sbmlsim.simulator.rr_worker

Classes for running simulations with SBML models.

Module Contents

Classes

SimulationWorkerRR

Worker running simulations with roadrunner.

Attributes

logger

sbmlsim.simulator.rr_worker.logger[source]
class sbmlsim.simulator.rr_worker.SimulationWorkerRR[source]

Worker running simulations with roadrunner.

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

set_model(model_state)[source]

Set model for simulator and updates the integrator settings.

Parameters:

model_state (bytes) –

Return type:

None

set_timecourse_selections(selections=None)[source]

Set the timecourse selections.

If the selections are None the complee selections will be used.

Raises:

RuntimeError –

Parameters:

selections (Optional[Iterator[str]]) –

Return type:

None

get_timecourse_selections()[source]

Get timecourse selections.

Return type:

List[str]

set_integrator_settings(**kwargs)[source]

Set integrator settings.

Keys are:

variable_step_size [boolean] stiff [boolean] absolute_tolerance [float] relative_tolerance [float]

Return type:

sbmlsim.model.rr_model.roadrunner.Integrator

get_integrator_setting(key)[source]

Get integrator setting for given key.

Parameters:

key (str) –

Return type:

Any

_timecourse(simulation)[source]

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