mdentropy
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Analyze correlated motions in MD trajectories with only a few lines of Python.
MDEntropy
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
Documentation
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!
Requirements
-
python
>=3.4 -
numpy
>=1.10.4 -
scipy
>=0.17.0 -
scikit-learn
>=0.17.0 -
msmbuilder
>=3.5.0 -
nose
(optional, for testing)
Citing
Please cite:
@article{mdentropy,
author = {Carlos X. Hern{\'{a}}ndez and Vijay S. Pande},
title = {{MDEntropy: Information-Theoretic Analyses for Molecular Dynamics}},
month = nov,
year = 2017,
doi = {10.21105/joss.00427},
url = {https://doi.org/10.21105/joss.00427}
}