OpenMMSolvation: Support for non-cubic boxes and defined box properties

[IAlibay]

Fixes #585

In this PR:

• Allows for defining the additional openmm keywords to addSolvent
• New OpenMM solvation settings + docstring

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/.

[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/protocols/openmm_afe/equil_solvation_afe_method.py:

Line 669:1: W293 blank line contains whitespace

• In the file openfe/protocols/openmm_utils/omm_settings.py:

Line 15:80: E501 line too long (83 > 79 characters)
Line 115:80: E501 line too long (80 > 79 characters)
Line 144:80: E501 line too long (139 > 79 characters)

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

Line 90:42: E225 missing whitespace around operator

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

Line 453:9: E128 continuation line under-indented for visual indent
Line 473:34: E251 unexpected spaces around keyword / parameter equals
Line 473:36: E251 unexpected spaces around keyword / parameter equals

Comment last updated at 2024-03-11 14:52:46 UTC

[IAlibay]

These solvation settings need OpenMM 8.0. Overall supporting multiple major versions of OpenMM is probably unwise as we'll need to test them all so I would suggest bumping up the minimum version?

Otherwise we can add a version check to the validator.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.92%. Comparing base (fd91902) to head (1cc7652).
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #673      +/-   ##
==========================================
+ Coverage   91.76%   91.92%   +0.15%     
==========================================
  Files         133      133              
  Lines        9748     9890     +142     
==========================================
+ Hits         8945     9091     +146     
+ Misses        803      799       -4     

Flag	Coverage Δ
fast-tests	91.92% <100.00%> (+0.15%)	⬆️

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[IAlibay]

This inherits the name from OpenMM, it's not amazingly named.

I.e. if you know what it is in OpenMM this makes sense, but if you don't then it may not...

[IAlibay]

I've handed this over to @hannahbaumann to drive forward whilst I'm OOO in case folks feel like pushing this for 1.0.

[mattwthompson]

@hannahbaumann Josh Mitchell (@Yoshanuikabundi) wrote openff.interchange.components._packmol but I'm the point person in case you run into issues, or have any questions about why something is the way it is in OpenFF's infrastructure