Simplify analysis coordinate generation - Githubissues

rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

https://rinikerlab.github.io/reeds/

MIT License

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Simplify analysis coordinate generation #86

Closed candidechamp closed 2 years ago

candidechamp commented 2 years ago

Description

This PR was made to simplify the code deciding which coordinates would be passed for the next simulations (placed in analysis/next in the RE_EDS_general_analysis.py).

A new input variable was given to the input_dict to allow to select for either SSM or final conformations to be given.

Many functions in the file management module were removed to avoid any confusion.

Todos

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

[x] Test analysis of lower bound search.
[x] Test analysis of energy offset estimation (with/out asking for SSM).
[x] Test analysis of optimization with LRTO
[x] Test analysis of optimization (with/out asking for SSM) with GRTO

Notes:

LRTO will not work with the SSM next coordinates (I think this is ok as sending the SSM coordinates between optimization steps is probably something we will want to remove entirely at one point anyways, I just need to test it thoroughly.)

GRTO can in principle be used by also adding replicas at the same time, and the code will not handle this specific case at the moment.

Status

[ ] Ready to go

lgtm-com[bot] commented 2 years ago

This pull request introduces 2 alerts when merging cb15575b634d9f3da4a6378e6d13691089994bea into 1dcb3676d4689e35cb6172e14820246f173d9fef - view on LGTM.com

new alerts:

1 for Unused local variable
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lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert when merging 9b722f3503eda1dcc5b23df5301ab900620af783 into 1dcb3676d4689e35cb6172e14820246f173d9fef - view on LGTM.com

new alerts:

1 for Unused import

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lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert when merging a8243444d2f57877a370083b523011dc07510e44 into 1dcb3676d4689e35cb6172e14820246f173d9fef - view on LGTM.com

new alerts:

1 for Unused import

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lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert when merging be993ae6783addcf4cfe65cbe81ec88545fa0e0e into 1dcb3676d4689e35cb6172e14820246f173d9fef - view on LGTM.com

new alerts:

1 for Unused import

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lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert when merging a78f34c858aefd3bd619abf808793e540d4e1857 into 1dcb3676d4689e35cb6172e14820246f173d9fef - view on LGTM.com

new alerts:

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lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert when merging a465c21a1a56165f84dfdde97dd0d8daa53f6769 into 5316007fef5bffe49c384e5c7d67c0dfa3c44e45 - view on LGTM.com

new alerts:

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epbarros commented 2 years ago

I tested the s-optimization on my water replacement system and it worked without a problem. Ok to merge