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model.model_roadrunner

RoadRunner model.

RoadrunnerSBMLModel 

RoadrunnerSBMLModel(
    source,
    base_path=None,
    changes=None,
    sid=None,
    name=None,
    selections=None,
    ureg=None,
    settings=None,
)

Bases: AbstractModel

Roadrunner model wrapper.

Load the model into roadrunner, with changes, selections and settings.

Q_ property 

Q_

Quantity to create quantities for model changes.

from_abstract_model staticmethod 

from_abstract_model(
    abstract_model,
    selections=None,
    ureg=None,
    settings=None,
)

Create from AbstractModel.

load_roadrunner_model classmethod 

load_roadrunner_model(source)

Load model from given source.

:param source: path to SBML model or SBML string :param state_path: path to rr state :return: roadrunner instance

get_state_path staticmethod 

get_state_path(sbml_path)

Get path of the state file.

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

copy_roadrunner_model classmethod 

copy_roadrunner_model(r)

Copy roadrunner model by using the state.

parse_units 

parse_units(ureg)

Parse units from SBML model.

set_timecourse_selections classmethod 

set_timecourse_selections(r, selections=None)

Set the model selections for timecourse simulation.

set_integrator_settings staticmethod 

set_integrator_settings(r, **kwargs)

Set integrator settings.

Keys are

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

set_default_settings staticmethod 

set_default_settings(r, **kwargs)

Set default settings of integrator.

parameter_df staticmethod 

parameter_df(r)

Create GlobalParameter DataFrame.

:return: pandas DataFrame

species_df staticmethod 

species_df(r)

Create FloatingSpecies DataFrame.

:return: pandas DataFrame