sbml¶

Reading, writing and validating SBML documents with libsbml.

The counterpart of sbml2cellml.cellml for the SBML side: errors are returned as messages instead of printed, SBMLValidationError is raised by the callers which want to stop on them.

SBMLValidationError ¶

Bases: ValueError

An SBML document has errors.

document_to_string ¶

document_to_string(doc)

Serialize a document to SBML xml.

Parameters:

Name	Type	Description	Default
`doc`	`SBMLDocument`	SBML document.	required

Returns:

Type	Description
`str`	The SBML xml.

write_document ¶

write_document(doc, sbml_path)

Write a document as SBML file.

Parameters:

Name	Type	Description	Default
`doc`	`SBMLDocument`	SBML document.	required
`sbml_path`	`Path`	path of the file, overwritten if it exists.	required

read_document ¶

read_document(sbml_path)

Read an SBML file.

Parameters:

Name	Type	Description	Default
`sbml_path`	`Path`	path of the SBML file.	required

Returns:

Type	Description
`SBMLDocument`	The document.

Raises:

Type	Description
`SBMLValidationError`	if the file cannot be read or has no model.

validate_document ¶

validate_document(doc)

Check the consistency of a document.

Runs the libsbml consistency checks (units, identifiers, MathML, SBO, modeling practice). Unit problems are reported by libsbml as warnings and are not part of the result. The error log of the document is cleared before the check.

Parameters:

Name	Type	Description	Default
`doc`	`SBMLDocument`	SBML document.	required

Returns:

Type	Description
`list[str]`	The messages of severity error or fatal, empty for a consistent document.