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Add temporary fix for periodic dihedrals #327

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rmatsum836
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PR Summary:

Addressing issues raised in #323 and #326. Two changes in forcefield.py:

  • when verbose=True, compare the openmm dihedrals to both parmed rb_torsions and dihedrals. This allows a system with periodic dihedrals to be compared with structure.dihedrals.
  • Raise separate errors/warnings for when openmm dihedrals != parmed dihedrals vs openmm dihedrals < parmed dihedrals. The motivation for this is in the case of Foyer should identify missing parameters when it fails #323, there were more parmed dihedrals than openmm dihedrals because a single dihedral type contained multiple dihedrals. I don't think this should raise an error, so in this case I raise a warning and a separate message instead.

This is very much a temporary fix, and I expect dihedrals will be handled much better with the new backend. This is also just an idea, so feel free to tell me if it's a bad one.

PR Checklist


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

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codecov bot commented Mar 10, 2020

Codecov Report

Merging #327 into master will increase coverage by 0.03%.
The diff coverage is 71.42%.

@@            Coverage Diff             @@
##           master     #327      +/-   ##
==========================================
+ Coverage   84.78%   84.82%   +0.03%     
==========================================
  Files          14       14              
  Lines        1275     1278       +3     
==========================================
+ Hits         1081     1084       +3     
  Misses        194      194              

@daico007
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Closing this PR since the issue has been fixed by #335

@daico007 daico007 closed this Jun 12, 2020
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2 participants