* 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>
* cleanup a bunch of g++ warnings
* make it work with clang
* remove some additional warnings based on CI builds
* fix that version number
* stop being verbose when building
* TautomerQuery class
* working test
* Comment header
* Merge with master. Greg's suggestions. More tests. Python wrapper
* Updated Pattern Fingerprints to merge with master. Reset email
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Greg suggestions of 6_2_2020
* Explicit types in Java TautomerQueryTests class
* Update Code/GraphMol/QueryOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* get windows dll builds working
* Removed tautomer query wrappers from RDKit namespace
* Fixes from evaluation
* Template molecule identification fix. Greg's suggestion
* Final check search functor for evaluating template matches as they are found
Co-authored-by: Gareth Jones <gjones@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
* switch from using `[D0]` to `[*]` to ensure single atom fragments are correctly handled in the pattern fingerprint;
Fixes#1496
* update expected reaction similarity results
