PyEnzyme
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Core layer
PyEnzyme
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Index
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B
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C
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D
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E
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F
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G
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I
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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)
add_object() (in module pyenzyme.enzymeml.databases.dataverse)
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.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)
create_citation_metadatablock() (in module pyenzyme.enzymeml.databases.dataverse)
create_enzymeml_metadatablock() (in module pyenzyme.enzymeml.databases.dataverse)
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_fit_parameters() (pyenzyme.thinlayers.TL_Copasi.ThinLayerCopasi 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)
kinetic_law_params() (in module pyenzyme.enzymeml.databases.dataverse)
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.databases
pyenzyme.enzymeml.databases.dataverse
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
pyenzyme.thinlayers
pyenzyme.thinlayers.TL_Copasi
pyenzyme.thinlayers.TL_Pysces
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)
optimize() (pyenzyme.thinlayers.TL_Copasi.ThinLayerCopasi method)
(pyenzyme.thinlayers.TL_Pysces.ThinLayerPysces method)
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)
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.databases
module
pyenzyme.enzymeml.databases.dataverse
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
pyenzyme.thinlayers
module
pyenzyme.thinlayers.TL_Copasi
module
pyenzyme.thinlayers.TL_Pysces
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_fit_parameters() (pyenzyme.thinlayers.TL_Copasi.ThinLayerCopasi 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)
ThinLayerCopasi (class in pyenzyme.thinlayers.TL_Copasi)
ThinLayerPysces (class in pyenzyme.thinlayers.TL_Pysces)
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)
unit_dict (pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument 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() (in module pyenzyme.enzymeml.databases.dataverse)
(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)
validate() (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
write() (pyenzyme.thinlayers.TL_Copasi.ThinLayerCopasi method)
(pyenzyme.thinlayers.TL_Pysces.ThinLayerPysces method)
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)
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