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README.md

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

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

MODE-TASK can be used with a variety of Python enviroments and package managers, below are some of the options:

Virtual environment using Python 2 and pip:

sudo apt install virtualenvwrapper python-dev python-pip
virtualenv venv
source venv/bin/activate
pip install -r requirements.txt

Virtual environment using Python 3 and pip3:

sudo apt install virtualenvwrapper python3-dev python3-pip
virtualenv venv
source venv/bin/activate
pip3 install setuptools
pip3 install -r requirements.txt

Conda (Python version depends on Conda installation):

conda create -n mode_task
source activate mode_task
conda install -c conda-forge numpy
conda install -c conda-forge cython
conda install -c omnia mdtraj
conda install -c conda-forge scipy
conda install -c conda-forge pandas
conda install -c conda-forge sklearn-contrib-lightning
conda install -c conda-forge matplotlib

Now :

conda install -c nizamibilal1064 mode-task

It will install the mode-task in /home/user/miniconda2/pkgs

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 guarentee can not 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 equasions. 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
doi pubmed

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