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
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:
or
You can also use conda to install all dependencies:
Create alias for your bash
Run PyRod
Load conda environment (optional)
Feed config file to pyrod
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.