Port test_pqr.py to BaseReaderTest/BaseWriterTest

[virvihuta]

Refs #516

Changes made in this Pull Request:

• ported test_pqr.py to use the new BaseReaderTest/BaseWriterTest classes
• added a small hand written 5-atom test.pqr fixture (COORDINATES_PQR in datafiles.py), since pqr is single-frame and the existing pqr files are way too big for what BaseReference expects
• renamed the old test classes to TestPQRReaderOld/TestPQRWriterOld, kept them intact so the tests still run against the real adk_open.pqr file
• overrode test_get_writer_1/2 and test_no_container in the new classes since PQRWriter doesnt track n_atoms the way BaseWriterTest assumes

LLM / AI generated code disclosure

yes

used claude to explain domain specific naming conventions in the pqr file format (atom naming like N/CA/C/O/CB, residue codes like MET) since Im not coming from a biochem background, help navigating the codebase when I couldnt find something myself and review my code before submitting. All the actual code, the design decisions and the test.pqr file contents are mine.

PR Checklist

• [ x ] Issue raised/referenced?
• [ x ] Tests updated/added?
• Documentation updated/added?
• [ x ] package/CHANGELOG file updated?
• [ x ] Is your name in package/AUTHORS? (If it is not, add it!)
• [ x ] 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 #33814332 | 📁 Comparing 0dcbe2c against latest (83bc9a2)

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2 files changed

± index.html
± documentation_pages/analysis/wbridge_analysis.html

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (83bc9a2) to head (0dcbe2c).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5449   +/-   ##
========================================
  Coverage    93.87%   93.87%           
========================================
  Files          182      182           
  Lines        22510    22510           
  Branches      3202     3202           
========================================
  Hits         21131    21131           
  Misses         917      917           
  Partials       462      462           

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