Export ODEs to PottersWheel (pysb.export.potterswheel)

Module containing a class for converting a PySB model to an equivalent set of ordinary differential equations for integration or analysis in PottersWheel.

For information on how to use the model exporters, see the documentation for pysb.export.

Output for the Robertson example model

The PottersWheel code produced will follow the form as given below for pysb.examples.robertson:

% A simple three-species chemical kinetics system known as "Robertson's
% example", as presented in:
% 
% H. H. Robertson, The solution of a set of reaction rate equations, in Numerical
% Analysis: An Introduction, J. Walsh, ed., Academic Press, 1966, pp. 178-182.
% 
% PottersWheel model definition file
% save as robertson.m
function m = robertson()

m = pwGetEmptyModel();

% meta information
m.ID          = 'robertson';
m.name        = 'robertson';
m.description = '';
m.authors     = {''};
m.dates       = {''};
m.type        = 'PW-1-5';

% dynamic variables
m = pwAddX(m, 's0', 1.000000e+00);
m = pwAddX(m, 's1', 0.000000e+00);
m = pwAddX(m, 's2', 0.000000e+00);

% dynamic parameters
m = pwAddK(m, 'k1', 4.000000e-02);
m = pwAddK(m, 'k2', 3.000000e+07);
m = pwAddK(m, 'k3', 1.000000e+04);
m = pwAddK(m, 'A_0', 1.000000e+00);
m = pwAddK(m, 'B_0', 0.000000e+00);
m = pwAddK(m, 'C_0', 0.000000e+00);

% ODEs
m = pwAddODE(m, 's0', '-k1*s0 + k3*s1*s2');
m = pwAddODE(m, 's1', 'k1*s0 - k2*power(s1, 2) - k3*s1*s2');
m = pwAddODE(m, 's2', 'k2*power(s1, 2)');

% observables
m = pwAddY(m, 'A_total', '1.000000 * s0');
m = pwAddY(m, 'B_total', '1.000000 * s1');
m = pwAddY(m, 'C_total', '1.000000 * s2');

% end of PottersWheel model robertson
class pysb.export.potterswheel.PottersWheelExporter(model, docstring=None)[source]

A class for returning the PottersWheel equivalent for a given PySB model.

Inherits from pysb.export.Exporter, which implements basic functionality for all exporters.

export(self)[source]

Generate the PottersWheel code for the ODEs of the PySB model associated with the exporter.

Returns:
string

String containing the PottersWheel code for the ODEs.