sbmlsim.model

Package for encoding models.

Submodules

Package Contents

Classes

AbstractModel

Abstract base class to store a model in sbmlsim.

ModelChange

ModelChange.

RoadrunnerSBMLModel

Roadrunner model wrapper.
class sbmlsim.model.AbstractModel(source, sid=None, name=None, language=None, language_type=LanguageType.SBML, base_path=None, changes=None, selections=None)[source]

Bases: object

Abstract base class to store a model in sbmlsim.

Depending on the model language different subclasses are implemented.

Parameters

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

  • sid (Optional[str]) –

  • name (Optional[str]) –

  • language (Optional[str]) –

  • language_type (LanguageType) –

  • base_path (Optional[pathlib.Path]) –

  • changes (Dict) –

  • selections (List[str]) –

class LanguageType

Bases: enum.Enum

Language types.

SBML = 1
CELLML = 2
class SourceType

Bases: enum.Enum

Source types.

PATH = 1
URN = 2
URL = 3
__repr__(self)

Get string representation.

Return type

str

normalize(self, uinfo)

Normalize values to model units for all changes.

Parameters

uinfo (sbmlsim.units.UnitsInformation) –

to_dict(self)

Convert to dictionary.

class sbmlsim.model.ModelChange[source]

Bases: object

ModelChange.

Structural change to a model.

CLAMP_SPECIES = clamp_species
static clamp_species(r, species_id, formula=True, speed=10000.0)

Clamp/free species to certain value or formula.

This is only an approximative clamp, i.e. not working instantenious. Depending on the model kinetics different speed settings are required. FIXME: time cannot be used in formula due to https://github.com/sys-bio/roadrunner/issues/601 FIXME: concentrations and amounts are not handled (uses native species setting

i.e., amount or concentration definition.

Parameters

r (roadrunner.RoadRunner) –

class sbmlsim.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) –

IntegratorSettingKeys
property Q_(self)

Quantity to create quantities for model changes.

Return type

sbmlsim.units.Quantity

property r(self)

Roadrunner instance.

Return type

roadrunner.RoadRunner

get_state_path(self)

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)

Load model from given source.

Parameters
Returns

roadrunner instance

Return type

roadrunner.RoadRunner

classmethod copy_roadrunner_model(cls, r)

Copy roadrunner model by using the state.

Parameters

r (roadrunner.RoadRunner) –

Returns

Return type

roadrunner.RoadRunner

parse_units(self, ureg)

Parse units from SBML model.

Parameters

ureg (sbmlsim.units.UnitRegistry) –

Return type

sbmlsim.units.UnitsInformation

classmethod set_timecourse_selections(cls, r, selections=None)

Set the model selections for timecourse simulation.

Parameters

  • r (roadrunner.RoadRunner) –

  • selections (List[str]) –

Return type

List[str]

static set_integrator_settings(r, **kwargs)

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)

Set default settings of integrator.

Parameters

r (roadrunner.RoadRunner) –

static parameter_df(r)

Create GlobalParameter DataFrame.

Returns

pandas DataFrame

Parameters

r (roadrunner.RoadRunner) –

Return type

pandas.DataFrame

static species_df(r)

Create FloatingSpecies DataFrame.

Returns

pandas DataFrame

Parameters

r (roadrunner.RoadRunner) –

Return type

pandas.DataFrame