sbmlsim.model.rr_model
¶
RoadRunner model.
Module Contents¶
Classes¶
Roadrunner model wrapper. |
Attributes¶
- 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
- 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:
source (sbmlsim.model.model_resources.Source) – path to SBML model or SBML string
state_path (pathlib.Path) – path to rr state
- 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:
- 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) –