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Handle some edge cases with preset charges #1070

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Handle some edge cases with preset charges #1070

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@mattwthompson mattwthompson commented Oct 3, 2024 •
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Description

This PR better handles user inputs around the charge_from_molecules argument from the toolkit. Resolves #1057 #1058 #1059

Checklist

  • Error if charge_from_molecules contains any molecule without partial charges
  • Error if charge_from_molecules contains any duplicate molecules (defined by isomorphism, approximated by SMILES without hydrogens)
  • Test behavior discussed in Partial charge assignment using charge_from_molecules on virtual sites / charge increments can be unexpected. #1050
  • Add tests
  • Lint
  • Update docstrings
    • Update from_smirnoff docstring
    • Add user guide
      • Describe charge assignment hierarchy
      • Describe limitations with preset charges
      • Add FAQ entry I guess we don't have an FAQ here, maybe should check openff-docs

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@mattwthompson mattwthompson changed the base branch from main to develop October 3, 2024 18:26
@mattwthompson mattwthompson linked an issue Oct 3, 2024 that may be closed by this pull request
charge_from_molecules silently ignores isomorphic molecules in list, only using the first entry #1058
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@mattwthompson mattwthompson mentioned this pull request Oct 3, 2024
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codecov bot commented Oct 3, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.61%. Comparing base (7b571ca) to head (23a4c26).

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@mattwthompson mattwthompson mentioned this pull request Oct 4, 2024
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@mattwthompson mattwthompson marked this pull request as ready for review October 4, 2024 20:08
Yoshanuikabundi
Yoshanuikabundi reviewed Oct 9, 2024
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These are great improvements I think. I think the documentation changes from #1048 could be merged with this so that the charge hierarchy is only documented once, which might improve findability - I think if there is similar documentation in two places, people sometimes read one place carefully, then later find the second place and think they're already familiar with it coz it looks the same.

My notes are mostly just adding more detail to what you've written, but this is great!

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@mattwthompson mattwthompson added this to the 0.4.1 milestone Oct 11, 2024
@mattwthompson mattwthompson linked an issue Oct 16, 2024 that may be closed by this pull request
Partial charge assignment using charge_from_molecules on virtual sites / charge increments can be unexpected. #1050
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