Commit Graph

8 Commits

Author SHA1 Message Date
Ric
90d22c94c5 Fixes #6664 (#6692)
* add some testing

* fix issue

* update doctests
2023-09-07 12:32:38 +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
Riccardo Vianello
88c5d80b33 unused targetBondLength argument in the CDXML parser's scaleBonds (#6469)
* fix unused targetBondLength argument in scaleBonds

* Replace literal with named constant in call to scaleBonds

* small fix in response to review
2023-07-04 16:54:29 +02:00
Greg Landrum
fcfbb7b083 Fix a couple CDXML issues (#6463)
* Scale bonds, make the Wedge detection cleaner, add more tests

* Readd comment

* Use document bond length

* Adds roundtrip test through a molblock

* a bit of cleanup

* change expected results for a bogus structure
add a non-ambiguous version of it

* fixes #6462

* document incompatibility

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
2023-06-15 05:05:33 +02:00
Ric
bc8d2e7556 Fix build warnings (#6235)
* un/signed comparisons in molops

* reference in loop in EmbeddedFrag.cpp

* un/signed comparison in filtercatalogtest.cpp

* un/signed comparison in Descriptors/catch_tests.cpp

* un/signed comparisons in DetermineBonds.cpp

* drop unused 'params' arg from static functions in MolInterchange/Writer.cpp

* un/signed comparisons in MolDraw2D/catch_tests.cpp

* unused var in SubgraphUtils.cpp

* 'move' preventing copy ellision in CDXMLParser.cpp

* fix infinite recursive call in SubstructLibraryWrap.cpp
2023-03-30 19:21:51 +02:00
Brian Kelley
6d10f90a8b Add wavy stereo bond support to cdxml (#5755)
* Add wavy stereo bonds

* Add wavy single bonds

* Single bonds have bond stereo stripped

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
2022-11-17 04:58:46 +01:00
Greg Landrum
1f4584b2ca run clang_format (#5676) 2022-11-01 04:14:26 +01:00
Brian Kelley
d1985caaa7 cdxml parser (#5273) 2022-09-28 05:49:27 +02:00