Add keywords to filter residues in Janin analysis #2899
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- fix #2898 - filter CYSH (actually, CYS*) - updated documentation with Henry Mull's Technical Report - added Ramachandran reference - plots have degree symbol on ticks - updated example plots and made sure that they show what's stated in the caption - test added - update CHANGELOG
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Looks good, thank you @orbeckst; just a missing '>' in a reference means that the docs don't build.
If you wanted to be ultimately flexible and accommodate ncAAs etc, you could pass in keywords instead of hardcoding, e.g. Janin.__init__(u, select_protein="protein", select_remove="resname ALA CYS* GLY PRO SER THR VAL") but that's up to you.
FIX: Janin analysis now correctly only selects from the provided input atomgroup Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>
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@lilyminium can I please leave it to you to handle the PR? Ping me if I need to do anything else. Thanks! |
Codecov Report
@@ Coverage Diff @@
## develop #2899 +/- ##
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- Coverage 92.89% 92.85% -0.04%
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Files 187 187
Lines 24587 24593 +6
Branches 3192 3186 -6
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- Hits 22840 22837 -3
- Misses 1701 1710 +9
Partials 46 46
Continue to review full report at Codecov.
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Looks good, thank you -- I'll merge now :-) |
Fixes MDAnalysis#2898 - add select_protein and select_remove keywords to Janin analysis - filter CYS* by default - updated docs and plots - made plots prettier (degree symbol on ticks)
Fixes #2898
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