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Hbond update

Open jaclark5 opened this issue 3 years ago • 3 comments
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Fixes #3847

Changes made in this Pull Request:

  • Added warning when distance or angle cutoffs produce zero hbonds to clarify a returned value of NaN
  • Guess_donor uses bonding information when available since it calls hydrogen types anyway
  • If resnames and names are not available, atom types are used. This is inclusive to LAMMPS users.
  • Change min max constraints to match inclusive language in the documentation.

PR Checklist

  • [x] Tests?
  • [x] Docs?
  • [x] CHANGELOG updated?
  • [X] Issue raised/referenced?

jaclark5 avatar Sep 21 '22 22:09 jaclark5

I expect these changes will spur discussion so I didn't bother with the tests yet.

jaclark5 avatar Sep 21 '22 22:09 jaclark5

It won't break the output. I've been using it with success for quite some time. I actually forgot I made some of these changes but I want to merge them and then stay current with the package.

jaclark5 avatar Sep 22 '22 12:09 jaclark5

Codecov Report

Base: 94.34% // Head: 94.38% // Increases project coverage by +0.03% :tada:

Coverage data is based on head (0a16b13) compared to base (6bc52ec). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #3848      +/-   ##
===========================================
+ Coverage    94.34%   94.38%   +0.03%     
===========================================
  Files          194      194              
  Lines        25226    25242      +16     
  Branches      3402     3406       +4     
===========================================
+ Hits         23800    23825      +25     
+ Misses        1377     1368       -9     
  Partials        49       49              
Impacted Files Coverage Δ
...DAnalysis/analysis/hydrogenbonds/hbond_analysis.py 98.85% <100.00%> (+0.11%) :arrow_up:
package/MDAnalysis/due.py 76.66% <0.00%> (+29.99%) :arrow_up:

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codecov[bot] avatar Sep 22 '22 13:09 codecov[bot]

@jaclark5 I've not forgotten about this, it's at the top of my review list over the next few days.

IAlibay avatar Nov 30 '22 00:11 IAlibay

/azp run

IAlibay avatar Dec 02 '22 23:12 IAlibay

Azure Pipelines successfully started running 1 pipeline(s).

azure-pipelines[bot] avatar Dec 02 '22 23:12 azure-pipelines[bot]

Thank you @jaclark5 , nice work! 🎉

orbeckst avatar Dec 07 '22 16:12 orbeckst