.. protex documentation master file, created by
   sphinx-quickstart on Thu Mar 15 13:55:56 2018.
   You can adapt this file completely to your liking, but it should at least
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Welcome to protex's documentation!
=========================================================
.. image:: ./assets/images/protex_logo.gif
   :class: logo-gif

**Protex** is an lightweight object-oriented python
extension to easily enable bond breaking and formation in molecular
dynamics simulations.
It uses the fast and lightweight `OpenMM <https://openmm.org>`_ package for the underlying molecular dynamics simulations.


.. toctree::
   :maxdepth: 2
   :caption: Contents:

   ./documentation_pages/getting_started
   ./documentation_pages/quickstart
   ./documentation_pages/detailed_example
   ./documentation_pages/use_cases
   ./documentation_pages/api



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`