MODE-TASK

Collection of tools for analysing normal modes and performing principal component analysis

pyMODE-TASK - a PyMol plugin for MODE-TASK is available here.

Installation

1. Download the project:

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

C++ scripts can be called from within a python environment using their corresponding ANM.py and getEigenVectors.py scripts. If the binaries do not exist the Python wrapper will attempt to complile them. To compile the C++ yourself, use the following commands:

sudo apt install g++
g++ -I cpp/src/ ANM.cpp -o ANM

Create and activate the MODE-TASK environment:

You can either run:

conda create -n mode-task pandas conda-forge::matplotlib conda-forge::mdtraj conda-forge::sklearn-contrib-lightning

or you can use the provided YAML file:

conda env create -f mode-task.yml
conda activate mode-task

Usage

For more detailed documentation on installation and usage of the tool suite please see our ReadTheDocs site.

Contributing to the project

Questions and issues can be posted to the issue tracker.

Pull requests are welcome and will be reviewed however a guarantee cannot me made as to your request being accepted.

To contribute to the documentation see here. The documentation is hosted by ReadTheDocs and makes use of reStructuredText for markdown with Latex for mathematical equations. See here for a more detailed guideline on creating documentation for ReadTheDocs.

Citation

MODE-TASK: Large-scale protein motion tools

Caroline Ross, Bilal Nizami, Michael Glenister, Olivier Sheik Amamuddy, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop;

Bioinformatics, Volume 34, Issue 21, 1 November 2018