.. AMPAL documentation master file, created by
   sphinx-quickstart on Fri Apr 13 11:42:52 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

AMPAL Documentation
===================

Welcome to the documentation for the AMPAL module. AMPAL stands for Atom,
Monomer, Polymer, Assembly and Ligand and is a simple, intuitive and
Pythonic framework for representing biomolecular structure.


.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   Installation <installation>
   Introduction to AMPAL <AMPAL_Introduction_and_Selections>
   Advanced Selections <Advanced_Selections_and_Analysis>
   API Reference <modules>



Indices and Search
==================

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