add plots to show the change in maxContrib state

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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add plots to show the change in maxContrib state #96

Closed eruijsena closed 1 year ago

eruijsena commented 1 year ago

Calculate and plot the number of times a trajectory switches its maximally contributing state to another. The calculation is based on the GROMOS-format repdat.

The plots are generated with plotly, thereby adding a new dependency to REEDS.

These analysis functions are not yet added anywhere in the pipeline.

eruijsena commented 1 year ago

The functions are now updated to use the ExpandedRepdat recently introduced in pygromos. (It is instantiated from a Repdat object: exp_repdat = ExpandedRepdat(repdat))