Lily Wang

+1! How much do you think it would break if the non-stereogenic value were changed from `None` to another value e.g. `stereochemistry: Optional[Literal["R", "S", ""]]`, where `""` is non-stereogenic and...

I don't have an immediate idea of where this comes from -- maybe looping over the distance matrix calculation? -- but I get a 1.2-2x speedup that saves 180 milliseconds...

> Either an extra description with instructions on how to debug plugin failures (simple) or a way to infer whether the user meant to load a force field through a...

> molecule = Molecule.from_xyz_unsafe(xyzfile) If you made the entrypoint `from_unsafe_xyz_data` or something that does not depend on it being a file, you could route `from_qcschema` through it too.

> The ToolkitAM1BCCHandler should try to assign ELF10 charges if OE is available, but just single-conformer AM1 charges if only AmberTools is available (for runtime reasons) > AmberTools assign_partial_charges with...

> Should these exceptions be grouped into a single file (maybe openforcefield/exceptions.py) or, as it stands now, scattered across files closer to where they'd be raised, or something in between?...

Please let me know if this should be a separate issue. On the topic of custom exceptions -- why is MessageException? Last week during a session with @j-wags we wondered...

Is #986 on the radar of this PR or should I open a PR? It currently raises vanilla Key- and IndexErrors.

> I'm almost always writing with one particular erroring line of code in mind You can still do this with XYZError, but for people who want to `except` a general...

> Trust the QCArchive molecule's geometry, symbols, and connectivity, and build the molecule from that. IMO this is the only reasonable way to handle this if the QC stack is...