rdkit

mirror of https://github.com/rdkit/rdkit.git synced 2026-06-05 22:04:27 +08:00

Files

Greg Landrum 253f172353 Allow identification of chemistry problems (#2587 )

* add AtomValenceException

* refactor a bit and add KekulizeException

* add copy ctor and copy() method

* add detectChemistryProblems

* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts

* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.

* cleanup and finish the python wrappers for the new exceptions

* make sure things are truly polymorphic

* wrap shared_ptrs of the new exception types

* expose DetectChemistryProblems()

* get the java wrappers building again

* transfer those changes to the c# wrapper

* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue

* response to review

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

csharp_wrapper

Allow identification of chemistry problems (#2587 )

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

gmwrapper

Allow identification of chemistry problems (#2587 )

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

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

first pass at switching to a normal download (#2609 )

2019-08-19 13:45:25 -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

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

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

Allow identification of chemistry problems (#2587 )

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

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