Collection of tools for analysing normal modes and performing principal component analysis
pyMODE-TASK - a PyMol plugin for MODE-TASK is available here.
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
conda install -c nizamibilal1064 mode-task
It will install the mode-task in /home/user/miniconda2/pkgs
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.
MODE-TASK: Large-scale protein motion tools
Caroline Ross, Bilal Nizami, Michael Glenister, Olivier Sheik Amamuddy, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop;