ENH: add subselection keyword argument to AlignTraj (Issue #5380)

[AkshitBoora]

Fixes #5380

Changes made in this Pull Request:

• Added a subselection keyword argument to AlignTraj.__init__ that accepts
  a selection string or AtomGroup. When provided, only the selected atoms are
  written to the output trajectory, enabling a performance/memory trade-off
  while the superposition/RMSD fit is still computed using the atoms defined by
  select. Raises TypeError for invalid types.
• Added a new guide "Performance and memory trade-offs when aligning
  sub-systems" to the MDAnalysis.analysis.align module docstring,
  demonstrating three usage patterns: fit-only selection, subselection output,
  and in-memory alignment.
• Added 4 unit tests covering string subselection, AtomGroup subselection,
  in-memory subselection, and invalid type handling.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes

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!)
• I have read and understand the current AI Policy
• 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 #34152690 | 📁 Comparing c884ebc against latest (ceb2e3e)

  🔍 Preview build  

4 files changed

± index.html
± documentation_pages/analysis/align.html
± documentation_pages/analysis/wbridge_analysis.html
± _modules/MDAnalysis/analysis/align.html

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.88%. Comparing base (c882e5c) to head (c884ebc).
⚠️ Report is 2 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5464   +/-   ##
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  Coverage    93.87%   93.88%           
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  Files          182      182           
  Lines        22522    22530    +8     
  Branches      3206     3208    +2     
========================================
+ Hits         21143    21152    +9     
+ Misses         917      916    -1     
  Partials       462      462           

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[IAlibay]

@AkshitBoora you declared "yes" to the use of AI generated code. Given that our AI policy does not generally allow for AI generated code, please tell us how AI tools were used in this contribution.

[AkshitBoora]

@AkshitBoora you declared "yes" to the use of AI generated code. Given that our AI policy does not generally allow for AI generated code, please tell us how AI tools were used in this contribution.

Hi @IAlibay, I have used AI for understanding the codebase and the issue. All the code was generated by me. Since I have used AI for understanding the codebase that's why I have declared "Yes".
Sorry for misunderstanding , I will change the usage of AI from "Yes" to "No"