Warn if `Molecule.from_smiles` is provided a full atom map

[mattwthompson]

https://github.com/openforcefield/openff-toolkit/issues/1186#issuecomment-1767128056

There are a few corner cases I've left uncovered - a full atom map, but one with ambiguous or confusing indices, or what to do if given a partial atom map - for simplicity. This just warns if the atom mapping is as long as the number of atoms.

• If a user has partial atom maps, I'm not sure if directing them to use Molecule.from_mapped_smiles is a net positive
• If a user has funky atom maps, this warning may or may not be thrown (the criteria being a simple length check opens up some accidental collisions) and I'm not sure it's worth the effort to deeply consider, at least here, the numerous ways this input can be partially garbled.

Happy to update the language of the warning itself; I understand what I wrote but am not confident I'm using the best terms to describe the details.

I didn't think too deeply about adversarial cases, this handles the specific thing I care about:

In [1]: from openff.toolkit import Molecule

In [2]: Molecule.from_smiles("[H:2][O:1][H:3]")
<ipython-input-2-74b6c4f20a48>:1: AtomMappingWarning: Warning! Fully mapped SMILES pattern passed to `from_smiles`. The atom map is stored as a property in `Molecule._properties`, but these indices are NOT used to determine atom ordering. To use these indices for atom ordering, use `Molecule.from_mapped_smiles`.
  Molecule.from_smiles("[H:2][O:1][H:3]")
Out[2]:
<IPython.core.display.SVG object>

In [3]: Molecule.from_mapped_smiles("[H:2][O:1][H:3]")
Out[3]: <IPython.core.display.SVG object>

• [x] Tag issue being addressed
• [x] Add tests
  • [x] Warn if Molecule.from_smiles is provided a full atom map
  • [x] Do not warn if Molecule.from_smiles is provided a partial atom map
• [ ] Update docstrings/documentation, if applicable
• [x] Lint codebase
• [ ] Update changelog

[codecov[bot]]

Codecov Report

Merging #1747 (baadb96) into main (b4ec518) will decrease coverage by 0.03%. The diff coverage is 100.00%.

Additional details and impacted files

[mattwthompson]

Examples still failing and still my responsibility - not in context here, though

[mattwthompson]

Thank you!