Commit Graph

10 Commits

Author SHA1 Message Date
Brian Kelley
b417465e93 Adds MolToCDXMLBlock to FileParsers (#9291)
* Adds MolToCDXMLBlock to FileParsers

* Simplified code, removed warning

* Fix C# wrapper for MolToCDX

* Add C# test, fix cscode in swig

* Fix typo in tests

* Set default format to CDXML for MolToCDXML

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Add CDXML writer smoke tests

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2026-05-29 05:36:35 +02:00
Greg Landrum
8fc241495c Fixes #9107 (#9111)
* Fixes #9107

always include std_unique_ptr.i when using modern SWIG

* allow java tests to build without chemdraw support
2026-02-13 14:11:10 -05:00
Brian Kelley
cf269aa813 Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
* Fist pass at CDX support

* Enable CDX support for reading (also) in the CDXMLParser API

* Add cdxml test files

* Update swig wrappers for CDXMLFormat and Parameters

* Add constructor to ChemDrawParserParams

* Add Java SWIG support for ChemDraw

* Add chemdraw define to rdconfig

* Add missing chemdraw deps

* Remove direct expat link

* Fix Java linkages for ChemDraw

* Remove bad merge code

* Remove bad merge code

* Fix csharp builds

* Add sniffer for the ChemDraw DataStream

* Include filesystem

* Fix test on windows

* Add more CDX tests

* Ensure streams are open in binary mode to support CDX on windows

* Fix text to show that a Block is the text input, not a file

* Fix CSharp test

* Disable CDX tests when not building chemdraw

* Turn back on chemdraw

* Response to review

* Turn off chemdraw support for the limited external test

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
2025-08-29 04:39:22 +02:00
Greg Landrum
a57060225f Fixes #6479 (#6482)
* make sure we don't try to access an SG which no longer exists

* Fixes #6479
updates a bunch of tests to support this

* test ring stereo too

* update expected results from the tests
2023-07-13 19:29:06 +02:00
Greg Landrum
a8c8e9a8e1 Add canonicalization of stereo groups (enhanced stereo) (#6051)
* add function to canonicalize enhanced stereo representations

* use enhanced stereo in canonicalization

* Fixes #6045
enables the doc tests for EnumerateStereoisomers.py
Re-enables the BRICS tests

* some things work... tests need to be updated

* c++ and python tests pass

* update expected psql results

* run the canonicalization on SMILES generation;
c++ and python tests pass

* cartridge and java tests pass

* update doctests
2023-02-08 04:21:51 +01:00
Brian Kelley
d1985caaa7 cdxml parser (#5273) 2022-09-28 05:49:27 +02:00
Kevin Burk
7bd9f7b434 Remove extra newline from Kekulize error message. (#5022)
* Remove extra newline from Kekulize error message.

* Fix test for exception message.
2022-02-22 04:48:14 +01:00
Steve Roughley
b1fd950eb2 Added getMessage method to exceptions (#3700)
* Added getMessage method to exceptions

* Added test cases to WrapperTests.java

* Corrected typo in test case

* Corrected test case error
2021-01-14 06:53:37 +01:00
Paolo Tosco
ffa524c87b - added SWIG Java wrappers for ResonanceMolSupplier and
getResonanceSubstructMatches()
- added a few tests
2015-11-02 22:45:41 +00:00
Greg Landrum
c7ef21088b add initial version of new swig wrappers 2011-04-07 05:22:00 +00:00