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Update polymer.py to add clarity to the docs for persistent length #4901

Merged
merged 4 commits into from
Feb 7, 2025
Merged

Update polymer.py to add clarity to the docs for persistent length #4901

merged 4 commits into from
Feb 7, 2025

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tanishy7777
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@tanishy7777 tanishy7777 commented Feb 1, 2025 •
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Fixes #4900

Changes made in this Pull Request:
Adds

.. math::

   C(n) = \langle \cos\theta_{i, i+n} \rangle =
           \langle \mathbf{a_i} \cdot \mathbf{a_{i+n}} \rangle
           
where :math:`\mathbf{a}_i \text{ and } \mathbf{a}_{i+n}` are unit vectors
along the bonds. (Because for two vectors a and b, 
:math:`\mathbf{a} \cdot \mathbf{b} = |\mathbf{a}| |\mathbf{b}| \cos{\alpha}`)
– see 
`Wikipedia <https://en.wikipedia.org/wiki/Dot_product#Geometric_definition>`_.

PR Checklist

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

Developers certificate of origin

📚 Documentation preview 📚: https://mdanalysis--4901.org.readthedocs.build/en/4901/

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codecov bot commented Feb 1, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.63%. Comparing base (f260c4a) to head (6fda256).
Report is 6 commits behind head on develop.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #4901      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21795    22861    +1066     
  Branches      3067     3067              
===========================================
+ Hits         20413    21406     +993     
- Misses         931     1004      +73     
  Partials       451      451

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RMeli
RMeli requested changes Feb 2, 2025
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Can you please merge develop into your branch, to make the linter check happy again (hopefully)?

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tanishy7777 commented Feb 4, 2025 •
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Can you please merge develop into your branch, to make the linter check happy again (hopefully)?

I tried merging develop but it was showing Already up to date. So I ran black and flake8 on package and testsuite. I think it's fixed now.

darker -r upstream/develop package/MDAnalysis -L flake8
darker -r upstream/develop testsuite/MDAnalysisTests -L flake8

orbeckst
orbeckst requested changes Feb 5, 2025
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Thanks for fixing the docs. Please see comment inline.

package/MDAnalysis/analysis/polymer.py Outdated
Comment on lines 128 to 130
along the bonds. (Because for two vectors :math:`\mathbf{a}` and :math:`\mathbf{b}`,
:math:`\mathbf{a} \cdot \mathbf{b} = |\mathbf{a}| |\mathbf{b}| \cos{\alpha}`,
where :math:`\alpha` is the angle between the two vectors.)
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We don't need the wikipedia link in the docs – I know that I had that in our discussion on discord but it's really elementary. Just remove the sentence with (Because ... .).

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@tanishy7777 tanishy7777 Feb 7, 2025 •
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We don't need the wikipedia link in the docs – I know that I had that in our discussion on discord but it's really elementary. Just remove the sentence with (Because ... .).

yeah it felt basic but I though I would add it for the sake of completeness, but yeah its probably not needed.

@orbeckst orbeckst enabled auto-merge (squash) February 7, 2025 16:47
orbeckst
orbeckst approved these changes Feb 7, 2025
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Looks good to me. Thank you!

@RMeli I enabled auto-merge.

@orbeckst orbeckst merged commit 084b8cc into MDAnalysis:develop Feb 7, 2025
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amruthesht pushed a commit to amruthesht/mdanalysis that referenced this pull request Feb 19, 2025
@tanishy7777 @RMeli @amruthesht
Update polymer.py to add clarity to the docs for persistent length (M…
e666f8b 
…DAnalysis#4901)

* Fixes MDAnalysis#4900
* Update doc string in polymer.py: make clear that we are using unit vectors along bonds

---------

Co-authored-by: Rocco Meli <[email protected]>
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@orbeckst orbeckst orbeckst approved these changes

@RMeli RMeli RMeli approved these changes

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Make the docs for Persistent length more clear
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@tanishy7777 @orbeckst @RMeli