Fix typo in test_resume.py

[zhang-ivy]

Description

Fixes typo that causes the test to be run in solvent instead of vacuum.

Motivation and context

Resolves #990

How has this been tested?

Change log

[ijpulidos]

I see that the tests are failing because it detects a charge difference and tries to use the get_water_indices from the PointMutationEngine here. I guess we shouldn't be changing from ALA to ASP if we don't want to deal with charges differences. Maybe changing to other similar residues with hydrophobic side chains should be enough (i.e. VAL), especially if all we are testing here is that the simulation can be resumed. Thoughts?

[zhang-ivy]

I think we want to make sure that the counterion isn't introduced for charge changing transformations in vacuum. I'll fix this.

[codecov]

Codecov Report

Merging #991 (41f11d8) into main (c9fa0c6) will increase coverage by 0.00%.
The diff coverage is 83.33%.

[mikemhenry]

I think we want to make sure that the counterion isn't introduced for charge changing transformations in vacuum. I'll fix this.

Yes that is a good point and something I didn't consider in the OG PR.

[mikemhenry]

@zhang-ivy I hate to open this can of worms on this PR, but do we need to make the same change for small molecules as well? I know @dominicrufa recently refactored this a bit and I'm not sure if he thought of that either.

[zhang-ivy]

@mikemhenry : Nope, I double checked and the counterion behavior is correct for small molecules!

[jchodera]

Thanks!

[ijpulidos]

Looks good to me! LGTM.

[zhang-ivy]

Ah, I need to update the PointMutationExecutor to not introduce a counterion if phase=vacuum was specified. We should keep the test as is. On May 3, 2022, at 19:49, Iván Pulido ***@***.***> wrote:  I see that the tests are failing because it detects a charge difference and tries to use the get_water_indices from the PointMutationEngine here<https://github.com/choderalab/perses/blob/main/perses/app/relative_point_mutation_setup.py#L368>. I guess we shouldn't be changing from ALA to ASP if we don't want to deal with charges differences. Maybe changing to other similar residues with hydrophobic side chains should be enough (i.e. VAL), especially if all we are testing here is that the simulation can be resumed. Thoughts? — Reply to this email directly, view it on GitHub<#991 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIPGJCRTK3XJJUUGPWYAEUTVIG3QVANCNFSM5VAKBJOQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>