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Package for creating and analysing hydrogels in ReaDDy

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Simulation and Numerical Integration for Hydrogel Degradation

This repository contains a variety of tools for simulating hydrogels. The main part of the code is for generating configurations and simulation systems for use with the software package called ReaDDy.

Then, in the theory folder, a numerical integration framework for integrating differential equations can be found. This is used for describing the enzymatic degradation of a hydrogel nanoparticle. This module in particular contains C++/Python code that is bound using pybind11. Also contained in the main repository, are Jupyter Notebooks with examples of how to use the hydrogels.theory module.


hydrogels is available on Linux, MacOS and Windows using Python 3.6, 3.7 and 3.8. It is not available yet on Python 3.9 because there is a dependency on SciPy which currently has no wheels built for Python 3.9.

At the time of writing it is only possible to install the package on a Linux architecture. This requires the following prerequisites:

  • gxx
  • pybind11
  • numpy
  • pandas
  • readdy
  • scipy

To install, do the following command from the main directory:

pip install .

And to test (also from the main directory):


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