sbmlsim.model
¶
Package for encoding models.
Submodules¶
Package Contents¶
Classes¶
Abstract base class to store a model in sbmlsim. |
|
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]) –
- __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) –