rdkit

mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00

Files

Maciej Wójcikowski 10fbd483bb [MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629 )

* Add parameter to skip proximity bonding during PDB reading

* Test proximityBonding flag

* Remove multivalent Hs and bonds to metals in PDB

* Add tests for multivalent Hs and metal unbinding

* Remove covalent bonds to waters

* Test unbinding of HOHs

* Refactor funxtions

* Rename flag for cosistency

* Include flavor in double bond perception

* Add metalorganic test (APW ligand)

* Validate input foe IsBlacklistedPair and minor changes.

2017-11-15 06:53:31 +01:00

csharp_wrapper

Fix #1413 (#1414 )

2017-05-20 09:46:29 -04:00

gmwrapper

Fixes Java wrapper build error with Boost 1.64 (#1613 )

2017-11-15 06:36:15 +01:00

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

Fix/java win64 memoryleak (#1159 )

2016-11-11 04:44:22 +01:00

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

Merge branch 'modern-cmake' of github.com:avaucher/rdkit into modern-cmake

2017-07-01 19:31:53 +02:00

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

Add a parameters structure for controlling the embedding options. (#1121 )

2016-11-01 11:39:03 +01:00

DiversityPick.h

add the useCache option to the java wrappers;

2016-02-26 08:07:03 +01:00

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

get the swig wrappers building. this required disabling the bitsSet version of the ctor for ExplicitBitVect

2014-04-12 07:12:09 +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

Fix #1413 (#1414 )

2017-05-20 09:46:29 -04:00

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

plug a fingerprint core leak in the SWIG wrappers

2013-03-29 17:17:08 +00:00

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

first pass, using google style

2015-11-14 14:58:11 +01:00

Inchi.i

add svn props

2011-07-01 04:43:39 +00:00

make_templates.py

Issue1071/yapf (#1078 )

2016-09-23 04:58:46 +02:00

MolDraw2D.i

Fix problems in the SWIG wrappers caused by #1546 (#1558 )

2017-09-11 16:08:47 +02:00

MolOps.i

Fix leak with renumberAtoms() in the SWIG wrappers (#1064 )

2016-09-13 12:24:08 -04:00

MolSupplier.i

fix SWIG wrappers for the resonance mol suppliers

2015-11-04 05:29:50 +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.i

add svn props

2011-07-01 04:43:39 +00:00

msvc_stdint.i

Fixes csharp build for 64 bit systems (#1098 )

2016-10-14 15:40:05 +02:00

parse_doxy_html.py

Issue1071/yapf (#1078 )

2016-09-23 04:58:46 +02:00

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

Find potential stereo bonds should return any (#1202 )

2016-12-17 05:37:30 +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

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

add support the new sequence readers to wrappers (#1181 ) (#1221 )

2016-12-21 04:42:17 +01:00

RWMol_doc.i

add svn props

2011-07-01 04:43:39 +00:00

RWMol.i

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629 )

2017-11-15 06:53:31 +01:00

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

Subgraphs.i

add svn props

2011-07-01 04:43:39 +00:00

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