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wiederm / endstate_correction

Endstate corrections from MM to QML potential
https://wiederm.github.io/endstate_correction/
MIT License
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Refractor the set up to allow potentially using amber as input and allow interface with BSS eaiser #53

Closed xiki-tempula closed 1 year ago

xiki-tempula commented 1 year ago

Description

@wiederm So I was thinking of adding a high-level interface to allow endstate_correction to be called by BioSimSpace in an easy fashion. This is to show how I think an interface can be. I have refactored the script/sampling.py and add an interface for amber.

Todos

Notable points that this PR has either accomplished or will accomplish.

Status

codecov-commenter commented 1 year ago

Codecov Report

Merging #53 (a365f51) into main (dc350fd) will increase coverage by 2.80%. The diff coverage is 80.00%.

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Additional details and impacted files
xiki-tempula commented 1 year ago

@wiederm Many thanks for the comments. I have changed some comments but I think some need discussion. Currently, you suggest that we hardcode it to take one sample every 1000 steps. Would it be better if we make this not hardcoded? I wonder what information do we want to extract from the trajectory name file? I think some of the information in the trajectory name might not really be necessary.

wiederm commented 1 year ago

Sorry @xiki-tempula , I didn't see your code changes! I resolved the merge conflicts --- but please review and see if these changes suite you!

wiederm commented 1 year ago

The code is now in a state that is ready for merge IMHO. If no more changes are required, I will wait for the review of @saratk1 and, if it also looks good to her, move ahead and merge.

xiki-tempula commented 1 year ago

@wiederm Many thanks for the comments. Would you mind using the review function to add comments? I felt it might facilitate the discussion before we commit to certain changes.

xiki-tempula commented 1 year ago

@wiederm Do you mind merge this one? I have changed the reporter and file name to dcd in this PR for the sake of clarity and not to bloats the PR too much as it is already quite big. I will change the reporter to hdf5 in the next PR.