Add explicit hydrogens if needed in from_openeye

[j-wags]

Summary

• Fixes Unexpected behavior: Parameter usage statistics incorrect when creating from SMILES without explicit hydrogens #362
• Adds test for same

Status

• Ready for review
• Ready for merge

[codecov-io]

Codecov Report

Merging #364 into master will increase coverage by 0.01%.
The diff coverage is 90%.

@@            Coverage Diff             @@
##           master     #364      +/-   ##
==========================================
+ Coverage   76.54%   76.56%   +0.01%     
==========================================
  Files          19       19              
  Lines        5585     5594       +9     
==========================================
+ Hits         4275     4283       +8     
- Misses       1310     1311       +1

Impacted Files	Coverage Δ
openforcefield/utils/toolkits.py	87.1% <90%> (+0.01%)	⬆️

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[andrrizzi]

I'm not entirely sure how we should do this, actually. Does this change make from_smiles(..., hydrogens_are_explicit=True) behave unexpectedly? I think that function calls from_openeye(). Maybe from_openeye() should take an argument to control this behavior as well.

[j-wags]

Wow. Great thinking, I had totally missed the possible consequences there.

So, the case where this would be a problem is if the user provided a SMILES with a specific explicit protonation state, and the toolkit misinterpreted it as having implicit hydrogens (even though the user set hydrogens_are_explicit=True).

To prevent this from happening, I've updated both OpenEyeToolkitWrapper and RDKitToolkitWrapper's from_smiles functions to assert that, if hydrogens_are_explicit=True, then there are zero implicit hydrogens on the molecule.

[andrrizzi]

Looks great, thank you! I've added only a few minor comments, but feel free to merge when you think it's ready.