8 Commits

Author	SHA1	Message	Date
Ric	3058ec4db8	Fixes #7023 (#7136) ... * reset to master, delete check * add the test	2024-02-06 15:57:21 +01:00
Greg Landrum	c9a46b34bc	Fixes #6975 (#6972)	2023-12-11 17:40:30 +01:00
Greg Landrum	2957ab4576	switch to catch2 v3 (#6898) ... * switch to catch2 v3 Fixes #6894 * fix a couple of problems noticed in the CI builds * more warning cleanup * changes in response to review	2023-11-15 06:45:42 +01:00
Ric	aa02c9afb0	Fixes #6633 (#6643) ... * add a test * add fix * ignore incorrect stereo bonds from inchi	2023-08-23 06:18:14 +02:00
Ric	d033aee043	Optionally forward Enhanced Stereo Group ids (#6560) ... * add id members to StereoGroup class * add optional read id argument to StereoGroup constructors * add functions forward Stereo Group Ids and assign the missing ones * update ops updating stereogroups to forward read id * update CX Smiles to parse/write stereogroup ids * Add test cases for stereo group id forwarding/canonicalization * update mol block (V3K only) to parse/write stereogroup ids * update pickling to parse/write stereogroup ids * update cdxml parser to store stereogroup ids * update mol interchange to parse/write stereogroup ids * update draw code with new stere group ids * update test * add some tests * Update Code/GraphMol/Wrap/rdmolfiles.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/Wrap/rdmolfiles.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/Canon.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/SmilesParse/CXSmilesOps.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * review --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>	2023-07-27 18:53:40 +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
Greg Landrum	9fa1df1cf6	Drop usage of CIP information from the canonicalization code (#5385) ... * stop using CIP codes in the atomic canonicalization this will change results in some cases, so lots of tests need to be updated. * stop breaking string literals... ARGH * tests now pass * update double bond canonicalization * update a python test * some cleanup * update expected results for cartridge	2022-07-13 05:40:23 +02:00