* 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>
* Support Chemical Markup Language, CML, for writing
Implement RDKit::MolToCMLBlock and RDKit::MolToCMLFile
http://www.xml-cml.org/
* a number of cleanups and fixes
1. stop writing the cml: namespace to the output. Tools like marvin can't read that and it's not nececssary
2. fix the H count
3. continue writing atom info for 2D confs
4. simplify the writing of atom parity
* make the conformer optional
write bond hash/wedge information
* update the expected python results
* Remove overloaded function
Co-authored-by: greg landrum <greg.landrum@gmail.com>
