sbmlsim.model.model

Models.

Functions for model loading, model manipulation and settings on the integrator. Model can be in different formats, main supported format being SBML.

Other formats could be supported like CellML or NeuroML.

Module Contents

Classes

AbstractModel

Abstract base class to store a model in sbmlsim.

Attributes

logger

sbmlsim.model.model.logger[source]
class sbmlsim.model.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[source]

Bases: enum.Enum

Language types.

SBML = 1[source]
CELLML = 2[source]
class SourceType[source]

Bases: enum.Enum

Source types.

PATH = 1[source]
URN = 2[source]
URL = 3[source]
__repr__()[source]

Get string representation.

Return type:

str

normalize(uinfo)[source]

Normalize values to model units for all changes.

Parameters:

uinfo (sbmlsim.units.UnitsInformation) –

to_dict()[source]

Convert to dictionary.