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

[IAlibay]

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Fixes #585

In this PR:

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

Developers certificate of origin

• [x] 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 690:1: 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 112:80: E501 line too long (80 > 79 characters) Line 141:80: 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 2024-08-27 13:21:57 UTC

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.57%. Comparing base (80d2a74) to head (a9d8fb5). Report is 130 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #673   +/-   ##
=======================================
  Coverage   92.57%   92.57%           
=======================================
  Files         134      134           
  Lines        9916     9917    +1     
=======================================
+ Hits         9180     9181    +1     
  Misses        736      736           

Flag	Coverage Δ
fast-tests	92.57% <100.00%> (+<0.01%)	:arrow_up:

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[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

[IAlibay]

This is low priority, but it would be amazing if we could get it merged sooner than later.

[IAlibay]

This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box?

I don't think it's a dumb question.

Looks like.. you can't? http://docs.openmm.org/development/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.addSolvent 🙈

I suspect the answer for setting a given density would be to do it manually, selecting a given box size / vectors and then setting the number of waters added manually?

[IAlibay]

This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box?

I don't think it's a dumb question.

Looks like.. you can't? http://docs.openmm.org/development/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.addSolvent 🙈

I suspect the answer for setting a given density would be to do it manually, selecting a given box size / vectors and then setting the number of waters added manually?

No... that doesn't work because it's not allowed. Good question indeed.

[IAlibay]

@hannahbaumann if you have time could you have another look at this? I'd like to get to a point where we can merge this but I definitely want your stamp of approval before we do!

[IAlibay]

This could use a changelog entry, otherwise it is good to go!

Good call, done!