Greg Landrum 5086391cdb Fix a bunch of edge cases in the pseudo 3d chiral assignment code. (#6669) ...

* 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

2023-08-31 17:30:16 +02:00

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