MSMExplorer: Data Visualizations for Biomolecular Dynamics

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)).

[1]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[2]  Mohammad M. Sultan,et al.  MSMBuilder: Statistical Models for Biomolecular Dynamics , 2016, bioRxiv.

[3]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[4]  Daniel Foreman-Mackey,et al.  corner.py: Scatterplot matrices in Python , 2016, J. Open Source Softw..

[5]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[6]  Aric Hagberg,et al.  Exploring Network Structure, Dynamics, and Function using NetworkX , 2008, Proceedings of the Python in Science Conference.

[7]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[8]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .