fixed error in verbose mode for missing dihedrals

[chrisiacovella]

PR Summary:

This is relate to a few recent issues posted.

#326
#323

1. There was a coding issue in the part of the code that would write out a missing RB dihedral when in verbose mode (undefined parameters referenced). Also, only ids were being output, not types (inconsistent with, e.g., how angles were outputted). The coding and formatting issues have been addressed.

2. Even when fixing that coding/formatting issues, the code only checked the RB torsions. So, when I was testing periodic torsions, it alerted that all dihedrals were missing. This bit now has two loops, first looping over proper_dihedrals and then rb_torsions in parmed structure.

PR Checklist

---

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

[codecov]

Codecov Report

Merging #335 into master will decrease coverage by 0.22%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##           master     #335      +/-   ##
==========================================
- Coverage   84.78%   84.55%   -0.23%     
==========================================
  Files          14       14              
  Lines        1275     1282       +7     
==========================================
+ Hits         1081     1084       +3     
- Misses        194      198       +4     

[rsdefever]

Hey @umesh-timalsina @justinGilmer looks like we are having some issues with the tests not running here as well.

[umesh-timalsina]

@rsdefever This branch needs a merge with the latest commit added by #334. The required checks have been modified.

[rsdefever]

@rsdefever This branch needs a merge with the latest commit added by #334. The required checks have been modified.

@chrisiacovella FYI

[justinGilmer]

Looking great, thanks @chrisiacovella ! A few questions/statements.

Can you review Ray’s PR #327 and see if there are other features included there that might be useful in verbose mode?

Also, can you merge the latest upstream master changes into this branch so we can check the tests? Some will fail due to #337 not being merged, but that is ok.

Assuming you have the mosdef-hub/foyer remote named origin

git fetch upstream
git merge upstream master
# assuming your remote is named origin
git push origin 

[chrisiacovella]

Totally didn't see Ray's PR when I put this together. I merged in his additions to the error messages. I think we are good to go whenever these checks complete. I'll merge it at that point.

[justinGilmer]

lgtm! @rmatsum836 or @daico007 can one of yall give it a once over? After that, its ready to merge.

[daico007]

LGTM