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.
Currently, install this package from source. Clone this repository and change directories into the package. Install a development version:
pip install -e .
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.
numpysvgwrite
The program uses a C extension, and so compilation requires the gcc compiler.
See the Documentation for this package.
To make sure everything is setup correctly you can run a set of Nose tests.
cd latticeproteins/
nosetests