Exporting to other formats (pysb.export)

Tools for exporting PySB models to a variety of other formats.

Exporting can be performed at the command-line or programmatically/interactively from within Python.

Command-line usage

At the command-line, run as follows:

python -m pysb.export model.py <format>

where model.py is a file containing a PySB model definition (i.e., contains an instance of pysb.core.Model instantiated as a global variable). [format] should be the name of one of the supported formats:

  • bngl

  • bng_net

  • json

  • kappa

  • potterswheel

  • sbml

  • pysb_flat

  • mathematica

  • matlab

  • stochkit

In all cases, the exported model code will be printed to standard out, allowing it to be inspected or redirected to another file.

Interactive usage

Export functionality is implemented by this module’s top-level function export. For example, to export the “Robertson” example model as SBML, first import the model:

from pysb.examples.robertson import model

Then import the export function from this module:

from pysb.export import export

Call the export function, passing the model instance and a string indicating the desired format, which should be one of the ones indicated in the list in the “Command-line usage” section above:

sbml_output = export(model, 'sbml')

The output (a string) can be inspected or written to a file, e.g. as follows:

with open('robertson.sbml', 'w') as f:
    f.write(sbml_output)

Implementation of specific exporters

Information on the implementation of specific exporters can be found in the documentation for the exporter classes in the package pysb.export:

exception pysb.export.CompartmentsNotSupported[source]

Compartments are not supported by this exporter

exception pysb.export.CustomSympyFunctionsNotSupported[source]

Custom sympy functions are not supported by this exporter

exception pysb.export.EnergyNotSupported[source]

Energy features are not supported by this exporter

exception pysb.export.ExportError[source]
class pysb.export.Exporter(model, docstring=None)[source]

Base class for all PySB model exporters.

Export functionality is implemented by subclasses of this class. The pattern for model export is the same for all exporter subclasses: a model is passed to the exporter constructor and the export method on the instance is called.

Parameters:
modelpysb.core.Model

The model to export.

docstringstring (optional)

The header comment to include at the top of the exported file.

Examples

Exporting the “Robertson” example model to SBML using the SbmlExporter subclass:

>>> from pysb.examples.robertson import model
>>> from pysb.export.sbml import SbmlExporter
>>> e = SbmlExporter(model)
>>> sbml_output = e.export()
docstring

Header comment to include at the top of the exported file.

export()[source]

The export method, which must be implemented by any subclass.

All implementations of this method are expected to return a single string containing the representation of the model in the desired format.

model

The model to export.

exception pysb.export.ExpressionsNotSupported[source]

Expressions are not supported by this exporter

exception pysb.export.FeatureNotSupportedError[source]
exception pysb.export.LocalFunctionsNotSupported[source]

Local functions are not supported by this exporter

pysb.export.export(model, format, docstring=None)[source]

Top-level function for exporting a model to a given format.

Parameters:
modelpysb.core.Model

The model to export.

formatstring

A string indicating the desired export format.

docstringstring (optional)

The header comment to include at the top of the exported file.

pysb.export.pad(text, depth=0)[source]

Dedent multi-line string and pad with spaces.