43:39 +00:00
SmilesParse.i
add support for replacements in smiles and smarts.
2011-07-07 05:45:31 +00:00
SmilesWrite.i
add svn props
2011-07-01 04:43:39 +00:00
SmilesWriter_doc.i
add svn props
2011-07-01 04:43:39 +00:00
StereoGroup.i
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
Streams.i
Adds gzstream stream, exposes to swig (#2314)
2019-03-18 05:32:42 +01:00
Subgraphs.i
add svn props
2011-07-01 04:43:39 +00:00
SubstructLibrary.i
Exposes substructlibrary to swig (#2337)
2019-03-12 16:35:22 +01:00
TDTMolSupplier_doc.i
add svn props
2011-07-01 04:43:39 +00:00
TDTWriter_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Trajectory.i
Java wrappers for Trajectory/Snapshot objects (#977)
2016-07-20 22:51:01 -04:00
Transform2D_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Transform3D_doc.i
add svn props
2011-07-01 04:43:39 +00:00
transforms.i
add svn props
2011-07-01 04:43:39 +00:00
types.i
add svn props
2011-07-01 04:43:39 +00:00