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tadhurst-cdd d5d4d194ec atropisomer handling added (#6903) 
* atropisomer handling added

* fixed non-used variables,  linking directives

* BOOST LIB start/stop fixes, linking fix

* Fixes for RDKIT CI errors

* minimalLib fix

* changed vector<enum> for java builds

* check for extra chars in CIP labeling

* removed wrong deprecated message

* fix ostrstream output error?

* restored _ChiralAtomRank to lowercase first letter

* changes for merged master

* Fixed catch label for new Catch package

* update expected psql results

* get swig wrappers building

* restore MolFileStereochem to FileParsers

* fix java wrapper for reapplyMolBlockWedging

* some suggestions

* move a couple functions out of Bond

* Merge branch 'master' into pr/atropisomers2

* merged master

* Renamed setStereoanyFromSquiggleBond

* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol

* fix for CI build

* attempt to fix java build in CI

* attempt to fix java build in CI #2

* New routine to remove non-explicit  3D-geneated chirality

* changed to use pair for atrop atoms and related bonds

* Changes as per PR reviews

* PR review respnses

* PR review reponse - more

* Fix merge from master

* fixing java ci after merge

* Updated the help doc for atripisomers

* update the atropisomer docs

* improve the images

* add the source CXSMILES

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2023-12-22 04:58:18 +01:00
..
csharp_wrapper
Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)
2023-12-19 04:44:06 +01:00
gmwrapper
cmake cleanup (#6814)
2023-11-10 15:32:54 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
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
cdxml parser (#5273)
2022-09-28 05:49:27 +02:00
ChemTransforms.i
Add depiction coordinates to molzip (#5993)
2023-01-28 04:46:39 +01:00
CMakeLists.txt
cmake cleanup (#6814)
2023-11-10 15:32:54 +01:00
Conformer_doc.i
add svn props
2011-07-01 04:43:39 +00:00
Conformer.i
- wrap types that are otherwise not accessible from SWIG wrappers (#6110)
2023-02-20 12:44:24 +01:00
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
Allow the sources of conformer generation failures to be retrieved (#5960)
2023-01-24 18:09:15 +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
SWIG pickling improvements (and other cleanup) (#6133)
2023-03-01 05:00:56 +01:00
extend_std_vector.i
Get the wrappers working with SWIG 4.0 (#5795)
2022-12-10 07:13:55 +01:00
FilterCatalog_doc.i
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
FilterCatalog.i
SWIG pickling improvements (and other cleanup) (#6133)
2023-03-01 05:00:56 +01:00
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
Get the wrappers working with SWIG 4.0 (#5795)
2022-12-10 07:13:55 +01:00
FMCS.i
Exclude MCSParametersInternal from SWIG (#6808)
2023-10-17 18:29:46 +02:00
ForceField.i
patch a leak
2013-12-06 03:39:00 +01:00
GeneralizedSubstruct.i
Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)
2023-12-19 04:44:06 +01:00
GenericRDKitException.h
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Inchi.i
add svn props
2011-07-01 04:43:39 +00:00
make_templates.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolBundle.i
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolDraw2D.i
- wrap types that are otherwise not accessible from SWIG wrappers (#6110)
2023-02-20 12:44:24 +01:00
MolEnumerator.i
Add support for SRUs to MolEnumerator (#4563)
2021-09-28 16:37:39 +02:00
MolHash.i
Fixes #2677 (#2687)
2019-10-03 18:07:26 -04:00
MolOps.i
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
MolStandardize.i
Dev/GSOC2018_MolVS_Integration (#2002)
2018-09-28 11:24:25 +02:00
MolSupplier.i
Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF (#4933)
2022-01-23 07:06:36 +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
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +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
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
RDKitExceptions.i
Added getMessage method to exceptions (#3700)
2021-01-14 06:53:37 +01:00
RDLogger.i
Expose RDLog to SWIG wrappers (#5749)
2023-04-14 09:26:56 +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
RGD with matching on tautomers of core (#6611)
2023-08-29 08:50:14 +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
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
RWMol_doc.i
add svn props
2011-07-01 04:43:39 +00:00
RWMol.i
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
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
std_tuple.i
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
StereoGroup.i
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
Streams.i
Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF (#4933)
2022-01-23 07:06:36 +01:00
Subgraphs.i
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
SubstanceGroup.i
Sgroup (#3390)
2020-09-09 04:59:08 +02:00
SubstructLibrary.i
support generalized substructure search in the SubstructLibrary (#6835)
2023-11-01 14:55:28 -04:00
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
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
types.i
add svn props
2011-07-01 04:43:39 +00:00