* handle bonds with zero length around chiral centers
* chirality perception fixes
- fix handling of T-shaped chirality
- catch zero-length bonds
- catch opposing bonds with opposite wedging
* another special case
* more quasi-linear handling
* more progress
* backup
* update
* remove some complication with the neighbor order sorting by just doing a sort
🤦
passing all tests again
* oh, isn't this fun?
* no more t-shaped three-coordinate chirality
* still a couple of tests failing
* all tests pass
* overlapping neighbors without wedges remove stereo
* add test for overlapping atoms with wedged bonds
* make warnings consistent to allow easy parsing
* more testing
* docs
* make sure we don't try to access an SG which no longer exists
* Fixes#6479
updates a bunch of tests to support this
* test ring stereo too
* update expected results from the tests
* backup
* backup
* passes a lot of tests
* cleanup; still failing some tests
* pay attention to bond starting points... duh
* all tests pass
* invert y coords
* Scale bonds, make the Wedge detection cleaner, add more tests
* Readd comment
* Use document bond length
* Adds roundtrip test through a molblock
* a bit of cleanup
* remove the old code since we aren't using it any more.
* changes in response to review
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Scale bonds, make the Wedge detection cleaner, add more tests
* Readd comment
* Use document bond length
* Adds roundtrip test through a molblock
* a bit of cleanup
* change expected results for a bogus structure
add a non-ambiguous version of it
* fixes#6462
* document incompatibility
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* add function to canonicalize enhanced stereo representations
* use enhanced stereo in canonicalization
* Fixes#6045
enables the doc tests for EnumerateStereoisomers.py
Re-enables the BRICS tests
* some things work... tests need to be updated
* c++ and python tests pass
* update expected psql results
* run the canonicalization on SMILES generation;
c++ and python tests pass
* cartridge and java tests pass
* update doctests
