Use Interchange for some OpenMM object creation

[mattwthompson]

Do not merge

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[pep8speaks]

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

• In the file openfe/protocols/openmm_afe/base.py:

Line 480:17: E225 missing whitespace around operator
Line 481:21: E251 unexpected spaces around keyword / parameter equals
Line 481:23: E251 unexpected spaces around keyword / parameter equals
Line 502:80: E501 line too long (82 > 79 characters)
Line 505:80: E501 line too long (91 > 79 characters)
Line 507:80: E501 line too long (82 > 79 characters)
Line 513:80: E501 line too long (85 > 79 characters)
Line 516:80: E501 line too long (133 > 79 characters)
Line 523:80: E501 line too long (84 > 79 characters)
Line 524:80: E501 line too long (95 > 79 characters)
Line 574:80: E501 line too long (116 > 79 characters)
Line 584:11: E111 indentation is not a multiple of four
Line 588:11: E111 indentation is not a multiple of four
Line 597:11: E111 indentation is not a multiple of four

Comment last updated at 2024-02-21 15:08:10 UTC

[IAlibay]

I was under the impressions that this was going into https://github.com/OpenFreeEnergy/openfe_skunkworks so maybe this isn't meant to aim towards a merge.

Just leaving the one comment in case stuff progresses whilst I'm out - mostly a style thing about moving selection logic to a separate class method to keep run pretty much just something where you can subclass and swap out methods.

[IAlibay]

(just in case this moves towards merge in the next couple of weeks): it may be better if this logic went into the getter than in the run of base - the idea here is that run should be kept pretty lean so it's easy to swap out class methods.

See https://github.com/OpenFreeEnergy/openfe/blob/ahfe-packmol/openfe/protocols/openmm_afe/base.py#L433 for example.

[mattwthompson]

I see the benefit of that design; it didn't come about naturally since the Interchange code path does not always need to call _get_system_generator

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (3cb55a2) 93.59% compared to head (bd41cc8) 90.78%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #703      +/-   ##
==========================================
- Coverage   93.59%   90.78%   -2.81%     
==========================================
  Files         133      133              
  Lines        9694     9713      +19     
==========================================
- Hits         9073     8818     -255     
- Misses        621      895     +274     

Flag	Coverage Δ
fast-tests	90.78% <100.00%> (?)
slow-tests	?

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