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choderalab / perses

Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
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Store initial and final topologies for all phases -- small molecule pipeline #1210

Closed ijpulidos closed 11 months ago

ijpulidos commented 1 year ago

Description

These changes make serialization of initial (old) and final (new) topologies for complex and solvent phases for the small molecule pipeline, adding the RelativeFEPSetup._serialize_topologies method which is called at the end of the constructor.

Note that while these changes do NOT break the API, it is a change in the behavior since now the stored objects are different.

Motivation and context

For extracting trajectories for debugging or visualization purposes, it is important to have the topologies available in PDB for the different phases and the initial and final states of the transformation.

Resolves #1154

How has this been tested?

Test written, need to check locally that the files make sense.

Change log

Storage of topologies for initial and final states of the transformation, for all phases of the simulation. Useful for extracting trajectories.
ijpulidos commented 1 year ago

Tested locally and visualizing the different generated PDB files for an example seem to work as expected.

codecov[bot] commented 11 months ago

Codecov Report

Merging #1210 (499b39e) into 0.10.x (4834ff7) will increase coverage by 0.07%. The diff coverage is 100.00%.

zhang-ivy commented 11 months ago

Left some comments, but otherwise looks good!