Brian Kelley cf9ea71384 First pass at MolZip (now with bond stereo!) (#3644) ...

* First pass at MolZip (sans bond stereo)

* Add support for bond stereo zipping

* Add molzip swig wrappers

* Add simple python wrapper/tests

* Remove smiles round tripping now that fragmentOnBonds is fixed

* Responses to review

* AtomMaps and Isotopes must explicitly be set

* Add molzip single molecule api isotope test

* Add missing %newobject

* Add better python docs, label test

* fix docs add a test for molzip

* Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Add missing case breaks

* Add more preconditions, move mark and restore to private functions

* Remove unused and redunddant code

* optimize get_other_atom

* Add single arg molzip test

* Update Code/GraphMol/Wrap/rough_test.py

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

2020-12-25 05:15:12 +01:00

..

csharp_wrapper

Clean up CMake files (#3417)

2020-11-28 08:00:39 +01:00

gmwrapper

support enumerating from lists of enumerators (#3664)

2020-12-25 05:14:46 +01:00

Abbreviations.i

Add support for abbreviations (#3406)

2020-09-28 17:09:46 -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

Sgroup (#3390)

2020-09-09 04:59:08 +02:00

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

Unset executable flag

2019-10-10 20:18:43 +09:00

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

First pass at MolZip (now with bond stereo!) (#3644)

2020-12-25 05:15:12 +01:00

CMakeLists.txt

Add support for abbreviations (#3406)

2020-09-28 17:09:46 -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

Improve Conformational Sampling of Small and Large Ring Molecules (#2999)

2020-03-23 14:57:46 +01:00

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

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

FilterCatalog.i

Add threaded runner for the filter catalog (#2718)

2019-10-19 07:42:14 +02:00

FilterCatalogParams_doc.i

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

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

Added support for Python FMCS functors (#3023)

2020-03-23 11:20:57 +01:00

ForceField.i

patch a leak

2013-12-06 03:39:00 +01:00

GenericRDKitException.h

Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

2020-04-01 14:30:07 +02:00

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

MolBundle.i

Support enumerating some mol file features into MolBundles (#3257)

2020-07-11 12:54:23 +02:00

MolDraw2D.i

Fixes #2896 (#2903)

2020-01-25 06:34:29 +01:00

MolEnumerator.i

Support enumerating some mol file features into MolBundles (#3257)

2020-07-11 12:54:23 +02:00

MolHash.i

Fixes #2677 (#2687)

2019-10-03 18:07:26 -04:00

MolOps.i

Allow identification of chemistry problems (#2587)

2019-08-28 14:15:55 -07:00

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

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

RDKitExceptions.i

Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

2020-04-01 14:30:07 +02:00

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

Allow Java to see RGroup labels in the std::map wrapper. (#2681)

2019-10-03 16:52:01 +02:00

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

Fix typo [ci skip]

2019-10-17 17:45:50 +09:00

ROMol.i

Fixes #2239 (#2693)

2019-10-07 07:51:07 +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

Allow identification of chemistry problems (#2587)

2019-08-28 14:15:55 -07:00

ScaffoldNetwork.i

Add ScaffoldNetwork to csharp (#3289)

2020-07-13 14:48:34 +02:00

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

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

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

SubstanceGroup.i

Sgroup (#3390)

2020-09-09 04:59:08 +02:00

SubstructLibrary.i

Exposes substructlibrary to swig (#2337)

2019-03-12 16:35:22 +01:00

TautomerQuery.i

Tautomer search (#3205)

2020-06-24 17:27:40 +02:00

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

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

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