* 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
* feed dummy perpendicular point for cross product to prevent zero error in normalization during atropisomer chirality, fixes#8602
* remove debug log
* move test, and check that no bonds
* Fixes#7983
move the call to cleanupAtropisomerStereoGroups() into assignStereochemistry()
* Additional tests from @susanhleung in #8323
* more testing
* changes in response to review
* changes for review
* 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
* test changes
* 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
* Merge branch 'master' into pr/specialQueries
* changes from previous PR
* Iclude false chiral
* rigorous enhnced stereo canoncalization
* Added more tests and clenup
* removed commented out code
* corrected init of SmilesWriteParams
* added MolFileStereoChem.h to the header files
* Renamed Rxn parser to MrvBlockToChemicalReaction
* To make catch2 work, and match the checksum
* Fixed Structchecker errors
* fix CI for DetermineBonds catch test
* error in catch_test for CI
* Allow custom smileWriteParams in GetMolLayers
* misnamed entry point
* ReactionFromMrvString change name
* remove adding writeParams to GetMolLayers
* make rigorous enhanced stereo the default, and fix tests
* only one abs group no longer needs Rigorous Enhanced treatment
* changed string_view to string in catch test
* Canonicalize Enhnaced Stereo only resturne unique smiles
* Now allows or and and groups together
* internal routines inside detail scope
* fix test error
* changed string back to string_view and fixed a CHECK
* Fixes for PR review tests
* Fix RDKit_Book.rst failure on build test
* fix xqm sql test
* updated expected files for cxsmiles_test
* Fixed removal of atom attrs
* Fixed tests after merge of master
* More efficient version of Stereo Groups Canonicalization
* Fixes for ctests
* removed debug code
* readded cipLabel test
* fix generalizedSubstruct/catch_tests.cpp error
* hueristics to improve speed
* Rationaized control of abs groups
* removed unused routine
* added rigorous stereo group treatment to test
* some suggested changes
* Changes per PR review and removed some changes to smiles
* Fixed CI errors
* changes per PR review
* more PR review vhanges and cleanup
* Fixed PSql PKL change
* changes as per PR review
* Restored error type for bad mols for canonicalizeStereoGroups and added a test
* Merge master and fix test in MolDraw2D
* Fix for randomize test error and other PR review comments
* Removed unsued variable to fix mac CI
* do not force aromatization in canonicalizeStereoGroups
* changes as per PR review
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* prefer wedging ring bonds for atropisomers
* update expected results
* handle 3D as well
* prefer wedging to larger rings
wedging bonds in 5 rings make later attempts at improving kekulization very difficult
update expected results
* extend those changes to 3D
* update tests for those changes
* avoid wedging atropisomers if possible
response to review
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
* changes for CIP test errors
* Updated internal doc to match what it does
* changes per PR review
* removed cout statements in tests
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
