.. SM_ConfGen 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
   contain the root `toctree` directive.

Welcome to Small Molecule Conformer Generation's documentation!
=========================================================
``SM_ConfGen`` is a Python package providing a method of generating ligand 
conformers from Temperature Replic Exchange Molecular Dynamics (TREMD) 
simulations in GROMACS.

.. toctree::
   getting_started
   :maxdepth: 2
   :caption: Getting started:

.. toctree::
   theory
   :maxdepth: 2
   :caption: Theory:

.. toctree::
   simulations
   :maxdepth: 2
   :caption: Launching SM_ConfGen simulations:



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

* :ref:`genindex`