pyenzyme.enzymeml.tools.enzymemlreader module

class pyenzyme.enzymeml.tools.enzymemlreader.ComplexFactory[source]

Bases: pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory

Returns an un-initialized complex species object

enzymeml_part: str = 'complex_dict'
get_species(**kwargs) → pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies[source]

Return a new species object

class pyenzyme.enzymeml.tools.enzymemlreader.EnzymeMLReader[source]

Bases: object

readFromFile(path: str) → pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument[source]

Reads EnzymeML document to an object layer EnzymeMLDocument class.

Parameters

path (str) – Path to .omex container or folder destination for plain .xml

class pyenzyme.enzymeml.tools.enzymemlreader.ProteinFactory[source]

Bases: pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory

Returns an un-initialized protein species object

enzymeml_part: str = 'protein_dict'
get_species(**kwargs) → pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies[source]

Return a new species object

class pyenzyme.enzymeml.tools.enzymemlreader.ReactantFactory[source]

Bases: pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory

Returns an un-initialized reactant species object

enzymeml_part: str = 'reactant_dict'
get_species(**kwargs) → pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies[source]

Return a new species object

pyenzyme.enzymeml.tools.enzymemlreader.species_factory_mapping(sbo_term: str) → pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory[source]

Maps from SBOTerms to the appropriate species using a factory