Package for creating and analysing hydrogels in ReaDDy
Project description
hydrogels
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.
Pre-requisites:
hydrogels
is available on Linux, MacOS and Windows using Python 3.6
, 3.7
, 3.8
, and 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
networkx
softnanotools
starpolymers
Installing most these packages is generally trivial and can be done using either pip
or anaconda
. However install readdy
is typically done only by using anaconda
.
# optional - only add if you don't have it already
conda config --add channels conda-forge
# install readdy
conda install -c readdy readdy
In our continuous integration, we provide a method for installing readdy
via pip
, but in some environments, in particular on local machines, problems locating HDF5
can arise, hence we recommend using conda
instead. Here is how to build readdy
manually using pip
:
git clone https://github.com/readdy/readdy
pushd readdy
pip install .
popd
Installing hydrogels
To install, do the following command from the main directory:
pip install .
And to test (also from the main directory):
pytest --import-mode=importlib
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