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


MDEntropy is actively being developed by researchers at Stanford University, with primary
application areas in computational protein dynamics and drug design, and distributed
under the `MIT License <https://tldrlegal.com/l/mit>`_.
All development takes place on `GitHub <https://github.com/msmbuilder/mdentropy>`_.

To cite MDEntropy, please use the following reference:

.. code:: bibtex

  @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}
  }

.. raw:: html

   <div style="display:none">

.. toctree::
   :maxdepth: 2

   installation
   examples/index
   api
   contributing
   publications
   changelog

.. raw:: html

   </div>

.. Indices and tables
.. ==================
..
.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`