pyenzyme.enzymeml.core package#
Submodules#
- Abstract Classes
AbstractSpeciesAbstractSpecies.boundaryAbstractSpecies.constantAbstractSpecies.creator_idAbstractSpecies.idAbstractSpecies.init_concAbstractSpecies.meta_idAbstractSpecies.nameAbstractSpecies.ontologyAbstractSpecies.unitAbstractSpecies.uriAbstractSpecies.vessel_idAbstractSpecies.set_meta_idAbstractSpecies.unitdef()
AbstractSpeciesDataclassAbstractSpeciesDataclass.boundaryAbstractSpeciesDataclass.constantAbstractSpeciesDataclass.creator_idAbstractSpeciesDataclass.idAbstractSpeciesDataclass.init_concAbstractSpeciesDataclass.meta_idAbstractSpeciesDataclass.nameAbstractSpeciesDataclass.ontologyAbstractSpeciesDataclass.unitAbstractSpeciesDataclass.uriAbstractSpeciesDataclass.vessel_id
AbstractSpeciesFactory
- Creator
- EnzymeML Base Class
- EnzymeMLDocument
EnzymeMLDocumentEnzymeMLDocument.complex_dictEnzymeMLDocument.createdEnzymeMLDocument.creator_dictEnzymeMLDocument.doiEnzymeMLDocument.file_dictEnzymeMLDocument.global_parametersEnzymeMLDocument.levelEnzymeMLDocument.logEnzymeMLDocument.measurement_dictEnzymeMLDocument.modifiedEnzymeMLDocument.nameEnzymeMLDocument.protein_dictEnzymeMLDocument.pubmedidEnzymeMLDocument.reactant_dictEnzymeMLDocument.reaction_dictEnzymeMLDocument.urlEnzymeMLDocument.versionEnzymeMLDocument.vessel_dictEnzymeMLDocument.addComplex()EnzymeMLDocument.addCreator()EnzymeMLDocument.addFile()EnzymeMLDocument.addGlobalParameter()EnzymeMLDocument.addMeasurement()EnzymeMLDocument.addProtein()EnzymeMLDocument.addReactant()EnzymeMLDocument.addReaction()EnzymeMLDocument.addReactions()EnzymeMLDocument.addVessel()EnzymeMLDocument.add_identifierEnzymeMLDocument.applyModelInitialization()EnzymeMLDocument.checkUnitConsistency()EnzymeMLDocument.exportKineticParameters()EnzymeMLDocument.exportMeasurementData()EnzymeMLDocument.fromFile()EnzymeMLDocument.fromJSON()EnzymeMLDocument.fromTemplate()EnzymeMLDocument.generateInitialValueTemplate()EnzymeMLDocument.getAny()EnzymeMLDocument.getCreator()EnzymeMLDocument.getDoi()EnzymeMLDocument.getFile()EnzymeMLDocument.getFileDict()EnzymeMLDocument.getFilesList()EnzymeMLDocument.getLevel()EnzymeMLDocument.getMeasurement()EnzymeMLDocument.getMeasurementDict()EnzymeMLDocument.getModified()EnzymeMLDocument.getName()EnzymeMLDocument.getProtein()EnzymeMLDocument.getProteinDict()EnzymeMLDocument.getProteinList()EnzymeMLDocument.getPubmedID()EnzymeMLDocument.getReactant()EnzymeMLDocument.getReactantDict()EnzymeMLDocument.getReactantList()EnzymeMLDocument.getReaction()EnzymeMLDocument.getReactionDict()EnzymeMLDocument.getReactionList()EnzymeMLDocument.getSpeciesIDs()EnzymeMLDocument.getUnitDef()EnzymeMLDocument.getUnitDict()EnzymeMLDocument.getUnitString()EnzymeMLDocument.getUrl()EnzymeMLDocument.getVersion()EnzymeMLDocument.getVessel()EnzymeMLDocument.get_created()EnzymeMLDocument.in_ipynb()EnzymeMLDocument.printDocument()EnzymeMLDocument.printMeasurements()EnzymeMLDocument.printReactionSchemes()EnzymeMLDocument.start_loggerEnzymeMLDocument.toDataFrame()EnzymeMLDocument.toFile()EnzymeMLDocument.toXMLString()EnzymeMLDocument.unifyMeasurementUnits()EnzymeMLDocument.uploadToDataverse()EnzymeMLDocument.validateDocument()EnzymeMLDocument.visualize()
- EnzymeReaction
EnzymeReactionEnzymeReaction.creator_idEnzymeReaction.eductsEnzymeReaction.idEnzymeReaction.meta_idEnzymeReaction.modelEnzymeReaction.modifiersEnzymeReaction.nameEnzymeReaction.ontologyEnzymeReaction.phEnzymeReaction.productsEnzymeReaction.reversibleEnzymeReaction.temperatureEnzymeReaction.temperature_unitEnzymeReaction.uriEnzymeReaction.addEduct()EnzymeReaction.addModifier()EnzymeReaction.addProduct()EnzymeReaction.apply_initial_values()EnzymeReaction.convert_temperature_unitEnzymeReaction.fromEquation()EnzymeReaction.getEduct()EnzymeReaction.getEducts()EnzymeReaction.getId()EnzymeReaction.getMetaid()EnzymeReaction.getModel()EnzymeReaction.getModifier()EnzymeReaction.getModifiers()EnzymeReaction.getName()EnzymeReaction.getPh()EnzymeReaction.getProduct()EnzymeReaction.getProducts()EnzymeReaction.getReversible()EnzymeReaction.getStoichiometricCoefficients()EnzymeReaction.getTemperature()EnzymeReaction.getTempunit()EnzymeReaction.get_reaction_scheme()EnzymeReaction.setModel()EnzymeReaction.set_meta_idEnzymeReaction.unitdef()
ReactionElement
- Exceptions
- Measurement
MeasurementMeasurement.creator_idMeasurement.global_timeMeasurement.global_time_unitMeasurement.idMeasurement.nameMeasurement.phMeasurement.species_dictMeasurement.temperatureMeasurement.temperature_unitMeasurement.uriMeasurement.addData()Measurement.addReplicates()Measurement.convert_temperature_unitMeasurement.exportData()Measurement.getGlobalTime()Measurement.getGlobalTimeUnit()Measurement.getId()Measurement.getName()Measurement.getProtein()Measurement.getProteins()Measurement.getReactant()Measurement.getReactants()Measurement.getSpeciesDict()Measurement.printMeasurementScheme()Measurement.temperature_unitdef()Measurement.unifyUnits()Measurement.updateReplicates()
- MeasurementData
MeasurementDataMeasurementData.init_concMeasurementData.measurement_idMeasurementData.protein_idMeasurementData.reactant_idMeasurementData.replicatesMeasurementData.unitMeasurementData.addReplicate()MeasurementData.check_id_occurencesMeasurementData.getInitConc()MeasurementData.getProteinID()MeasurementData.getReactantID()MeasurementData.getReplicates()MeasurementData.getUnit()MeasurementData.get_id()MeasurementData.setMeasurementIDs()MeasurementData.unifyUnits()MeasurementData.unitdef()
- Ontology
DataTypesEnzymeMLPartSBOTermSBOTerm.ACID_BASE_REACTIONSBOTerm.BIOCHEMICAL_REACTIONSBOTerm.CATALYSTSBOTerm.CONFORMATIONAL_TRANSITIONSBOTerm.CONVERSIONSBOTerm.DEGRADATIONSBOTerm.DIMERSBOTerm.DISSOCIATIONSBOTerm.ESSENTIAL_ACTIVATORSBOTerm.GENESBOTerm.INHIBITORSBOTerm.INTERACTORSBOTerm.IONSBOTerm.IONISATIONSBOTerm.ISOMERISATIONSBOTerm.K_CATSBOTerm.K_MSBOTerm.MACROMOLECULAR_COMPLEXSBOTerm.MICHAELIS_MENTENSBOTerm.NON_COVALENT_BINDINGSBOTerm.NON_ESSENTIAL_ACTIVATORSBOTerm.POTENTIATORSBOTerm.PRODUCTSBOTerm.PROTEINSBOTerm.PROTEIN_COMPLEXSBOTerm.RADICALSBOTerm.REDOX_REACTIONSBOTerm.SMALL_MOLECULESBOTerm.SPONTANEOUS_REACTIONSBOTerm.SUBSTRATESBOTerm.V_MAX
- Protein
ProteinProtein.boundaryProtein.constantProtein.creator_idProtein.ecnumberProtein.idProtein.init_concProtein.meta_idProtein.nameProtein.ontologyProtein.organismProtein.organism_tax_idProtein.sequenceProtein.uniprotidProtein.unitProtein.uriProtein.vessel_idProtein.clean_sequenceProtein.fromUniProtID()Protein.getBoundary()Protein.getConstant()Protein.getEcnumber()Protein.getId()Protein.getInitConc()Protein.getMetaid()Protein.getName()Protein.getOrganism()Protein.getOrganismTaxId()Protein.getSboterm()Protein.getSequence()Protein.getSubstanceUnits()Protein.getUniprotID()Protein.getVessel()Protein.set_meta_id
- Reactant
ReactantReactant.boundaryReactant.chebi_idReactant.constantReactant.creator_idReactant.idReactant.inchiReactant.init_concReactant.meta_idReactant.nameReactant.ontologyReactant.smilesReactant.unitReactant.uriReactant.vessel_idReactant.fromChebiID()Reactant.getBoundary()Reactant.getConstant()Reactant.getId()Reactant.getInchi()Reactant.getInitConc()Reactant.getMetaid()Reactant.getName()Reactant.getSboterm()Reactant.getSmiles()Reactant.getSubstanceUnits()Reactant.getVessel()
- Replicate
ReplicateReplicate.creator_idReplicate.dataReplicate.data_typeReplicate.data_unitReplicate.idReplicate.is_calculatedReplicate.measurement_idReplicate.species_idReplicate.timeReplicate.time_unitReplicate.uriReplicate.check_data_completenessReplicate.data_unitdef()Replicate.getData()Replicate.getDataUnit()Replicate.getIsCalculated()Replicate.getMeasurement()Replicate.getReactant()Replicate.getReplica()Replicate.getTimeUnit()Replicate.getType()Replicate.time_unitdef()
- Unit Definition
- Utils
- Vessel