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Adds checking if the RB_to_OPLS dihedral conversion is exact when the standard OPLS format does not have a constant (i.e., f0/2) - #436

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bc118:RB_to_OPLS_xml_checks
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Adds checking if the RB_to_OPLS dihedral conversion is exact when the standard OPLS format does not have a constant (i.e., f0/2)#436
bc118 wants to merge 16 commits into
mosdef-hub:mainfrom
bc118:RB_to_OPLS_xml_checks

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@bc118

@bc118 bc118 commented Jun 29, 2021

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This adds checking if the RB_to_OPLS dihedral conversion is exact when the standard OPLS format does not have a constant (i.e., f0/2). If the RB is not directly convertible to the standard OPLS, then it prints a list. Then, it compares to the printed list with a user input list of known dihedrals that are not analytically perfect, and if it is not in the list, it throws an error. This will also help catch other random user-entered errors for the dihedrals in the MoSDeF standard FF XMLs.

NOTE:
We need to replace the manually input RB_to_OPLS conversion in the check_xml_dihedrals_RB_to_OPLS.py file with the mBuild version, once foyer updates to this new mBuild.

Let me know everyone's thoughts.

PR Checklist


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

bc118 and others added 2 commits June 29, 2021 15:37
…n the standard OPLS format does not have a constant (i.e., f0/2). If the RB is not directly convertible to the standard OPLS, then it prints a list. Then, it compares to the printed list with a user input list of known dihedrals that are not analytically perfect, and if it is not in the list, it throws an error. This will also help catch other random user-entered errors for the dihedrals in the MoSDeF standard FF XMLs.
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lgtm-com Bot commented Jun 29, 2021

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This pull request introduces 2 alerts when merging f72d4d5 into 3b91082 - view on LGTM.com

new alerts:

  • 1 for Unused local variable
  • 1 for Unused import

@codecov

codecov Bot commented Jun 29, 2021

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Codecov Report

❌ Patch coverage is 96.40288% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.46%. Comparing base (78dbdaf) to head (a28f785).
⚠️ Report is 321 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #436      +/-   ##
==========================================
+ Coverage   73.88%   75.46%   +1.57%     
==========================================
  Files          17       18       +1     
  Lines        1842     1981     +139     
==========================================
+ Hits         1361     1495     +134     
- Misses        481      486       +5     
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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lgtm-com Bot commented Jun 29, 2021

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This pull request introduces 2 alerts when merging 3902bb6 into 3b91082 - view on LGTM.com

new alerts:

  • 1 for Unused local variable
  • 1 for Unused import

@lgtm-com

lgtm-com Bot commented Jun 29, 2021

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This pull request introduces 2 alerts when merging f56a3a0 into fc44f80 - view on LGTM.com

new alerts:

  • 1 for Unused local variable
  • 1 for Unused import

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2 participants