Fix: Incorrect capped_distance in some triclinic box situations

[BradyAJohnston]

Fixes #4906

In triclinic boxes where both b_x and c_y are non-zero (e.g. truncated octahedra), the nsgrid and pkdtree methods of capped_distance / self_capped_distance miss pairs within the cutoff. This affects bond guessing, selections, etc. Reproduced with the issue's struc.txt and the truncated-octahedron script; both now match bruteforce.

Changes made in this Pull Request:

• _triclinic_pbc: fix the a-axis wrapping bound, which could leave coordinates just outside the primary image (affects apply_PBC, pkdtree and nsgrid)
• FastNS.coord2cellxyz: fix the same missing term in the x cell index (as suspected here)
• FastNS._prepare_box: size grid cells from the box's perpendicular widths, so cells are never thinner than the cutoff
• Add regression tests for apply_PBC, capped_distance, self_capped_distance and FastNS in skewed boxes

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

I did use Claude to scan through and track down the issue, but I wrote the code and the tests.

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)
• LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

[read-the-docs-community]

Documentation build overview

📚 MDAnalysis | 🛠️ Build #35038979 | 📁 Comparing a3e37a8 against latest (6ae1589)

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1 file changed

± documentation_pages/analysis/wbridge_analysis.html

[BradyAJohnston]

Seems one of the old snapshots is failing but I'm pretty sure they are just incorrectly snapshotted values, looking into it

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (6ae1589) to head (a3e37a8).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5481   +/-   ##
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  Coverage    93.87%   93.87%           
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  Files          184      184           
  Lines        22645    22645           
  Branches      3220     3220           
========================================
  Hits         21257    21257           
  Misses         923      923           
  Partials       465      465           

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[IAlibay]

This looks great, unfortunately I won't have time to review. I'm going to un-request my review here and pick on someone else ;)