ModPipe
=======

ModPipe is a completely automated software pipeline that can calculate 
protein structure models for a large number of sequences with almost no
manual intervention. In the simplest case, it takes as input a sequence
identifier and a configuration file and produces one or more comparative 
models for that sequence.

.. toctree::
   :maxdepth: 2

   intro
   running
   configurationfile
   fold-assignments
   cmdline
   developing
   using-lib

Reference:

.. toctree::
   :maxdepth: 1

   modules/index

Appendices:

.. toctree::
   :maxdepth: 2

   file-formats
   modweb
   modbase-import
   install-ext
   databases
   copying
   changes

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

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