Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Open
wants to merge 16 commits into
base: main
Choose a base branch
from

Conversation

bc118
Copy link

@bc118 bc118 commented Jun 29, 2021

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.
@lgtm-com
Copy link
Contributor

lgtm-com bot commented Jun 29, 2021

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
Copy link

codecov bot commented Jun 29, 2021

Codecov Report

Merging #436 (a28f785) into master (78dbdaf) will increase coverage by 1.57%.
The diff coverage is 96.40%.

@@            Coverage Diff             @@
##           master     #436      +/-   ##
==========================================
+ Coverage   73.88%   75.46%   +1.57%     
==========================================
  Files          17       18       +1     
  Lines        1842     1981     +139     
==========================================
+ Hits         1361     1495     +134     
- Misses        481      486       +5     

@lgtm-com
Copy link
Contributor

lgtm-com bot commented Jun 29, 2021

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
Copy link
Contributor

lgtm-com bot commented Jun 29, 2021

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants