sbmlsim.simulator.rr_simulator_abstract

Classes for running simulations with SBML models.

Module Contents

Classes

SimulatorAbstractRR

Abstract base class for roadrunner simulator.

Attributes

logger

sbmlsim.simulator.rr_simulator_abstract.logger[source]
class sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR[source]

Bases: abc.ABC

Abstract base class for roadrunner simulator.

abstract static from_sbml(self, sbml_path)[source]

Set model from SBML.

Parameters

sbml_path (pathlib.Path) –

Return type

Any

abstract set_model(model_state)[source]

Set model from state.

Parameters

model_state (str) –

Return type

None

abstract set_timecourse_selections(selections)[source]

Set timecourse selections.

Parameters

selections (Iterator[str]) –

Return type

None

abstract set_integrator_settings(**kwargs)[source]

Set integrator settings.

Return type

None

abstract _run_timecourses(simulations)[source]

Execute timecourse simulations.

Parameters

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

Return type

List[pandas.DataFrame]

run_timecourse(simulation)[source]

Run single timecourse.

Parameters

simulation (sbmlsim.simulation.TimecourseSim) –

Return type

sbmlsim.xresult.XResult

run_scan(scan)[source]

Run scan simulation.

Parameters

scan (sbmlsim.simulation.ScanSim) –

Return type

sbmlsim.xresult.XResult