sbmlsim.model.model_roadrunner

RoadRunner model.

Module Contents

Classes

RoadrunnerSBMLModel

Roadrunner model wrapper.

Attributes

logger

sbmlsim.model.model_roadrunner.logger[source]
class sbmlsim.model.model_roadrunner.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) –

IntegratorSettingKeys[source]
property Q_(self)[source]

Quantity to create quantities for model changes.

Return type

sbmlsim.units.Quantity

property r(self)[source]

Roadrunner instance.

Return type

roadrunner.RoadRunner

get_state_path(self)[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 load_roadrunner_model(cls, source, state_path=None)[source]

Load model from given source.

Parameters
Returns

roadrunner instance

Return type

roadrunner.RoadRunner

classmethod copy_roadrunner_model(cls, r)[source]

Copy roadrunner model by using the state.

Parameters

r (roadrunner.RoadRunner) –

Returns

Return type

roadrunner.RoadRunner

parse_units(self, ureg)[source]

Parse units from SBML model.

Parameters

ureg (sbmlsim.units.UnitRegistry) –

Return type

sbmlsim.units.UnitsInformation

classmethod set_timecourse_selections(cls, 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