-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
1 changed file
with
15 additions
and
69 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,82 +1,28 @@ | ||
| <img src="https://img.shields.io/badge/python-2.7%2C%203.6-blue.svg" align="right"><img src="https://travis-ci.com/RUBi-ZA/MODE-TASK.svg?branch=master" align="right"><img src="https://readthedocs.org/projects/pymode-task/badge/?version=latest" align="right"> <img src='https://anaconda.org/nizamibilal1064/mode-task/badges/version.svg' align="right"> <img src='https://anaconda.org/nizamibilal1064/mode-task/badges/downloads.svg' align="right"> | ||
| # MDM-TASK-web | ||
|
|
||
| # MODE-TASK | ||
| **MDM-TASK-web** is web server for MD-TASK and MODE-TASK and can be accessed here: [https://mdmtaskweb.rubi.ru.ac.za](https://mdmtaskweb.rubi.ru.ac.za) | ||
|
|
||
| Collection of tools for analysing normal modes and performing principal component analysis | ||
|
|
||
| Take a look at our web application [MDM-TASK-web](https://mdmtaskweb.rubi.ru.ac.za/) and find the [BioRxiv article here](https://www.biorxiv.org/content/10.1101/2021.01.29.428734v1) | ||
|
|
||
| pyMODE-TASK - a PyMol plugin for MODE-TASK is [available here](https://github.com/RUBi-ZA/pyMODE-TASK). | ||
| If you use MDM-TASK-web in your work, please cite the following: | ||
| - [MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics](https://doi.org/10.1016/j.csbj.2021.08.043) | ||
| - [MODE-TASK: large-scale protein motion tools](https://academic.oup.com/bioinformatics/article/34/21/3759/5021681) | ||
|
|
||
| ## Installation | ||
|
|
||
| *Download the project:* | ||
| ```bash | ||
| git clone https://github.com/RUBi-ZA/MODE-TASK.git | ||
| cd MODE-TASK | ||
| Clone the MDM-TASK-web branch | ||
| ``` | ||
|
|
||
| *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:* | ||
| git clone -b mdmtask-dev https://github.com/RUBi-ZA/MODE-TASK | ||
| ``` | ||
| sudo apt install g++ | ||
| g++ -I cpp/src/ ANM.cpp -o ANM | ||
| Go inside the cloned MODE-TASK folder and run the following to create the working environment named "mdmtaskweb" | ||
| ``` | ||
|
|
||
| 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:* | ||
| ```bash | ||
| sudo apt install virtualenvwrapper python-dev python-pip | ||
| virtualenv venv | ||
| source venv/bin/activate | ||
| pip install -r requirements.txt | ||
| conda env create -f environment.yml | ||
| ``` | ||
| *Virtual environment using Python 3 and pip3:* | ||
| ```bash | ||
| sudo apt install virtualenvwrapper python3-dev python3-pip | ||
| virtualenv venv | ||
| source venv/bin/activate | ||
| pip3 install setuptools | ||
| pip3 install -r requirements.txt | ||
| Activate the conda environment | ||
| ``` | ||
| *Conda (Python version depends on Conda installation):* | ||
| ```bash | ||
| 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 activate mdmtaskweb | ||
| ``` | ||
| Now <img src='https://anaconda.org/nizamibilal1064/mode-task/badges/installer/conda.svg'>: | ||
|
|
||
| ```bash | ||
| conda install -c nizamibilal1064 mode-task | ||
| In order to use ANM.py and getEigenVectors.py, ANM.cpp needs to be compiled. The following may be used to do so, from the MODE-TASK directory: | ||
| ``` | ||
| 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](http://mode-task.readthedocs.io/en/latest/index.html) site. | ||
|
|
||
| ## Contributing to the project | ||
|
|
||
| Questions and issues can be posted to the [issue tracker](https://github.com/RUBi-ZA/MODE-TASK/issues). | ||
|
|
||
| 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](https://github.com/RUBi-ZA/MODE-TASK/tree/master/docs). The documentation is hosted by [ReadTheDocs](https://readthedocs.org/) and makes use of reStructuredText for markdown with Latex for mathematical equasions. See [here](https://docs.readthedocs.io/en/latest/getting_started.html) 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;* | ||
| sudo apt install g++ | ||
| g++ -I src/cpp/src/ src/ANM.cpp -o src/ANM | ||
| [Bioinformatics, Volume 34, Issue 21, 1 November 2018](https://academic.oup.com/bioinformatics/article/34/21/3759/5021681) <br/> | ||
| [](https://academic.oup.com/bioinformatics/article/34/21/3759/5021681) | ||
| [](https://www.ncbi.nlm.nih.gov/pubmed/29850770) | ||
| ``` |