README.md

This package is no longer actively mantained

Python CRN

A CRN simulator based on David Soloveichik's Mathematica CRN Simulator

Version & Promises

Currently this is in a pre-alpha state, but already has some reasonable features. No guarantees are made for backward-compatibility. That is, some of the API calls might change, some of the reaction literals syntax might change, etc.

Dependencies

The package is written for Python 3.6+ and definitely won't work on an older Python version.

The current list of dependencies are

numpy
scipy
sympy
stochpy

Examples

A simple example of creating a crn, simulating it, and plotting it, is given here. An explanation of this code in detail can be found in crn/examples/basic_example.py.

from crn import *

a, a1, a2, b, c, t, z = species("A A1 A2 B C T Z")

sys = CRN(
    a >> a1 + a2,
    a1 + b >> t,
    c >> z,
    (a2 >> z).k(2.5),
    z + t >> 0)

sys.simulate({a: 2.5, b: 2.0}, t=5).plot("sim.png", title="Example Simulation")

This will output:

More examples will be added soon in the crn/examples/ folder.

Installation

Install using pip or pip3 depending on your setup.

pip3 install crn

Note: StochPy is not Python 3 ready. So, when crn is imported, it actually runs lib2to3 on the files that need to be modified within StochPy.