14.8.8. steps.API_1.utilities.sbml
- class Interface(filename, timeunits_def=1.0, volunits_def=0.001, subsunits_def=1.0, volume_def=False, area_def=False, strict_mode=False)[source]
The interface to the SBML importer.
- getModel()[source]
Returns a reference to the steps.model.Model biocehmical model container object created during SBML import.
Syntax:
getModel()
- Arguments:
None
- Return:
steps.model.Model
- getGeom()[source]
Returns a reference to the steps.geom.Geom geoemtry container object created during SBML import.
Syntax:
getGeom()
- Arguments:
None
- Return:
steps.geom.Geom
- setupSim(sim)[source]
Setup the simulation, initialising molecule counts, compartment volumes and SBML ‘boundary conditions” to those specified in the SBML file, which may differ from default values through mechanisms such as Initial Assignments. This function is NOT called internally and must be called by the user.
Syntax:
setupSim(sim)
- Arguments:
steps.solver.API sim (steps.solver.Wmdirect or steps.solver.Wmrk4 solver object)
- Return
None
- updateSim(sim, simdt)[source]
Update the simulation solver state, which may impact any variables in the simulation that can be altered within Rules and Events. Time since last update given as argument dt in seconds.
Syntax:
updateSim(sim, dt)
- Arguments:
steps.solver.API sim (steps.solver.Wmdirect or steps.solver.Wmrk4 solver object)
float dt
- Return
None