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Move angles to results.angles for dihedral classes#3266

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IAlibay merged 5 commits intoMDAnalysis:developfrom
IAlibay:results-dihedrals
May 6, 2021
Merged

Move angles to results.angles for dihedral classes#3266
IAlibay merged 5 commits intoMDAnalysis:developfrom
IAlibay:results-dihedrals

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@IAlibay
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@IAlibay IAlibay commented May 6, 2021

Towards #3261

Changes made in this Pull Request:

  • Moves angles to results.angles for Dihedral/Ramachandran/Janin classes.

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

@IAlibay IAlibay added this to the 2.0 milestone May 6, 2021
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codecov bot commented May 6, 2021

Codecov Report

Merging #3266 (77570fc) into develop (b6ae72f) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff            @@
##           develop    #3266   +/-   ##
========================================
  Coverage    93.02%   93.03%           
========================================
  Files          172      172           
  Lines        22704    22714   +10     
  Branches      3193     3193           
========================================
+ Hits         21121    21131   +10     
  Misses        1533     1533           
  Partials        50       50           
Impacted Files Coverage Δ
package/MDAnalysis/analysis/dihedrals.py 100.00% <100.00%> (ø)

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minor doc thing — will add it directly & then approve

Comment on lines +195 to 200
.. attribute:: results.angles

Contains the time steps of the :math:`\phi` and :math:`\psi` angles for
each residue as an ``n_frames×n_residues×2`` :class:`numpy.ndarray` with
content ``[[[phi, psi], [residue 2], ...], [time step 2], ...]``.

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add versionadded:: 2.0.0

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There's a versionchanged that mentions it below (mainly bringing this up because I don't think I've been adding versionadded in the previous PRs), but we can start doing this if you want too (it's not exactly a lot of work).

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I know and that's (=changes) good. I find that the versionadded completes the picture. I put it in the general instructions in #3261 . We can update whenever, though.

:inherited-members:

.. attribute:: angles
.. attribute:: results.angles
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add versionadded:: 2.0.0

- versionadded
- small improvements about ref=True (based on user list question)
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pep8speaks commented May 6, 2021

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-05-06 22:38:56 UTC

@IAlibay IAlibay merged commit a43c0a0 into MDAnalysis:develop May 6, 2021
@IAlibay IAlibay deleted the results-dihedrals branch May 6, 2021 23:31
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3 participants