PyRID: A Brownian dynamics simulator for reacting and interacting particles written in Python.

Disclaimer: PyRID is currently in early state development (version 0.1). As such, there is no guaranty that any of the functions are bug free. Careful validation of any results is recommended.

PyRID is a tool for particle based reaction diffusion simulations and is highly influenced and inspired by

• ReaDDy
• MCell
• Sarkas

PyRID is an attempt to combine several features of the above mentioned tools, which include

• unimolecular and bimolecular Reactions (ReaDDy, MCell)
• pair-interactions (ReaDDy)
• mesh based compartments and surface diffusion (MCell)
• pure Python implementation (Sarkas)

Documenttaion

Go to the PyRID documentation -> https://moritzb90.github.io/PyRID_doc/

Installation

1. Install Anaconda Python distribution (recommended):

   Anaconda

2. Download PyRID-0.0.1.tar.gz from the GitHub repository and extract it:

   PyRID on GitHub

3. Open Anaconda Prompt on your computer.

4. Go to the directory to which you downloaded PyRID-0.0.1.tar.gz:

   $ cd <your directory>
   

5. Create a new environment:

   conda create -n pyrid-env python=3.9
   
   conda activate pyrid-env
   

6. Pip install PyRID and install numba and h5py via conda:

   pip install PyRID-0.0.1.tar.gz
   conda install numba
   conda install h5py
   

To run your PyRID Python scripts you can use, e.g., Spyder or Jupyter Lab, which both come with the Anaconda distribution.