* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* 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
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
* fix for calculation of prinicipal moments of inertia
* fix a typo
update expected values
* PMI and NPR tests working
* cleanup some of the other descriptors and tests
* Test against Moments.py descriptors
* add new tests from Brian
* remove some warnings
* update .gitignore
* foundation for 3D descriptors
move PBF into core
* cleanup work
* a bit more cleanup
* move the principal moments calc to MolTransforms
* cleanup
* cleanups
* add caching of the principal moments and values
* do not include the 3D descriptors in MolDescriptors.h
* the properties are computed
* add PMI descriptors and tests
* add tests for NPR descriptors
* return 0 when the largest PMI is zero
* PMI edge case tests
* NPR edge case tests
* PBF edge case tests
* PBF edge case tests
* more edge cases
* add a few more 3d descriptors
* add defns to docs
* tests for the new descriptors
* add versions to new descriptors
* add 3d descriptors to python wrapper
* add eigen support to the travis build
* try to get non-windows builds working
* remove computeCovarianceMatrix() from java wrapper
* make pmi property names "private"
the horrible cross-library exception handling mess on linux. This may well break things on windows, which
might want these things static. Regardless, even as it is, this should be considered experimental
