sbmlsim.model.rr_model

RoadRunner model.

Module Contents

Classes

RoadrunnerSBMLModel

Roadrunner model wrapper.

Attributes

logger

IntegratorSettingKeys

sbmlsim.model.rr_model.logger[source]
sbmlsim.model.rr_model.IntegratorSettingKeys[source]
class sbmlsim.model.rr_model.RoadrunnerSBMLModel(source, base_path=None, changes=None, sid=None, name=None, selections=None, ureg=None, settings=None)[source]

Bases: sbmlsim.model.AbstractModel

Roadrunner model wrapper.

Parameters:

  • source (Union[str, pathlib.Path, sbmlsim.model.AbstractModel]) –

  • base_path (pathlib.Path) –

  • changes (Dict) –

  • sid (str) –

  • name (str) –

  • selections (List[str]) –

  • ureg (sbmlsim.units.UnitRegistry) –

  • settings (Dict) –

property Q_: sbmlsim.units.Quantity[source]

Quantity to create quantities for model changes.

Return type:

sbmlsim.units.Quantity

property r: roadrunner.RoadRunner[source]

Roadrunner instance.

Return type:

roadrunner.RoadRunner

get_state_path()[source]

Get path of the state file.

The state file is a binary file which allows fast model loading.

Return type:

Optional[pathlib.Path]

classmethod loda_model_from_source(source, state_path=None)[source]

Load model from given source.

Parameters:
Returns:

roadrunner instance

Return type:

roadrunner.RoadRunner

classmethod copy_roadrunner_instance(r)[source]

Copy roadrunner model by using the state.

Parameters:

r (roadrunner.RoadRunner) –

Return type:

roadrunner.RoadRunner

parse_units(ureg)[source]

Parse units from SBML model.

Parameters:

ureg (sbmlsim.units.UnitRegistry) –

Return type:

sbmlsim.units.UnitsInformation

classmethod set_timecourse_selections(r, selections=None)[source]

Set the model selections for timecourse simulation.

Parameters:

  • r (roadrunner.RoadRunner) –

  • selections (List[str]) –

Return type:

List[str]

static set_integrator_settings(r, **kwargs)[source]

Set integrator settings.

Keys are:

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

Parameters:

r (roadrunner.RoadRunner) –

Return type:

roadrunner.Integrator

static set_default_settings(r, **kwargs)[source]

Set default settings of integrator.

Parameters:

r (roadrunner.RoadRunner) –

static parameter_df(r)[source]

Create GlobalParameter DataFrame.

Returns:

pandas DataFrame

Parameters:

r (roadrunner.RoadRunner) –

Return type:

pandas.DataFrame

static species_df(r)[source]

Create FloatingSpecies DataFrame.

Returns:

pandas DataFrame

Parameters:

r (roadrunner.RoadRunner) –

Return type:

pandas.DataFrame