MDEntropy: Information-Theoretic Analyses for Molecular Dynamics

Abstract

MDEntropy is a Python package for information-theoretic (IT) analysis of data generated from molecular dynamics simulations. While correlation studies have long been of interest to the molecular dynamics (MD) community (McCammon, Gelin, and Karplus 1977, McClendon et al. (2009)), IT tools to analyze MD trajectories have been much less developed. MDEntropy seeks to fill this niche by providing an easy-to-use Python API that works seamlessly with other Python packages, such as mdtraj, msmbuilder, and numpy (R. T. McGibbon et al. 2015, Walt, Colbert, and Varoquaux (2011), M. P. Harrigan et al. (2017)).