* atropisomer bond atoms are checked explicitly for SP2 hybridization
before, we checked only on totalDegree = 2 or 3,
but this causes false positives for something like a chiral sulfoxide
since the S is tetrahedral (sp3) but has only 3 substituents.
the hybridization code relies on totalDegree,
but modified to include and making sure to include conjugation
so while this is more expensive per molecule, it is closer to intent
Closes#8973
* assert we got no warnings on sulfinamides
* cleanup
* bring back degree based check, quick pass so that we don't run expensive calc on all mols with wedge bonds
* bring conformer back
* Include macrocycles in atropisomer calculation
Previously, atropisomeric bonds were sanitized away if they were part of a "ring bond", which happens in macrocyclic systems.
None of the existing test cases fail if that sanitization check is removed.
The sanitization step is removed to support biaryls that are part of a larger macrocyclic system.
A set of test cases is included that cover potential macrocyclic atropisomeric systems
* Remove unmentioned files
* Keep ring check, and narrow it to when bond is in as many rings as atoms
* exclude atropisomer bonds if in rings < 8 atoms
Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
* Clarify macrocycle behavior in RDKit book
* fix typo
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Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
* New tests for speical query atoms and atropisomers
* fixed error, and used unique_ptrs
* Removed test that makes GraphMol depend on GenericGroups
* More to remove GraphMol dependency on GenericGroups
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
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Co-authored-by: greg landrum <greg.landrum@gmail.com>
