Preparation layer
=================

The first layer of the library provides utilities for preparing the simulation
by loading the requisite files, modifying them and outputting results. The layer
is independent of the simulation layers; more appropriate storage formats can
be used in the simulation layer without having to modify any of the files here.

.. toctree::
   :maxdepth: 2
   :caption: Modules

   cmap
   seq
   pdb/index
   model
   param