Greg Landrum fbb1e6baaa Add v2 API to FileParsers (#7077) ...

* basic approach to v2api

* does not work, backup commit

* well, that now compiles

* cleaner

* more cleanup and testing

* get the SWIG wrappers to build

* swig wrappers now build

* switch back to using references to default values

* adjust to new catch version

* move the implementation to v2 and call it from v1

* update the parameter object too

* move debugParse down

* a couple of review changes

* make v2 naming consistent with Python

* first pass at v2 for the ctab parsers

* move a the writing functionality to a different header

this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code

* do v2 of the tpl parser

* fix missing dependency

* Mol2 parser

* move over the XYZ parser

* switch over the PDB parsers too

* get mac and java builds working (hopefully)

2024-01-28 05:11:54 +01:00

..

csharp_wrapper

Update C# exception handling (#7081)

2024-01-23 06:11:36 +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

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

Point3D_doc.i

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

point.i

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QueryAtom_doc.i

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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

[v2 API] SMILES/SMARTS parsers (#6203)

2024-01-19 17:17:51 +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

Add v2 API to FileParsers (#7077)

2024-01-28 05:11:54 +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

[v2 API] SMILES/SMARTS parsers (#6203)

2024-01-19 17:17:51 +01:00

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