6. Analysis

New in version 0.8.0.

The mdpow.analysis module contains tools for analyzing whole sets (ensembles) of FEP simulations and a framework to write new analysis tools [Lescoulie2021].

6.1. Analysis tools

MDPOW analysis tools are based on the Ensemble Analysis Framework. They generally take as an input the top level directory of a complete FEP run and then collect individual simulations and run a specific analysis over all FEP simulations. They then make data available (typically, as a pandas.DataFrame).

• 6.1.1. Solvation Shell Analysis
• 6.1.2. Dihedral Analysis

6.2. Ensemble Analysis Framework

The Ensemble Analysis framework [Lescoulie2021] allows for the construction analysis tools that work with whole sets (ensembles) of FEP simulations. They generally follow (and can use) standard MDAnalysis analysis classes.

The Ensemble Objects and Ensemble Analysis base class sections assume a basic understanding of object oriented programming in Python and are for users who wish to construct their own analyses. The code in the Analysis tools serves as example implementations and is described in more detail in [Lescoulie2021].

• 6.2.1. Ensemble Analysis base class
• 6.2.2. Ensemble Objects

6.3. References

[Lescoulie2021]

(1, 2, 3) A. Lescoulie, “SPIDAL Summer REU 2021: Upgrading MDPOW and adding analysis functionality,” Technical Report, Arizona State University, Tempe, AZ, 2021. doi: 10.6084/m9.figshare.17156018