* 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
* backup
* simple first pass, passes all tests
* cleanup a bunch of existing uses
* ensure that we can safely add atoms/bonds while in edit mode
* add context manager on python side
* handle exceptions properly in those
* changes in response to review
* 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
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@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
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
* 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
* 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
