pyenzyme.enzymeml.tools.enzymemlwriter module#

class pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter[source]#

Bases: object

static addFileToArchive(archive, file_path, target_path, format, description)[source]#
static appendAttribute(attributeName, value)[source]#
appendInitConcData(measurement_annot: XMLNode, measurement_data_dict: Dict[str, MeasurementData], species_type: str)[source]#

Adds individual intial concentration data to the enzymeml:measurement annotation.

Parameters

  • measurement_annot (XMLNode) – The SBML XMLNode for the measurement annotation.

  • measurement_data_dict (Dict[str, MeasurementData]) – The EnzymeMLDocument measurement data.

  • species_type (str) – The type of species in the measurement_data_dict.

appendMultiAttributes(attributeName, object, objectMapping, annotationNode)[source]#
appendOptionalAttribute(attributeName, object, objectName, annotationNode)[source]#
appendReplicateData(species: Dict[str, MeasurementData], format_annot: XMLNode, data_columns: Dict[str, List[float]]) → Dict[str, List[float]][source]#

Extracts all time course data from the replicate objects and adds them to the the enzymeml:format annotation.

Parameters

  • species (Dict[str, MeasurementData]) – Reactant/Protein measurement data.

  • format_annot (XMLNode) – The SBML XMLNode representing the format annotation.

Returns

The time course data from the replicate objects.

Return type

List[List[float]]

convertEnzymeMLToSBML(model: Model, enzmldoc)[source]#

Manages the conversion of EnzymeML to SBML.

Parameters

  • model (libsbml.Model) – The blank SBML model, where the EnzymeML document is converted to.

  • enzmldoc (EnzymeMLDocument) – The EnzymeML document to be converted.

setupXMLNode(name, namespace=True)[source]#
toFile(enzmldoc, path: str, name: Optional[str] = None)[source]#

Writes EnzymeMLDocument object to an .omex container

Parameters

  • enzmldoc (String) – Previously created instance of an EnzymeML document

  • path (String) – EnzymeML file is written to this destination

  • name (String) – Name of the target EnzymeML file. Defaults to ‘None’ and thus uses the doc name.

toSBML(enzmldoc)[source]#

Returns libSBML model.

Parameters

enzmldoc (EnzymeMLDocument) – Previously created instance of an EnzymeML document

toXMLString(enzmldoc)[source]#

Converts EnzymeMLDocument to XML string.

Parameters

enzmldoc (EnzymeMLDocument) – Previously created instance of an EnzymeML document

writeElements(reaction_elements: List[ReactionElement], createFunction: Callable)[source]#

Writes SpeciesReference elements to the SBML document.

Parameters

  • reaction_elements (List[ReactionElement]) – List of reaction elements containing information on stoichiometry, species_id and ontology.

  • createFunction (Callable) – Function that creates either an educt, product or modifier list to the SBML document.

writeMeasurementData(measurement: Measurement, measurement_annot: XMLNode, format_annot: XMLNode, data_columns: Dict[str, List[float]]) → None[source]#

Writes measurement metadata as columns to the SBML document annotation enzymeml:column.

Parameters

  • measurement (Measurement) – EnzymeML measurement that is written to SBML.

  • measurement_annot (XMLNode) – The SBML XMLNode the measurement metadata is written to.

  • format_annot (XMLNode) – The SBML XMLNode the column information is written to.

Returns

The time course data from the replicate objects.

Return type

List[List[float]]

writeReplicateData(replicate: Replicate, format_annot: XMLNode) → None[source]#

Writes column information to the enzymeml:format annotation.

Parameters

  • replicate (Replicate) – Replicate holding the time course data.

  • format_annot (XMLNode) – The enzymeml:format annotation node.

writeTimeData(measurement: Measurement, format_annot: XMLNode, data_columns: dict)[source]#