`MDPath <https://github.com/NDoering99/mdpath>`_ documentation
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**MDPath** is a Python package designed to calculate and visualize allosteric communication pathways in proteins using molecular dynamics (MD) simulations. It employs mutual information calculations to identify connected residues and graph-building techniques to map out pathways between them. This documentation will guide you through the installation, usage, and functionalities of MDPath, providing detailed instructions and examples to help you explore protein dynamics and interactions effectively.

.. toctree::
   :maxdepth: 1
   :caption: User Guide

   installation
   faq

.. toctree::
   :maxdepth: 1
   :caption: MDPath
   
   running_mdpath
   mdpath_outputs
   running_mdpath_tools
   mdpath_visualization

.. toctree::
   :maxdepth: 1
   :caption: API Docs

   mdpath_api

.. toctree::
   :maxdepth: 1
   :caption: Contributing to MDPath

   developer_guide