2 Commits

Author	SHA1	Message	Date
Greg Landrum	86141183c1	Moving towards getting all tests to pass when using the new stereo code (#8409) ... * Fixes #8379 * check in some working tests * test passes * test passes * test passes * test passes * test passes * ensure that the invariants flush the streams on failure * tests pass * test passes * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * tests pass * Fixes #8391 * tests pass * fix a test with legacy not clear why this was not causing problems before * make a test work * Fixes #8396 * gcc builds work * fingerprint tests pass * mention backwards incompatible change * fix a problem with FindMolChiralCenters * more testing details * enable the test status output * Fixes #8432 fix a bug in double-bond stereo handling for template matching * all depictor tests pass * use the new-stereo chiral ranks in the depiction code * always assign new-stereo chiral ranks * make _ChiralAtomRank a computed property This is analogous to _CIPRank * tweak to the way the atom ordering is computed for 2D coordinate generation * update two expected results * backup * response to review * tests pass * tests pass --------- Co-authored-by: = <=>	2025-04-15 14:00:32 +02:00
Riccardo Vianello	3f7caf0147	Extend RDKit::MolStandardize with a validation and standardization Pipeline (#7582) ... * Extend RDKit::MolStandardize with a validation and standardization Pipeline * suggested changes * apply clang-format * apply yapf * MolStandardize::FeaturesValidation optionally disallow dative bonds * add allowDativeBondType to MolStandardize::PipelineOptions * apply clang-format * make the API of other validation classes more consistent with MolStandardize::FeaturesValidation * apply clang-format * PipelineStage to enum class remove virtual functions from Pipeline class be explicit about enums * light refactoring to avoid what I think is an unnecessary call to `parse` * a bit of modernization * make the pipeline configurable * make parse and serialize configurable too * switch to storing pipeline stages using uints * add a simple test for providing a pipeline * update pointer alignment for clang-format * test modifying the parser and serializer * update swig requirement * changes in response to review * changes in response to review * rename PipelineResult's *MolBlock members to *MolData * upgrade swig to 4.2 in the CI environments * add a few missing export directives --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>	2024-07-30 17:09:16 +02:00