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PyRod - Tracing water molecules in molecular dynamics simulations
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configs added point properties component Jun 16, 2019
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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.


Clone this repository

Open a new terminal and clone this repository

git clone ~/pyrod

Install dependencies

PyRod is written in python 3.6 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


python3 -m pip install --upgrade MDAnalysis

You can also use conda to install all dependencies:

conda config --add conda-forge
conda create -n pyrod mdanalysis python=3.6

Create alias for your bash

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

Run PyRod

Load conda environment (optional)

source activate pyrod

Feed config file to pyrod

pyrod /path/to/pyrod_config_file.cfg


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

License Information

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

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