LatticeGPM

LatticeGPM is a python package for building complete binary sequence spaces from protein lattice models. Lattice models provide a nice way to simulate the relationships between sequence, conformation, and function. Sequence Space provides a metaphor for thinking about evolution of sequence and function through this space. All lattice model calculations are done using Dr. Jesse Bloom's latticeproteins package here.

Dependencies

The main dependency for this repository is the seqspace module found here.

To run the notebooks, IPython and Jupyter notebooks must be installed.

Also, for constructing notebooks, NetworkX must be properly installed.

Examples/Tutorials.

Check out the tutorials here.

Installation

Git must be installed to clone and contribute to this project

Setting up for use.

• Clone this repo locally:

git clone https://github.com/<user-name>/latticegpm

• Navigate to this directory, and install this python package with

python setup.py develop

Setting up for development.

• Fork this repository on Github
• Clone that repository locally

    git clone https://github.com/<user-name>/latticegpm

• Navigate to this directory, and install (softly) this python package with

cd latticegpm
python setup.py develop

• Add another remote link to the master version, call it upstream.

git remote add upstream https://github.com/harmslab/latticegpm

• Start a branch locally from local master

git checkout -B <branch-name>

• Make changes and commit to that branch.

git commit -a -m "<commit message>"

• Push to your fork on github (which you called upstream).

git push upstream <branch-name>

• Pull request the branch on Github into this master repository on Github.