PyJess

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

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 during his PhD in the Thornton group.

PyJess is a Python module that provides bindings to Jess using Cython. 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 Installation page to find other ways to install ``pyjess`.

Library

• Installation
  • PyPi
  • Arch User Repository
  • Piwheels
  • GitHub + pip
  • GitHub + setuptools
• Contributing
  • Coding guidelines
  • Setting up a local repository
  • Running tests
• API Reference
  • Molecule
  • Template
  • Jess
• Changelog
  • Unreleased
  • v0.1.1 - 2024-04-18
  • v0.1.0 - 2024-04-18

License

This library is provided under the MIT License. The JESS code is distributed under the MIT License 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 during his PhD project at the European Molecular Biology Laboratory in the Zeller team.