sbmlsim.simulator

Package for simulator.

Submodules

Package Contents

Classes

SimulatorWorker

Worker running simulations.

SimulatorSerial

Serial simulator using a single core.
class sbmlsim.simulator.SimulatorWorker[source]

Worker running simulations.

Implements the timecourse simulation once which can be reused by the different simulators.

_timecourse(self, simulation)

Timecourse simulation.

Requires for all timecourse definitions in the timecourse simulation to be unit normalized. The changes have no units any more for parallel simulations. You should never call this function directly!

Parameters

simulation (sbmlsim.simulation.TimecourseSim) – Simulation definition(s)

Returns

DataFrame with results

Return type

pandas.DataFrame

class sbmlsim.simulator.SimulatorSerial(model=None, **kwargs)[source]

Bases: sbmlsim.simulator.simulation.SimulatorWorker

Serial simulator using a single core.

A single simulator can run many different models. See the parallel simulator to run simulations on multiple cores.

set_model(self, model)

Set model for simulator and updates the integrator settings.

This should handle caching and state saving.

set_integrator_settings(self, **kwargs)

Set settings in the integrator.

set_timecourse_selections(self, selections)

Set timecourse selection in model.

property r(self)

Get the RoadRunner model.

Return type

roadrunner.roadrunner.ExecutableModel

property uinfo(self)

Get model unit information.

Return type

sbmlsim.units.UnitsInformation

property Q_(self)

Get model unit information.

Return type

pint.Quantity

run_timecourse(self, simulation)

Run single timecourse.

Parameters

simulation (sbmlsim.simulation.TimecourseSim) –

Return type

sbmlsim.result.XResult

run_scan(self, scan)

Run a scan simulation.

Parameters

scan (sbmlsim.simulation.ScanSim) –

Return type

sbmlsim.result.XResult

_timecourses(self, simulations)
Parameters

simulations (List[sbmlsim.simulation.TimecourseSim]) –

Return type

List[pandas.DataFrame]