AAriam / pyrod

PyRod - Tracing water molecules in molecular dynamics simulations

PyRod is a python software developed to generate dynamic molecular interaction fields (dMIFs) and pharmacophore features based on analyzing the protein environment of water molecules in molecular dynamcis simulations. Check the PyRod wiki for more information on installation and usage. The employed algorithms are described in the PyRod publication in JCIM.

Installation

Clone this repository

Open a new terminal and clone this repository

git clone https://github.com/schallerdavid/pyrod.git ~/pyrod

Install dependencies

PyRod is written in python 3.8 and uses MDAnalysis (>= 0.19.0, is shipped with NumPy and SciPy), NumPy and SciPy which can be easily installed using pip:

pip3 install --upgrade MDAnalysis

or

python3 -m pip install --upgrade MDAnalysis

You can also use conda to install all dependencies:

conda create -n pyrod -c conda-forge mdanalysis python=3.8

Create alias for your bash

echo 'alias pyrod="python3 ~/pyrod/pyrod.py"' >> ~/.bashrc

Run PyRod

Load conda environment (optional)

source activate pyrod

Feed config file to pyrod

pyrod /path/to/pyrod_config_file.cfg

Example

An example Jupyter Notebook for visualization of dMIFs using NGLView is provided in the example directory.

Citation

Please cite our paper in JCIM when using PyRod for your research.

License Information

PyRod is published under GNU General Public License v2.0. For more information read LICENSE.