MDEntropy is a python library that allows users to perform information-theoretic analyses on molecular dynamics (MD) trajectories. It includes methods to calculate:
- Bias-Corrected Entropy
- Conditional Entropy
- Mutual Information
- Normalized Mutual Information
- Conditional Mutual Information
- Normalized Conditional Mutual Information
Full documentation can be found at http://msmbuilder.org/mdentropy/. For information about installation, please refer to our Installation page.
We also have example notebooks with common use cases for MDEntropy. Please feel free to add your own as a pull-request!
python
>=3.4numpy
>=1.10.4scipy
>=0.17.0scikit-learn
>=0.17.0msmbuilder
>=3.5.0nose
(optional, for testing)
Please cite:
@misc{mdentropy,
author = {Carlos X. Hern{\'{a}}ndez and Vijay S. Pande},
title = {msmbuilder/mdentropy: v0.3},
month = oct,
year = 2017,
doi = {10.5281/zenodo.1000997},
url = {https://doi.org/10.5281/zenodo.1000997}
}