sbmlsim.model

Package for encoding models.

Submodules

Package Contents

Classes

AbstractModel

Abstract base class to store a model in sbmlsim.

ModelChange

ModelChange.

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__()

Get string representation.

Return type

str

normalize(uinfo)

Normalize values to model units for all changes.

Parameters

uinfo (sbmlsim.units.UnitsInformation) –

to_dict()

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 (sbmlsim.model.rr_model.roadrunner.RoadRunner) –