* move molzip to its own file
* basics working
* more testing
* another test
* minor
* fix doxygen comment format
* fix alignment with co-directional exit vectors;
some modernization
* JSON parsing
python wrapper
* response to review
* response to review
* explicitly test that the first frag does not move
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Co-authored-by: = <=>
* Mostly working.
* Clear out debugging writes.
* Avoid a mol copy.
* Left some debugging in.
* Move the fix into fragmentOnBonds.
* Add test.
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Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
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Co-authored-by: = <=>
* Test routine working
* Fix python molzip signature clash
* Update SWIG bindings
* Add C++ and Python documentation
* Add C++ and Python documentation
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Initial development and test
* Sort of working tests
* Copy corodinates to new core
* Clear stereochemistry on core atoms with unlabelled rgroups
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Continuing development
* Updated development
* Fixed Chirality Issues
* All tests working
* Remove some unused code
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Working tests
* Tidy test code
* Adjust catch_rgd for stereochemistry in output cores
* Build ring info in output cores
* Fix Mac OS bug
* Fix for MCS and onlyMatchAtRGroups
* Brian's optimization suggestion
* Fix core group coordinate bug
* Test for replaceCore and multiple core bonds to chiral atom
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Changes in response to Greg's code review
* R group stereo bond attachment fix
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* MolZip now saves the bonddir when zipping
* Add test for saving bonddir in MolZip
* Save either the first or second bond dir, fix the test to actually test
* Add more comprehensive bonddir checking and atom reordering
* Fix the atom swaps after the consistency check
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* MolFragmenter: fix a leak when exceptions are thrown
* DistGeomHelpers: fix leaks when exceptions are thrown
* SubstructLibrary: fix usage of invalid memory
* clear up leaks found during ASAN testing
* First pass at MolZip (sans bond stereo)
* Add support for bond stereo zipping
* Add molzip swig wrappers
* Add simple python wrapper/tests
* Remove smiles round tripping now that fragmentOnBonds is fixed
* Responses to review
* AtomMaps and Isotopes must explicitly be set
* Add molzip single molecule api isotope test
* Add missing %newobject
* Add better python docs, label test
* fix docs add a test for molzip
* Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add missing case breaks
* Add more preconditions, move mark and restore to private functions
* Remove unused and redunddant code
* optimize get_other_atom
* Add single arg molzip test
* Update Code/GraphMol/Wrap/rough_test.py
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix bondstereo when fragmenting molecules with cis/trans E/Z
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add more tests for bond stereo
* Add test to ensure non-stereo atom bond breaks are preserved
* Remove extraneous test, fix another
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Sketch of a solution to preserve bond direction in fragmentOnBonds
* A bit of cleanup work based on Andrew's original commit for #1039
Add a couple of tests too
* forgot to save a file before the commit
