Add option to control whether water is alchemically changed into counterion for charge changes

[zhang-ivy]

Description

This PR allows the user to disable the introduction of counterion(s) for small molecule and protein mutation transformations.

Motivation and context

Resolves #1004

How has this been tested?

@ijpulidos : Could you make sure that specifying transform_waters_into_ions_for_charge_changes : False in the yaml actually controls the introduction of the counterion? If the changes I made are right, you should see a logger message that says Skipping counterion.

Note that I added a test (for protein mutations, but not small molecules) that checks that this option is working properly. You could adapt this test for a small molecule example, or it might be sufficient to just double check that you see the logger statement when you include the transform_waters_into_ions_for_charge_changes option in the yaml.

Change log

Add option for disabling the introduction of a counterion for charge changing transformations

[zhang-ivy]

Note that this PR should not be merged until #1024 has been merged, as I made some changes to the protein mutation API. Those changes will need to be carefully merged with these ones -- I can take care of that once #1024 is merged.

[codecov]

Codecov Report

Attention: Patch coverage is 91.30435% with 2 lines in your changes missing coverage. Please review.

Project coverage is 52.32%. Comparing base (a2cdad2) to head (fa0111a).
Report is 65 commits behind head on main.

Additional details and impacted files

[ijpulidos]

Looks good, great work. Just a couple of things:

• We need to use the option read from the YAML file.
• Do we want a test that directly computes the charges?

[ijpulidos]

LGTM!

[ijpulidos]

By the way, just confirmed locally that the YAML file option is working correctly.

[ijpulidos]

@zhang-ivy Could you please add what would need to appear in the changelog for these changes? Thanks!

[zhang-ivy]

@ijpulidos : Done!