[WIP] Net charge support in ABFEs

[IAlibay]

Fixes: #1662

Checklist

• Added a news entry

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

[codecov]

Codecov Report

❌ Patch coverage is 75.36232% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.80%. Comparing base (80cbc22) to head (cef9cb7).

Files with missing lines	Patch %	Lines
...e/protocols/openmm_afe/equil_binding_afe_method.py	60.00%	16 Missing ⚠️
openfe/protocols/openmm_afe/base.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1614      +/-   ##
==========================================
- Coverage   95.32%   92.80%   -2.52%     
==========================================
  Files         183      183              
  Lines       15765    15803      +38     
==========================================
- Hits        15028    14666     -362     
- Misses        737     1137     +400     

Flag	Coverage Δ
fast-tests	92.80% <75.36%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅

[christopherkottke]

I am very interested in this feature, and I appreciate the hard work that is being done on this package in general. Is the code here ready for testing / do you have a timeline for when it might be released?

[IAlibay]

Hi @christopherkottke,

It's been a while since I had a chance to work on this, looking at the tests it seems like there were a few things that needed fixing - probably not an overwhelming amount for a first draft.

I'll bring this up for discussion internally - one of the biggest blockers we had with this was that we just didn't have enough compute to run tests / benchmark. Is this something you might be interested in helping out with?

[christopherkottke]

Hi @IAlibay,

We could be interested in running tests / benchmarking, but we would want to know what these tests/benchmarks would look like and how computationally expensive you expect them to be.