Export to StochKit (pysb.export.stochkit)

Module containing a class to return the StochKit XML equivalent of a model

Contains code based on the gillespy <https://github.com/JohnAbel/gillespy> library with permission from author Brian Drawert.

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

class pysb.export.stochkit.StochKitExporter(model, docstring=None)[source]

A class for returning the Kappa for a given PySB model.

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

export(self, initials=None, param_values=None)[source]

Generate the corresponding StochKit2 XML for a PySB model

Parameters:
initials : list of numbers

List of initial species concentrations overrides (must be same length as model.species). If None, the concentrations from the model are used.

param_values : list

List of parameter value overrides (must be same length as model.parameters). If None, the parameter values from the model are used.

Returns:
string

The model in StochKit2 XML format