mosdef-hub / foyer

A package for atom-typing as well as applying and disseminating forcefields

https://foyer.mosdef.org

MIT License

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Integrate ele #395

Closed daico007 closed 3 years ago

daico007 commented 3 years ago

PR Summary:

Remove parmed element dependency in the atomtyping step. Relate to #391

PR Checklist

[ ] Includes appropriate unit test(s)
[ ] Appropriate docstring(s) are added/updated
[ ] Code is (approximately) PEP8 compliant
[ ] Issue(s) raised/addressed?

codecov[bot] commented 3 years ago

Codecov Report

Merging #395 (8558fe4) into master (26791e1) will decrease coverage by 0.09%. The diff coverage is 40.00%.

@@            Coverage Diff             @@
##           master     #395      +/-   ##
==========================================
- Coverage   71.47%   71.38%   -0.10%     
==========================================
  Files          16       16              
  Lines        1553     1555       +2     
==========================================
  Hits         1110     1110              
- Misses        443      445       +2

umesh-timalsina commented 3 years ago

While we are at it can we also take care of https://github.com/mosdef-hub/foyer/blob/a3ec0177507d847ec53136d8c49f424ce188f8a1/foyer/forcefield.py#L16-L17 imports here and remove foyer/element.py

daico007 commented 3 years ago

While we are at it can we also take care of

https://github.com/mosdef-hub/foyer/blob/a3ec0177507d847ec53136d8c49f424ce188f8a1/foyer/forcefield.py#L16-L17

imports here and remove foyer/element.py

I think the we still need the OpenMM elem here, they are used to infer OpenMM Element objects. I don't think the OpenMM forcefield will accept 3rd party Element object.

justinGilmer commented 3 years ago

Also, the RTD build has failed. It seems to be missing ele? Although im not entirely sure yet.

daico007 commented 3 years ago

I added ele to the docs build yml, let see if that fixes the issue