sbmlutils.comp

Package for SBML comp.

Submodules

Package Contents

Functions

create_ExternalModelDefinition(doc_comp, emd_id, source)

Create comp ExternalModelDefinition.

create_ports(model[, portRefs, idRefs, unitRefs, ...])

Create ports for given model.

flatten_sbml(sbml_path, sbml_flat_path[, leave_ports])

Flatten given SBML file.

flatten_sbml_doc(doc[, sbml_flat_path, leave_ports])

Flatten SBMLDocument.
sbmlutils.comp.create_ExternalModelDefinition(doc_comp, emd_id, source)[source]

Create comp ExternalModelDefinition.

Parameters:

  • doc_comp (libsbml.CompSBMLDocumentPlugin) – SBMLDocument comp plugin

  • emd_id (str) – id of external model definition

  • source (str) – source

Returns:

Return type:

libsbml.ExternalModelDefinition

sbmlutils.comp.create_ports(model, portRefs=None, idRefs=None, unitRefs=None, metaIdRefs=None, portType=factory.PortType.PORT, suffix=factory.PORT_SUFFIX)[source]

Create ports for given model.

Helper function to create port creation. :param model: SBML model :param portRefs: dict of the form {pid:portRef} :param idRefs: dict of the form {pid:idRef} :param unitRefs: dict of the form {pid:unitRef} :param metaIdRefs: dict of the form {pid:metaIdRef} :param portType: type of port :param suffix: suffix to use in port generation

Returns:

Parameters:

  • model (libsbml.Model) –

  • portRefs (Optional[Any]) –

  • idRefs (Optional[Any]) –

  • unitRefs (Optional[Any]) –

  • metaIdRefs (Optional[Any]) –

  • portType (sbmlutils.factory.PortType) –

  • suffix (str) –

Return type:

List[sbmlutils.factory.Port]

sbmlutils.comp.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_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