mepster / latticeproteins

2d protein lattice model simulator in Python

Latticeproteins

latticeproteins is a 2d protein lattice simulator. It enumerates all possible conformations for an L-length chain of amino acids on a two-dimensional grid (no crossing). Many thermodynamic properties can be calculated from energy landscape constructed from the full ensemble of conformations.

Install

Currently, install this package from source. Clone this repository and change directories into the package. Install a development version:

pip install -e .

Credit

This is a fork of the latticeprotein simulator written by Jesse Bloom. There are some pretty significant differences between the two packages. Mainly, I've added Numpy as a key dependency of this module to speed up computation and improve memory efficiency. All credit goes to Jesse for the original implementation, so please cite Jesse's papers if you use this software:

• Protein stability promotes evolvability
• Stability and the evolvability of function in a model protein

This maintains the GNU Public License of the original package.

Dependencies

• numpy
• svgwrite

The program uses a C extension, and so compilation requires the gcc compiler.

Documentation

See the Documentation for this package.

Testing

To make sure everything is setup correctly you can run a set of Nose tests.

cd latticeproteins/
nosetests