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MSMExplorer is a Python package for visualizing data generated from biomolecular dynamics. While molecular visualizations have been a large focus of the molecular dynamics (MD) community (Humphrey, Dalke, and Schulten 1996, Schrödinger, LLC (2015)), data visualizations for the analyses of MD trajectories have been less developed. MSMExplorer seeks to fill this niche by providing publication-quality statistical plots with an easy-to-use Python API that works seamlessly with commonly used Python libraries, such as numpy and scikit-learn (Walt, Colbert, and Varoquaux 2011, Pedregosa et al.(2011)). Additionally, plots are generated using already established plotting libraries, like seaborn, to provide a consistent aesthetic (Waskom et al. 2016, Hunter (2007), Hagberg, Schult, and Swart (2008), Foreman-Mackey (2016)).

Plotting functionality in MSMExplorer is centered around the statistical tools available in msmbuilder (MP Harrigan et al. 2017). Because of this focus, in addition to standard time-series plots, users can choose to plot more involved measures, such as Gibbs free energy and implied timescales estimated from Markov models.