Move structural analysis methods to child classes in SepTop Protocol

[IAlibay]

Fixes #2041

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[hannahbaumann]

pre-commit.ci autofix

[IAlibay]

I wouldn't include a news item for this - it's an internal re-arrangement for somewhat private unit methods. Putting it in the human-readable changelog is probably more likely to confuse users than anything else.

[hannahbaumann]

Ok, I removed it!

[codecov]

Codecov Report

❌ Patch coverage is 98.27586% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 90.58%. Comparing base (d8a6d37) to head (a0739d6).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_septop/base_units.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2049      +/-   ##
==========================================
- Coverage   95.19%   90.58%   -4.62%     
==========================================
  Files         213      213              
  Lines       21104    21138      +34     
==========================================
- Hits        20091    19147     -944     
- Misses       1013     1991     +978     

Flag	Coverage Δ
fast-tests	90.58% <98.27%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅

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Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main

$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main