tadhurst-cdd d5d4d194ec atropisomer handling added (#6903) ...

* 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>

2023-12-22 04:58:18 +01:00

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