Document that topology charges are ignored

[mattwthompson]

Description

Resolves #1059

Checklist

• Document details relevant to from_smirnoff _without_ charge_from_molecules silently assigns all isormophic molecules the same partial charges #1059

[davidlmobley]

I read the updated doc strings, and I'm not sure the changes make the implications sufficiently clear for a use case like Irfan's. Should it explicitly say somewhere that in no case can isomorphic molecules end up with different charge sets?

[IAlibay]

@mattwthompson this seems to address #1059 but not #1058 is this intended? (the fixes says 1058, the linked issue is 1059..)

[mattwthompson]

Whoops, yes, this is meant to address #1059!

[mattwthompson]

Should it explicitly say somewhere that in no case can isomorphic molecules end up with different charge sets?

Separate issue (due to my mistake) but in #1070 I'm adding an error when charge_from_molecules includes any isomorphic molecules

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.59%. Comparing base (ea65f20) to head (ca7ded6).
Report is 5 commits behind head on develop.

Additional details and impacted files