Hotfix: structural analysis

[IAlibay]

Fixes #926

TODO:

• Move structural analysis writing to npz
• Write results accessor
• Tests
• News
• Fix CI

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[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 3 lines in your changes missing coverage. Please review.

Project coverage is 92.84%. Comparing base (117ce98) to head (f4a7930).
Report is 149 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_rfe/equil_rfe_methods.py	57.14%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #937      +/-   ##
==========================================
- Coverage   94.59%   92.84%   -1.75%     
==========================================
  Files         134      134              
  Lines        9931     9934       +3     
==========================================
- Hits         9394     9223     -171     
- Misses        537      711     +174     

Flag	Coverage Δ
fast-tests	92.84% <83.33%> (?)
slow-tests	?

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[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file openfe/tests/protocols/test_openmm_equil_rfe_protocols.py:

Line 2112:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-09-18 02:06:06 UTC

[IAlibay]

@hannahbaumann @dotsdl - I think this should work, fixing the giant JSON results file issue whilst keeping the same things around as before (there's deeper issues with structural analysis correctness, but we'll need to deal with this later).

[hannahbaumann]

Thanks, @IAlibay , just the one comment, other than that it looks good to me!

[dotsdl]

LGTM! Some comments to address, but none major or blocking. Thanks @IAlibay!