smeΒΆ

Spatial Model Editor Python interface

Python bindings to a subset of the functionality available in the full GUI Spatial Model Editor

https://spatial-model-editor.readthedocs.io/

Functions

open_example_model()

opens a built in example spatial model

open_file(filename)

opens a sme or SBML file containing a spatial model

open_sbml_file(filename)

opens an SBML file containing a spatial model

Classes

Compartment

a compartment where species live

CompartmentList

CompartmentList: a list of Compartment

Membrane

a membrane where two compartments meet

MembraneList

MembraneList: a list of Membrane

Model

the spatial model

Parameter

a parameter of the model

ParameterList

ParameterList: a list of Parameter

Reaction

a reaction between species

ReactionList

ReactionList: a list of Reaction

ReactionParameter

a parameter of a reaction

ReactionParameterList

ReactionParameterList: a list of ReactionParameter

SimulationResult

results at a single timepoint of a simulation

SimulationResultList

SimulationResultList: a list of SimulationResult

SimulatorType

Members:

Species

a species that lives in a compartment

SpeciesList

SpeciesList: a list of Species

Exceptions

InvalidArgument

RuntimeError