hjuinj acdfe26dea Improve Conformational Sampling of Small and Large Ring Molecules (#2999) ...

* improvements for smal anr large ring conformer generation

* add documentation and reorder parameters in EmbedParam

* resolve merge conflict due to coordMap null pointer

* minor changes to address merge comments

* reorder variables in EmbedParameters

* add regression test for small ring and macrocycle torsion preferences

* not apply small ring torsions to bridged ring systems

* fix and test for bridged small rings torsion pattern exclusion

* add ETKDGv3 and srETKDGv3 option to keep compatiblity for original ETKDG

* EKTDG version 3 related minor fix

* add reference to doc string

* Java wrapper for ETKDGv3

* fix doc

* change CPCI to shared_ptr, but it seems to be much slower

* minor modifications to small bridged ring systems, and share_ptr from previous commit is fine

* rollback from shared_ptr(map) to just map

* run clang-format

Co-authored-by: Shuzhe Wang <shuwang@eu-login-10.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-14.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-17.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-45.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-05.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-15.euler.ethz.ch>
Co-authored-by: greg landrum <greg.landrum@gmail.com>

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

..

csharp_wrapper

Fix to allow multistructure images in Java/C# and use MCS for c# wrapper (#2898)

2020-01-23 09:03:09 +01:00

gmwrapper

Add a scaffold network implementation (#2911)

2020-02-11 08:21:01 -05:00

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

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

Adds replaceCore function that takes a matchVect (#1013)

2016-08-17 04:40:59 +02:00

CMakeLists.txt

Add a scaffold network implementation (#2911)

2020-02-11 08:21:01 -05:00

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

Override what() in exceptions (Addresses #2920) (#2928)

2020-02-05 08:20:17 +01:00

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

Fixes #2896 (#2903)

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

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

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

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 a scaffold network implementation (#2911)

2020-02-11 08:21:01 -05:00

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

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

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