Index

A

ABSORPTION (pyenzyme.enzymeml.core.ontology.DataTypes attribute) AbstractSpeciesFactory (class in pyenzyme.enzymeml.core.abstract_classes) ACID_BASE_REACTION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) add_identifier() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument class method) addBaseUnit() (pyenzyme.enzymeml.core.unitdef.UnitDef method) addComplex() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addCreator() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addData() (pyenzyme.enzymeml.core.measurement.Measurement method) addEduct() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) addFile() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addFileToArchive() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter static method) addGlobalParameter() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addMeasurement() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addModifier() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) addParameter() (pyenzyme.enzymeml.models.kineticmodel.KineticModel method)

addProduct() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) addProtein() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addReactant() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addReaction() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addReactions() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) addReplicate() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) addReplicates() (pyenzyme.enzymeml.core.measurement.Measurement method) addVessel() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) appendAttribute() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter static method) appendInitConcData() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) appendMultiAttributes() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) appendOptionalAttribute() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) appendReplicateData() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) apply_initial_values() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) applyModelInitialization() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method)

B

BIOCHEMICAL_REACTION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) BIOMASS (pyenzyme.enzymeml.core.ontology.DataTypes attribute) boundary (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute)

C

calculateTransformValue() (pyenzyme.enzymeml.core.unitdef.UnitDef method) CATALYST (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) chebi_id (pyenzyme.enzymeml.core.reactant.Reactant attribute) ChEBIIdentifierError check_data_completeness() (pyenzyme.enzymeml.core.replicate.Replicate class method) check_empty_strings() (pyenzyme.enzymeml.core.creator.Creator class method) check_id_occurences() (pyenzyme.enzymeml.core.measurementData.MeasurementData class method) check_mail_consistency() (pyenzyme.enzymeml.core.creator.Creator class method) check_meta_id() (pyenzyme.enzymeml.core.unitdef.UnitDef class method) check_reactant_ids() (pyenzyme.enzymeml.core.complex.Complex class method) checkUnitConsistency() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) clean_sequence() (pyenzyme.enzymeml.core.protein.Protein class method) complex_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) ComplexFactory (class in pyenzyme.enzymeml.tools.enzymemlreader) CONCENTRATION (pyenzyme.enzymeml.core.ontology.DataTypes attribute) CONFORMATIONAL_TRANSITION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) constant (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymereaction.ReactionElement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute)

CONVERSION (pyenzyme.enzymeml.core.ontology.DataTypes attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) convert_temperature_unit() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction class method) (pyenzyme.enzymeml.core.measurement.Measurement class method) convertEnzymeMLToSBML() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) created (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) createGenerator() (pyenzyme.enzymeml.models.kineticmodel.KineticModel static method) creator_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) creator_id (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.replicate.Replicate attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute)

D

data (pyenzyme.enzymeml.core.replicate.Replicate attribute) data_type (pyenzyme.enzymeml.core.replicate.Replicate attribute) data_unit (pyenzyme.enzymeml.core.replicate.Replicate attribute) data_unitdef() (pyenzyme.enzymeml.core.replicate.Replicate method) DataError DataTypes (class in pyenzyme.enzymeml.core.ontology)

DEGRADATION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) deprecated_getter() (in module pyenzyme.enzymeml.core.utils) deprecated_method() (in module pyenzyme.enzymeml.core.utils) DIMER (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) DISSOCIATION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) doi (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute)

E

ecnumber (pyenzyme.enzymeml.core.protein.Protein attribute) ECNumberError educts (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) entityFromSBOTerm() (pyenzyme.enzymeml.core.ontology.EnzymeMLPart class method) enzymeml_part (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory attribute) (pyenzyme.enzymeml.tools.enzymemlreader.ComplexFactory attribute) (pyenzyme.enzymeml.tools.enzymemlreader.ProteinFactory attribute) (pyenzyme.enzymeml.tools.enzymemlreader.ReactantFactory attribute) EnzymeMLPart (class in pyenzyme.enzymeml.core.ontology)

EnzymeMLReader (class in pyenzyme.enzymeml.tools.enzymemlreader) EnzymeMLWriter (class in pyenzyme.enzymeml.tools.enzymemlwriter) equation (pyenzyme.enzymeml.models.kineticmodel.KineticModel attribute) (pyenzyme.enzymeml.models.kineticmodel.ModelFactory attribute) ESSENTIAL_ACTIVATOR (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) evaluate() (pyenzyme.enzymeml.models.kineticmodel.KineticModel method) exponent (pyenzyme.enzymeml.core.unitdef.BaseUnit attribute) exportData() (pyenzyme.enzymeml.core.measurement.Measurement method) exportKineticParameters() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) exportMeasurementData() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method)

F

family_name (pyenzyme.enzymeml.core.creator.Creator attribute) FEED (pyenzyme.enzymeml.core.ontology.DataTypes attribute) file_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) fromChebiID() (pyenzyme.enzymeml.core.reactant.Reactant class method) fromEquation() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction class method) (pyenzyme.enzymeml.models.kineticmodel.KineticModel class method)

fromFile() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument static method) fromJSON() (pyenzyme.enzymeml.core.enzymemlbase.EnzymeMLBase class method) (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument class method) fromTemplate() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument class method) fromUniProtID() (pyenzyme.enzymeml.core.protein.Protein class method)

G

GENE (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) generateInitialValueTemplate() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) get_created() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) get_id() (pyenzyme.enzymeml.core.enzymereaction.ReactionElement method) (pyenzyme.enzymeml.core.measurementData.MeasurementData method) (pyenzyme.enzymeml.core.unitdef.BaseUnit method) (pyenzyme.enzymeml.models.kineticmodel.KineticModel method) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter method) get_name() (pyenzyme.enzymeml.core.unitdef.BaseUnit method) get_reaction_scheme() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) get_species() (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory method) (pyenzyme.enzymeml.tools.enzymemlreader.ComplexFactory method) (pyenzyme.enzymeml.tools.enzymemlreader.ProteinFactory method) (pyenzyme.enzymeml.tools.enzymemlreader.ReactantFactory method) getAny() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getBoundary() (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) getConstant() (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) (pyenzyme.enzymeml.core.vessel.Vessel method) getCreator() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getData() (pyenzyme.enzymeml.core.replicate.Replicate method) getDataUnit() (pyenzyme.enzymeml.core.replicate.Replicate method) getDoi() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getEcnumber() (pyenzyme.enzymeml.core.protein.Protein method) getEduct() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getEducts() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getEquation() (pyenzyme.enzymeml.models.kineticmodel.KineticModel method) getExponentString() (pyenzyme.enzymeml.tools.unitparser.UnitParser method) getFile() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getFileDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getFilesList() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getFname() (pyenzyme.enzymeml.core.creator.Creator method) getFootprint() (pyenzyme.enzymeml.core.unitdef.UnitDef method) getGlobalTime() (pyenzyme.enzymeml.core.measurement.Measurement method) getGlobalTimeUnit() (pyenzyme.enzymeml.core.measurement.Measurement method) getGname() (pyenzyme.enzymeml.core.creator.Creator method) getId() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) (pyenzyme.enzymeml.core.measurement.Measurement method) (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) (pyenzyme.enzymeml.core.unitdef.UnitDef method) (pyenzyme.enzymeml.core.vessel.Vessel method) getInchi() (pyenzyme.enzymeml.core.reactant.Reactant method) getInitConc() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) getIsCalculated() (pyenzyme.enzymeml.core.replicate.Replicate method) getLevel() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getMail() (pyenzyme.enzymeml.core.creator.Creator method) getMeasurement() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.core.replicate.Replicate method) getMeasurementDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getMetaid() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) (pyenzyme.enzymeml.core.unitdef.UnitDef method) (pyenzyme.enzymeml.core.vessel.Vessel method) getModel() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getModified() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getModifier() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getModifiers() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getName() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) (pyenzyme.enzymeml.core.measurement.Measurement method) (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) (pyenzyme.enzymeml.core.unitdef.UnitDef method) (pyenzyme.enzymeml.core.vessel.Vessel method) (pyenzyme.enzymeml.models.kineticmodel.KineticModel method)

getOntology() (pyenzyme.enzymeml.core.unitdef.UnitDef method) getOrganism() (pyenzyme.enzymeml.core.protein.Protein method) getOrganismTaxId() (pyenzyme.enzymeml.core.protein.Protein method) getParameter() (pyenzyme.enzymeml.models.kineticmodel.KineticModel method) getParameters() (pyenzyme.enzymeml.models.kineticmodel.KineticModel method) getPh() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getProduct() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getProducts() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getProtein() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.core.measurement.Measurement method) getProteinDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getProteinID() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) getProteinList() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getProteins() (pyenzyme.enzymeml.core.measurement.Measurement method) getPubmedID() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReactant() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.core.measurement.Measurement method) (pyenzyme.enzymeml.core.replicate.Replicate method) getReactantDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReactantID() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) getReactantList() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReactants() (pyenzyme.enzymeml.core.measurement.Measurement method) getReaction() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReactionDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReactionList() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getReplica() (pyenzyme.enzymeml.core.replicate.Replicate method) getReplicates() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) getReversible() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getSboterm() (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) getSequence() (pyenzyme.enzymeml.core.protein.Protein method) getSize() (pyenzyme.enzymeml.core.vessel.Vessel method) getSmiles() (pyenzyme.enzymeml.core.reactant.Reactant method) getSpeciesDict() (pyenzyme.enzymeml.core.measurement.Measurement method) getSpeciesIDs() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getStoichiometricCoefficients() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getSubstanceUnits() (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) getTemperature() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getTempunit() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) getTimeUnit() (pyenzyme.enzymeml.core.replicate.Replicate method) getType() (pyenzyme.enzymeml.core.replicate.Replicate method) getUniprotID() (pyenzyme.enzymeml.core.protein.Protein method) getUnit() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) (pyenzyme.enzymeml.core.vessel.Vessel method) (pyenzyme.enzymeml.tools.unitcreator.UnitCreator method) getUnitDef() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getUnitDict() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getUnits() (pyenzyme.enzymeml.core.unitdef.UnitDef method) getUnitString() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getUrl() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getVersion() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) getVessel() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.core.protein.Protein method) (pyenzyme.enzymeml.core.reactant.Reactant method) given_name (pyenzyme.enzymeml.core.creator.Creator attribute) global_parameters (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) global_time (pyenzyme.enzymeml.core.measurement.Measurement attribute) global_time_unit (pyenzyme.enzymeml.core.measurement.Measurement attribute)

I

id (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.creator.Creator attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.replicate.Replicate attribute) (pyenzyme.enzymeml.core.unitdef.UnitDef attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) in_ipynb() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument static method) inchi (pyenzyme.enzymeml.core.reactant.Reactant attribute) INHIBITOR (pyenzyme.enzymeml.core.ontology.SBOTerm attribute)

init_conc (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) initial_value (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) INTERACTOR (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) ION (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) IONISATION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) is_calculated (pyenzyme.enzymeml.core.replicate.Replicate attribute) is_global (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) ISOMERISATION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute)

J

json() (pyenzyme.enzymeml.core.enzymemlbase.EnzymeMLBase method)

K

K_CAT (pyenzyme.enzymeml.core.ontology.SBOTerm attribute)

K_M (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) kind (pyenzyme.enzymeml.core.unitdef.BaseUnit attribute)

L

level (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute)

log (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) lower (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute)

M

MACROMOLECULAR_COMPLEX (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) mail (pyenzyme.enzymeml.core.creator.Creator attribute) measurement_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) measurement_id (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) (pyenzyme.enzymeml.core.replicate.Replicate attribute) MeasurementDataSpeciesIdentifierError meta_id (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.unitdef.UnitDef attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) MICHAELIS_MENTEN (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) MichaelisMentenKCat() (in module pyenzyme.enzymeml.models.michaelismenten) MichaelisMentenVMax() (in module pyenzyme.enzymeml.models.michaelismenten) model (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) ModelFactory (class in pyenzyme.enzymeml.models.kineticmodel) modified (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) modifiers (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) module pyenzyme pyenzyme.enzymeml pyenzyme.enzymeml.core pyenzyme.enzymeml.core.abstract_classes pyenzyme.enzymeml.core.complex pyenzyme.enzymeml.core.creator pyenzyme.enzymeml.core.enzymemlbase pyenzyme.enzymeml.core.enzymemldocument pyenzyme.enzymeml.core.enzymereaction pyenzyme.enzymeml.core.exceptions pyenzyme.enzymeml.core.measurement pyenzyme.enzymeml.core.measurementData pyenzyme.enzymeml.core.ontology pyenzyme.enzymeml.core.protein pyenzyme.enzymeml.core.reactant pyenzyme.enzymeml.core.replicate pyenzyme.enzymeml.core.unitdef pyenzyme.enzymeml.core.utils pyenzyme.enzymeml.core.vessel pyenzyme.enzymeml.models pyenzyme.enzymeml.models.kineticmodel pyenzyme.enzymeml.models.michaelismenten pyenzyme.enzymeml.tools pyenzyme.enzymeml.tools.enzymemlreader pyenzyme.enzymeml.tools.enzymemlwriter pyenzyme.enzymeml.tools.unitcreator pyenzyme.enzymeml.tools.unitparser

multiplier (pyenzyme.enzymeml.core.unitdef.BaseUnit attribute)

N

name (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.unitdef.UnitDef attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticModel attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) (pyenzyme.enzymeml.models.kineticmodel.ModelFactory attribute)

NON_COVALENT_BINDING (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) NON_ESSENTIAL_ACTIVATOR (pyenzyme.enzymeml.core.ontology.SBOTerm attribute)

O

ontology (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.enzymereaction.ReactionElement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.unitdef.UnitDef attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticModel attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute)

organism (pyenzyme.enzymeml.core.protein.Protein attribute) organism_tax_id (pyenzyme.enzymeml.core.protein.Protein attribute)

P

parameters (pyenzyme.enzymeml.models.kineticmodel.KineticModel attribute) (pyenzyme.enzymeml.models.kineticmodel.ModelFactory attribute) parse() (pyenzyme.enzymeml.tools.unitparser.UnitParser method) parse_equation() (pyenzyme.enzymeml.models.kineticmodel.ModelFactory static method) partFromSBOTerm() (pyenzyme.enzymeml.core.ontology.EnzymeMLPart class method) ParticipantIdentifierError participants (pyenzyme.enzymeml.core.complex.Complex attribute) PEAK_AREA (pyenzyme.enzymeml.core.ontology.DataTypes attribute) ph (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) POTENTIATOR (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) printDocument() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) printMeasurements() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) printMeasurementScheme() (pyenzyme.enzymeml.core.measurement.Measurement method) printReactionSchemes() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) PRODUCT (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) products (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) PROTEIN (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) PROTEIN_COMPLEX (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) protein_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) protein_id (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) ProteinFactory (class in pyenzyme.enzymeml.tools.enzymemlreader) pubmedid (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) pyenzyme module pyenzyme.enzymeml module pyenzyme.enzymeml.core module pyenzyme.enzymeml.core.abstract_classes module pyenzyme.enzymeml.core.complex module pyenzyme.enzymeml.core.creator module pyenzyme.enzymeml.core.enzymemlbase module

pyenzyme.enzymeml.core.enzymemldocument module pyenzyme.enzymeml.core.enzymereaction module pyenzyme.enzymeml.core.exceptions module pyenzyme.enzymeml.core.measurement module pyenzyme.enzymeml.core.measurementData module pyenzyme.enzymeml.core.ontology module pyenzyme.enzymeml.core.protein module pyenzyme.enzymeml.core.reactant module pyenzyme.enzymeml.core.replicate module pyenzyme.enzymeml.core.unitdef module pyenzyme.enzymeml.core.utils module pyenzyme.enzymeml.core.vessel module pyenzyme.enzymeml.models module pyenzyme.enzymeml.models.kineticmodel module pyenzyme.enzymeml.models.michaelismenten module pyenzyme.enzymeml.tools module pyenzyme.enzymeml.tools.enzymemlreader module pyenzyme.enzymeml.tools.enzymemlwriter module pyenzyme.enzymeml.tools.unitcreator module pyenzyme.enzymeml.tools.unitparser module

R

RADICAL (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) reactant_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) reactant_id (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) ReactantFactory (class in pyenzyme.enzymeml.tools.enzymemlreader)

reaction_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) readFromFile() (pyenzyme.enzymeml.tools.enzymemlreader.EnzymeMLReader method) REDOX_REACTION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) replicates (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) reversible (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute)

S

SBOTerm (class in pyenzyme.enzymeml.core.ontology) scale (pyenzyme.enzymeml.core.unitdef.BaseUnit attribute) sequence (pyenzyme.enzymeml.core.protein.Protein attribute) set_kinetic_model() (pyenzyme.enzymeml.core.enzymemlbase.EnzymeMLBase static method) set_meta_id() (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies class method) (pyenzyme.enzymeml.core.complex.Complex class method) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction class method) (pyenzyme.enzymeml.core.protein.Protein class method) (pyenzyme.enzymeml.core.unitdef.UnitDef class method) (pyenzyme.enzymeml.core.vessel.Vessel class method) setMeasurementIDs() (pyenzyme.enzymeml.core.measurementData.MeasurementData method) setModel() (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) setupXMLNode() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method)

SMALL_MOLECULE (pyenzyme.enzymeml.core.ontology.EnzymeMLPart attribute) (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) smiles (pyenzyme.enzymeml.core.reactant.Reactant attribute) species_dict (pyenzyme.enzymeml.core.measurement.Measurement attribute) species_factory_mapping() (in module pyenzyme.enzymeml.tools.enzymemlreader) species_id (pyenzyme.enzymeml.core.enzymereaction.ReactionElement attribute) (pyenzyme.enzymeml.core.replicate.Replicate attribute) SpeciesNotFoundError SPONTANEOUS_REACTION (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) start_logger() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument class method) stdev (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) stoichiometry (pyenzyme.enzymeml.core.enzymereaction.ReactionElement attribute) SUBSTRATE (pyenzyme.enzymeml.core.ontology.SBOTerm attribute)

T

temperature (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) temperature_unit (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) temperature_unitdef() (pyenzyme.enzymeml.core.measurement.Measurement method) time (pyenzyme.enzymeml.core.replicate.Replicate attribute) time_unit (pyenzyme.enzymeml.core.replicate.Replicate attribute)

time_unitdef() (pyenzyme.enzymeml.core.replicate.Replicate method) toDataFrame() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) toFile() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) toSBML() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) toXMLString() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) type_checking() (in module pyenzyme.enzymeml.core.utils)

U

unifyMeasurementUnits() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) unifyUnits() (pyenzyme.enzymeml.core.measurement.Measurement method) (pyenzyme.enzymeml.core.measurementData.MeasurementData method) uniprotid (pyenzyme.enzymeml.core.protein.Protein attribute) UniProtIdentifierError unit (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.measurementData.MeasurementData attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) UnitCreator (class in pyenzyme.enzymeml.tools.unitcreator) unitdef() (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies method) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction method) (pyenzyme.enzymeml.core.measurementData.MeasurementData method) (pyenzyme.enzymeml.core.vessel.Vessel method) (pyenzyme.enzymeml.models.kineticmodel.KineticParameter method)

UnitParser (class in pyenzyme.enzymeml.tools.unitparser) units (pyenzyme.enzymeml.core.unitdef.UnitDef attribute) update() (pyenzyme.enzymeml.models.kineticmodel.KineticParameter method) updateReplicates() (pyenzyme.enzymeml.core.measurement.Measurement method) uploadToDataverse() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) upper (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) uri (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction attribute) (pyenzyme.enzymeml.core.measurement.Measurement attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute) (pyenzyme.enzymeml.core.replicate.Replicate attribute) (pyenzyme.enzymeml.core.vessel.Vessel attribute) url (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute)

V

V_MAX (pyenzyme.enzymeml.core.ontology.SBOTerm attribute) validateDocument() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) value (pyenzyme.enzymeml.models.kineticmodel.KineticParameter attribute) version (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) vessel_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument attribute) vessel_id (pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies attribute) (pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass attribute) (pyenzyme.enzymeml.core.complex.Complex attribute) (pyenzyme.enzymeml.core.protein.Protein attribute) (pyenzyme.enzymeml.core.reactant.Reactant attribute)

visualize() (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument method) volume (pyenzyme.enzymeml.core.vessel.Vessel attribute)

W

writeElements() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) writeMeasurementData() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method)

writeReplicateData() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method) writeTimeData() (pyenzyme.enzymeml.tools.enzymemlwriter.EnzymeMLWriter method)