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ab5483dc51
* 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>