mdanalysis
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Hbond update
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?
I expect these changes will spur discussion so I didn't bother with the tests yet.
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.
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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@jaclark5 I've not forgotten about this, it's at the top of my review list over the next few days.
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Thank you @jaclark5 , nice work! 🎉