* very basics: actually parsing the new atom stereochem features
* add some input verification for the chiral permutations
* fix a typo
add quadruple bond SMILES/SMARTS extension
* add forgotten files
* patch from Roger
* add Roger's parsing examples
* typo
* new tests
* adjusted version of next PR from Roger:
- add SP2D hybridization for square planar (this may change)
- some modernizationof Chirality.cpp
- stop using < HybridizationType in Chirality.cpp (should probably do this elsewhere too)
- improved handling of hybridization assignment for new stereochem
- handle new stereo/hybridization in UFF
- tests for the above
* perception of non-tetrahedral stereo from 3D (from Roger S)
Basic testing of SP and TB based on opensmiles docs
* potential fixes for octahedral assignment
more tests
* docs update
need way more!
* map the TH tags directly to @ tags
* very basics of SMILES writing
this does not work with anything that changes the permutation order
like canonicalization or writing things in rings.
* start to support the getChiralAcross API
* more testing
* consistency
* add hasNonTetrahedralStereo() and getIdealAngleBetweenLigands()
* assignStereochemistry should only remove non-tetrahedral stereo
* re-simplify those tests
* cleanup matrix stream output
* initial pass at supporting nontet stereo in distgeom
* backup
* start on the reference docs
* TBP reference
* first pass at Oh finished
* update SP section
* more doc updates
* fix a typo
* add param to not remove Hs connected to non-tetrahedral atoms
* VERY basic coord generation for square planar
* TBP basics
* basic OH depiction
* start testing missing ligands
allow non-tet stereo in rings (ugly, but correct)
* add new TBP functions from Roger
* update depiction code for new API
* backup, the new tests work so far
* Finish the TB tests
* OH tests pass too
* cleanup
* first pass at getting correct SMILES with reordering
need way more testing than this
* ensure permutation 0 is correctly preserved
* some progress towards adding non-tetrahedral stereo to StereoInfo
* doc update
* add non-tet chiral classes to python wrappers
* make sure removeAllHs also gets neighbors of non-tetrahedral centers
more testing
* a bit of depictor cleanup
* make the assignment from 3D more tolerant
more testing
* improve the bulk testing
* cleanup
* remove a bit of redundant code
* ensure we don't write bogus permutation values to SMILES
* fix some rebase problems
* allow assignStereochemistryFrom3D() to be called without sanitization
* allow disabling the non-tetrahedral stereo when it's not explicit
* get that working on windows too
* Stop trying to assign hybridization to actinides
There's also some cleanup in this commit
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@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
* first round of cleanups based on PVS-studio suggestions
* a couple more
* a few more cleanups
* another round of cleanups
* undo one of those cleanups
we want the integer rounding behavior here
* add a comment to make that clear
* Fix for filter catalog PRECONDITION redundancy
* 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
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
* remove some debugging info
* move classes from .h to .cpp
* SWIG wrappers
* improve resonance structure sorting for degenerate resonance
structures
I will do all of the above ASAP
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
