parser¶

Parse SBML and antimony into the Model of sbmlutils.factory.

sbml_to_model is the inverse of create_model. A round trip SBML -> sbml_to_model -> create_model -> SBML preserves SBML core, see https://github.com/matthiaskoenig/sbmlutils/issues/469. It reads the unit definitions, the model units and conversionFactor, the function definitions, compartments, species and parameters, the reactions with their species references, modifiers and kinetic laws with local parameters, the initial assignments, rules, events with their trigger, priority, delay and event assignments, and constraints, and on each of these its id, name, metaid, sboTerm, notes, annotations and fbc key-value pairs. An element without math, which SBML allows from L3V2 on, is read without math. It also reads fbc:strict of the model, its gene products and objectives with their flux objectives, the gene product association of a reaction, as an infix string of gene product ids, its flux bounds, the charge and chemical formula of a species, and the user-defined constraints of the model with their components. A document which declares fbc version 1 is converted to fbc version 2 before it is read, see _convert_fbc_v1. Of distrib it reads the uncertainties of every element, with their uncert parameters and spans in the order of the document, and on each of those its type, value, variable, bounds, unit, definitionURL, math and the uncert parameters of an external distribution, see _parse_uncertainties. Of comp it reads the submodels of a model with their deletions, its ports, the replaced elements and the replacedBy of every element, each with the whole nested sBaseRef chain below it, and the model definitions and external model definitions of the document; a model definition is read by recursing into _parse_model_body, so everything of every package inside it is read as it is for the model of the document. An external model definition is preserved as the reference it is, source, modelRef and md5: the file it names is not opened and its content is not resolved into the document.

Not read are the model history, the content of the groups and layout packages, an uncertainty on an element which cannot carry one and a <comp:replacedBy> on an element which cannot carry one, both of which are reported (_drop_uncertainties, _drop_replaced_by; of the elements libsbml reads a replacement from at all, a species reference and a local parameter are the two whose replacement is dropped), a <comp:replacedElement> of an element which has neither an id nor a metaid, which sbmlutils.factory has no way to name and which is reported (_parse_replaced_elements), the comp:substanceConversionFactor libsbml reads on a submodel although comp version 1 does not define it, and of fbc the metadata of a gene product association and of the and, or and geneProductRef nodes of its association, which the infix string has no place for, and the fbc version 3 reaction2 of a flux objective and variable2 of a user-defined constraint component, which the factory has no field for. The fbc, distrib and comp packages a document declares are declared on the model. Math is read as an L3 infix string, in which an id named like a MathML constant or csymbol (pi, INF, NaN, time, avogadro) cannot be told apart from the constant, so such an id does not round trip.

antimony_to_sbml(source)

antimony_to_model(
    source,
    validate=False,
    promote=False,
    validation_options=None,
)

sbml_to_model(
    source,
    validate=False,
    promote=False,
    validation_options=None,
)