PyJess |Stars|
==============

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*A Python interface to Jess, a 3D template matching software.*

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Overview
--------

Jess is an algorithm for constraint-based structural template matching
proposed by Jonathan Barker & Janet Thornton. It can be used to identify
catalytic residues from a known template inside a protein structure. Jess
is an evolution of TESS, a geometric hashing algorithm developed by
Andrew Wallace *et al.*, removing some pre-computation and 
structural requirements from the original algorithm. Jess was further 
updated and maintained by `Ioannis Riziotis <https://github.com/iriziotis>`_
during his PhD in the `Thornton group <https://www.ebi.ac.uk/research/thornton/>`_.

PyJess is a Python module that provides bindings to Jess using
`Cython <https://cython.org/>`_. It allows creating templates, querying them
with protein structures, and retrieving the hits using a Python API without
performing any external I/O.

PyJess is available for all modern Python versions (3.6+).


Setup
-----

Run ``pip install pyjess`` in a shell to download the latest release from PyPI,
or have a look at the :doc:`Installation page <install>` to find other ways 
to install ``pyjess`.


Library
-------

.. toctree::
   :maxdepth: 2

   Installation <install>
   Contributing <contributing>
   API Reference <api/index>
   Changelog <changes>


License
-------

This library is provided under the `MIT License <https://choosealicense.com/licenses/mit/>`_.
The JESS code is distributed under the 
`MIT License <https://choosealicense.com/licenses/mit/>`_ as well.

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original JESS authors. It was developed
by* `Martin Larralde <https://github.com/althonos/>`_ *during his PhD project
at the* `European Molecular Biology Laboratory <https://www.embl.de/>`_ *in
the* `Zeller team <https://github.com/zellerlab>`_.