MD-TASK

Tool suite for analysing molecular dynamics trajectories using network analysis and PRS.

Introduction

MD-TASK consists of a suite of Python scripts that have been developed to analyze molecular dynamics trajectories. Detailed documentation can be found on our ReadTheDocs site.

Installation

Download the project:

git clone https://github.com/RUBi-ZA/MD-TASK.git
cd MD-TASK

Install dependencies and set up Python virtual environment:

sudo apt-get install virtualenvwrapper python-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libpng12-dev libfreetype6-dev python-tk r-base
virtualenv venv
source venv/bin/activate
pip install --upgrade pip
pip install numpy
pip install scipy
pip install matplotlib cython networkx natsort
pip install mdtraj

Install igraph package for R:

R
> install.packages("igraph")

Usage

The scripts are located in the root directory of the project. To run the scripts, ensure that the virtual environment is activated. For more info, find detailed documentation here.