sbmlutils.comp.flatten
¶
Helpers for model flattening.
Module Contents¶
Functions¶
|
Flatten given SBML file. |
|
Flatten SBMLDocument. |
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Convert all ExternalModelDefinitions to ModelDefinitions. |
Attributes¶
- sbmlutils.comp.flatten.flatten_sbml(sbml_path, sbml_flat_path, leave_ports=True)[source]¶
Flatten given SBML file.
- Parameters
sbml_path (pathlib.Path) – input path to SBML file to flatten (should be a comp model)
sbml_flat_path (pathlib.Path) – output path for flat SBML
leave_ports (bool) – boolean flag to leave ports in flattened model.
- Returns
flattened SBMLDocument
- Return type
libsbml.SBMLDocument
- sbmlutils.comp.flatten.flatten_sbml_doc(doc, sbml_flat_path=None, leave_ports=True)[source]¶
Flatten SBMLDocument.
Validation should be performed before the flattening and is not part of the flattening routine. If an output path is provided the file is written to the output path.
- Parameters
doc (libsbml.SBMLDocument) – SBMLDocument to flatten.
sbml_flat_path (Optional[pathlib.Path]) – Path to write flattended SBMLDocument to
leave_ports (bool) – flag to leave ports
- Returns
SBMLDocument
- Return type
libsbml.SBMLDocument
- sbmlutils.comp.flatten.flatten_external_model_definitions(doc, validate=False)[source]¶
Convert all ExternalModelDefinitions to ModelDefinitions.
I.e. the definition of models in external files are read and directly included in the top model. The resulting comp model consists than only of a single file.
The model refs in the submodel do not change in the process, so no need to update the submodels.
- Parameters
doc (libsbml.SBMLDocument) – SBMLDocument
validate (bool) – validation flag
- Returns
SBMLDocument with ExternalModelDefinitions replaced
- Return type
libsbml.SBMLDocument