EnzymeMLDocument
- pydantic model pyenzyme.enzymeml.core.enzymemldocument.EnzymeMLDocument[source]
Bases:
pyenzyme.enzymeml.core.enzymemlbase.EnzymeMLBase
Show JSON schema
{ "title": "EnzymeMLDocument", "type": "object", "properties": { "name": { "title": "Name", "description": "Title of the EnzymeML Document.", "type": "string" }, "level": { "title": "Level", "description": "SBML evel of the EnzymeML XML.", "default": 3, "inclusiveMinimum": 1, "inclusiveMaximum": 3, "type": "integer" }, "version": { "title": "Version", "description": "SBML version of the EnzymeML XML.", "default": 2, "type": "integer" }, "pubmedid": { "title": "Pubmedid", "description": "Pubmed ID reference.", "type": "string" }, "url": { "title": "Url", "description": "Arbitrary type of URL that is related to the EnzymeML document.", "type": "string" }, "doi": { "title": "Doi", "description": "Digital Object Identifier of the referenced publication or the EnzymeML document.", "type": "string" }, "created": { "title": "Created", "description": "Date the EnzymeML document was created.", "type": "string" }, "modified": { "title": "Modified", "description": "Date the EnzymeML document was modified.", "type": "string" }, "creators": { "title": "Creators", "description": "Dictionary mapping from creator IDs to creator describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Creator" } }, "vessels": { "title": "Vessels", "description": "Dictionary mapping from vessel IDs to vessel describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Vessel" } }, "proteins": { "title": "Proteins", "description": "Dictionary mapping from protein IDs to protein describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Protein" } }, "complexes": { "title": "Complexes", "description": "Dictionary mapping from complex IDs to complex describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Complex" } }, "reactants": { "title": "Reactants", "description": "Dictionary mapping from reactant IDs to reactant describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Reactant" } }, "reactions": { "title": "Reactions", "description": "Dictionary mapping from reaction IDs to reaction describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/EnzymeReaction" } }, "units": { "title": "Units", "description": "Dictionary mapping from unit IDs to unit describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/UnitDef" } }, "measurements": { "title": "Measurements", "description": "Dictionary mapping from measurement IDs to measurement describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/Measurement" } }, "files": { "title": "Files", "description": "Dictionary mapping from protein IDs to protein describing objects.", "type": "object", "additionalProperties": { "type": "object" } }, "global_parameters": { "title": "Global Parameters", "description": "Dictionary mapping from parameter IDs to global kinetic parameter describing objects.", "type": "object", "additionalProperties": { "$ref": "#/definitions/KineticParameter" } }, "log": { "title": "Log", "default": "", "type": "string" } }, "required": [ "name" ], "definitions": { "Creator": { "title": "Creator", "type": "object", "properties": { "given_name": { "title": "Given Name", "description": "Given name of the author or contributor.", "type": "string" }, "family_name": { "title": "Family Name", "description": "Family name of the author or contributor.", "type": "string" }, "mail": { "title": "Mail", "description": "Email address of the author or contributor.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the protein.", "pattern": "a[\\d]+", "type": "string" } }, "required": [ "given_name", "family_name", "mail" ] }, "Vessel": { "title": "Vessel", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the used vessel.", "template_alias": "Name", "type": "string" }, "volume": { "title": "Volume", "description": "Volumetric value of the vessel.", "template_alias": "Volume value", "exclusiveMinimum": 0, "type": "number" }, "unit": { "title": "Unit", "description": "Volumetric unit of the vessel.", "template_alias": "Volume unit", "type": "string" }, "constant": { "title": "Constant", "description": "Whether the volume of the vessel is constant or not.", "default": true, "type": "boolean" }, "meta_id": { "title": "Meta Id", "description": "Unique meta identifier of the vessel.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the vessel.", "pattern": "v[\\d]+", "template_alias": "ID", "type": "string" }, "uri": { "title": "Uri", "description": "URI of the vessel.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" } }, "required": [ "name" ] }, "SBOTerm": { "title": "SBOTerm", "description": "String enumeration used to assign ontologies derived from SBOTerms.", "enum": [ "SBO:0000176", "SBO:0000208", "SBO:0000181", "SBO:0000182", "SBO:0000179", "SBO:0000180", "SBO:0000209", "SBO:0000377", "SBO:0000177", "SBO:0000200", "SBO:0000672", "SBO:0000252", "SBO:0000251", "SBO:0000247", "SBO:0000327", "SBO:0000328", "SBO:0000336", "SBO:0000015", "SBO:0000011", "SBO:0000013", "SBO:0000020", "SBO:0000461", "SBO:0000462", "SBO:0000021", "SBO:0000296", "SBO:0000297", "SBO:0000607", "SBO:0000028", "SBO:0000025", "SBO:0000027", "SBO:0000186" ], "type": "string" }, "Protein": { "title": "Protein", "description": "Due to inheritance and type-checking issues, the dataclass has to be mixed in.", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the protein", "template_alias": "Name", "type": "string" }, "meta_id": { "title": "Meta Id", "description": "Unique meta identifier of the protein.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the protein.", "pattern": "p[\\d]+", "template_alias": "ID", "type": "string" }, "vessel_id": { "title": "Vessel Id", "description": "Identifier of the vessel in which the protein was stored.", "pattern": "v[\\d.]+", "template_alias": "Vessel", "type": "string" }, "init_conc": { "title": "Init Conc", "description": "Initial concentration of the protein.", "type": "number" }, "constant": { "title": "Constant", "description": "Whether the proteins concentration remains constant or not.", "default": true, "template_alias": "Constant", "type": "boolean" }, "boundary": { "title": "Boundary", "description": "Whether the protein is under any boundary conditions (SBML Technicality, better leave it to default)", "default": false, "type": "boolean" }, "unit": { "title": "Unit", "description": "Unit of the proteins intial concentration.", "type": "string" }, "ontology": { "description": "Ontology describing the characteristic of the protein.", "default": "SBO:0000252", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] }, "uri": { "title": "Uri", "description": "URI of the protein.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" }, "sequence": { "title": "Sequence", "description": "Amino acid sequence of the protein", "template_alias": "Sequence", "type": "string" }, "ecnumber": { "title": "Ecnumber", "description": "EC number of the protein.", "pattern": "(\\d+.)(\\d+.)(\\d+.)(\\d+)", "template_alias": "EC Number", "type": "string" }, "organism": { "title": "Organism", "description": "Organism the protein was expressed in.", "template_alias": "Source organism", "type": "string" }, "organism_tax_id": { "title": "Organism Tax Id", "description": "Taxonomy identifier of the expression host.", "type": "string" }, "uniprotid": { "title": "Uniprotid", "description": "Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database.", "template_alias": "UniProt ID", "type": "string" } }, "required": [ "vessel_id" ] }, "Complex": { "title": "Complex", "description": "Due to inheritance and type-checking issues, the dataclass has to be mixed in.", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the complex", "type": "string" }, "meta_id": { "title": "Meta Id", "description": "Unique meta identifier of the protein.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the protein.", "pattern": "c[\\d]+", "type": "string" }, "vessel_id": { "title": "Vessel Id", "description": "Identifier of the vessel in which the protein was stored.", "pattern": "v[\\d]+", "type": "string" }, "init_conc": { "title": "Init Conc", "description": "Initial concentration of the protein.", "inclusiveMinimum": 0.0, "type": "number" }, "constant": { "title": "Constant", "description": "Whether the proteins concentration remains constant or not.", "default": false, "type": "boolean" }, "boundary": { "title": "Boundary", "description": "Whether the protein is under any boundary conditions (SBML Technicality, better leave it to default)", "default": false, "type": "boolean" }, "unit": { "title": "Unit", "description": "Unit of the proteins intial concentration.", "type": "string" }, "ontology": { "description": "Ontology describing the characteristic of the protein.", "default": "SBO:0000296", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] }, "uri": { "title": "Uri", "description": "URI of the protein.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" }, "participants": { "title": "Participants", "description": "Array of IDs the complex contains", "type": "array", "items": { "type": "string" } } }, "required": [ "name", "vessel_id" ] }, "Reactant": { "title": "Reactant", "description": "Due to inheritance and type-checking issues, the dataclass has to be mixed in.", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the reactant.", "template_alias": "Name", "type": "string" }, "meta_id": { "title": "Meta Id", "description": "Unique meta identifier of the protein.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the protein.", "pattern": "s[\\d]+", "template_alias": "ID", "type": "string" }, "vessel_id": { "title": "Vessel Id", "description": "Identifier of the vessel in which the reactant was stored.", "template_alias": "Vessel", "type": "string" }, "init_conc": { "title": "Init Conc", "description": "Initial concentration of the reactant.", "type": "number" }, "constant": { "title": "Constant", "description": "Whether the reactants concentration remains constant or not.", "default": false, "template_alias": "Constant", "type": "boolean" }, "boundary": { "title": "Boundary", "description": "Whether the reactant is under any boundary conditions (SBML Technicality, better leave it to default)", "default": false, "type": "boolean" }, "unit": { "title": "Unit", "description": "Unit of the reactant intial concentration.", "type": "string" }, "ontology": { "description": "Ontology describing the characteristic of the reactant.", "default": "SBO:0000247", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] }, "uri": { "title": "Uri", "description": "URI of the protein.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" }, "smiles": { "title": "Smiles", "description": "Simplified Molecular Input Line Entry System (SMILES) encoding of the reactant.", "template_alias": "SMILES", "type": "string" }, "inchi": { "title": "Inchi", "description": "International Chemical Identifier (InChI) encoding of the reactant.", "template_alias": "InCHI", "type": "string" }, "chebi_id": { "title": "Chebi Id", "description": "Unique identifier of the CHEBI database. Use this identifier to initialize the object from the CHEBI database.", "type": "string" } }, "required": [ "vessel_id" ] }, "KineticParameter": { "title": "KineticParameter", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the estimated parameter.", "type": "string" }, "value": { "title": "Value", "description": "Numerical value of the estimated parameter.", "type": "number" }, "unit": { "title": "Unit", "description": "Unit of the estimated parameter.", "type": "string" }, "initial_value": { "title": "Initial Value", "description": "Initial value that was used for the parameter estimation.", "type": "number" }, "upper": { "title": "Upper", "description": "Upper bound of the estimated parameter.", "type": "number" }, "lower": { "title": "Lower", "description": "Lower bound of the estimated parameter.", "type": "number" }, "is_global": { "title": "Is Global", "description": "Specifies if this parameter is a global parameter.", "default": false, "type": "boolean" }, "stdev": { "title": "Stdev", "description": "Standard deviation of the estimated parameter.", "type": "number" }, "constant": { "title": "Constant", "description": "Specifies if this parameter is constant", "default": false, "type": "boolean" }, "ontology": { "description": "Type of the estimated parameter.", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] } }, "required": [ "name" ] }, "KineticModel": { "title": "KineticModel", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the kinetic law.", "type": "string" }, "equation": { "title": "Equation", "description": "Equation for the kinetic law.", "type": "string" }, "parameters": { "title": "Parameters", "description": "List of estimated parameters.", "type": "array", "items": { "$ref": "#/definitions/KineticParameter" } }, "ontology": { "description": "Type of the estimated parameter.", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] } }, "required": [ "name", "equation" ] }, "ReactionElement": { "title": "ReactionElement", "description": "Describes an element of a chemical reaction.", "type": "object", "properties": { "species_id": { "title": "Species Id", "description": "Internal identifier to either a protein or reactant defined in the EnzymeMLDocument.", "type": "string" }, "stoichiometry": { "title": "Stoichiometry", "description": "Positive float number representing the associated stoichiometry.", "exclusiveMinimum": 0, "type": "number" }, "constant": { "title": "Constant", "description": "Whether or not the concentration of this species remains constant.", "type": "boolean" }, "ontology": { "description": "Ontology defining the role of the given species.", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] } }, "required": [ "species_id", "stoichiometry", "constant", "ontology" ] }, "EnzymeReaction": { "title": "EnzymeReaction", "description": "Describes an enzyme reaction by combining already defined\nreactants/proteins of an EnzymeML document. In addition,\nthis class provides ways to integrate reaction conditions\nas well. It is also possible to add a kinetic law to this\nobject by using the KineticModel class.", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the reaction.", "template_alias": "Name", "type": "string" }, "reversible": { "title": "Reversible", "description": "Whether the reaction is reversible or irreversible", "template_alias": "Reversible", "type": "boolean" }, "temperature": { "title": "Temperature", "description": "Numeric value of the temperature of the reaction.", "template_alias": "Temperature value", "type": "number" }, "temperature_unit": { "title": "Temperature Unit", "description": "Unit of the temperature of the reaction.", "pattern": "kelvin|Kelvin|k|K|celsius|Celsius|C|c", "template_alias": "Temperature unit", "type": "string" }, "ph": { "title": "Ph", "description": "PH value of the reaction.", "template_alias": "pH value", "inclusiveMinimum": 0, "inclusiveMaximum": 14, "type": "number" }, "ontology": { "description": "Ontology defining the role of the given species.", "default": "SBO:0000176", "allOf": [ { "$ref": "#/definitions/SBOTerm" } ] }, "meta_id": { "title": "Meta Id", "description": "Unique meta identifier for the reaction.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the reaction.", "pattern": "r[\\d]+", "template_alias": "ID", "type": "string" }, "uri": { "title": "Uri", "description": "URI of the reaction.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" }, "model": { "title": "Model", "description": "Kinetic model decribing the reaction.", "allOf": [ { "$ref": "#/definitions/KineticModel" } ] }, "educts": { "title": "Educts", "description": "List of educts containing ReactionElement objects.", "template_alias": "Educts", "type": "array", "items": { "$ref": "#/definitions/ReactionElement" } }, "products": { "title": "Products", "description": "List of products containing ReactionElement objects.", "template_alias": "Products", "type": "array", "items": { "$ref": "#/definitions/ReactionElement" } }, "modifiers": { "title": "Modifiers", "description": "List of modifiers (Proteins, snhibitors, stimulators) containing ReactionElement objects.", "template_alias": "Modifiers", "type": "array", "items": { "$ref": "#/definitions/ReactionElement" } } }, "required": [ "name", "reversible" ] }, "BaseUnit": { "title": "BaseUnit", "description": "Base unit description including kind, exponent, scale and multiplier", "type": "object", "properties": { "kind": { "title": "Kind", "description": "Unit kind used to write SBML.", "type": "string" }, "exponent": { "title": "Exponent", "description": "Unit exponent.", "type": "number" }, "scale": { "title": "Scale", "description": "Unit scale.", "type": "integer" }, "multiplier": { "title": "Multiplier", "description": "Unit multiplier.", "type": "number" } }, "required": [ "kind", "exponent", "scale", "multiplier" ] }, "UnitDef": { "title": "UnitDef", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the SI unit.", "type": "string" }, "id": { "title": "Id", "description": "Interal Identifier of the SI unit.", "type": "string" }, "meta_id": { "title": "Meta Id", "description": "Interal meta identifier of the SI unit.", "type": "string" }, "units": { "title": "Units", "description": "List of SI baseunits.", "type": "array", "items": { "$ref": "#/definitions/BaseUnit" } }, "ontology": { "title": "Ontology", "description": "Ontology of the SI unit.", "type": "string" } } }, "DataTypes": { "title": "DataTypes", "description": "String enumeration used to assign replicate type ontologies", "enum": [ "conc", "abs", "feed", "biomass" ], "type": "string" }, "Replicate": { "title": "Replicate", "type": "object", "properties": { "id": { "title": "Id", "description": "Unique identifier of the replicate", "type": "string" }, "species_id": { "title": "Species Id", "description": "Unique identifier of the species that has been measured.", "pattern": "[s|r|p][\\d]+", "type": "string" }, "measurement_id": { "title": "Measurement Id", "description": "Unique identifier of the measurement that the replicate is part of.", "pattern": "m[\\d]+", "type": "string" }, "data_type": { "description": "Type of data that was measured (e.g. concentration)", "default": "conc", "allOf": [ { "$ref": "#/definitions/DataTypes" } ] }, "data_unit": { "title": "Data Unit", "description": "SI unit of the data that was measured.", "type": "string" }, "time_unit": { "title": "Time Unit", "description": "Time unit of the replicate.", "type": "string" }, "time": { "title": "Time", "description": "Time steps of the replicate.", "type": "array", "items": { "type": "number" } }, "data": { "title": "Data", "description": "Data that was measured.", "type": "array", "items": { "type": "number" } }, "is_calculated": { "title": "Is Calculated", "description": "Whether or not the data has been generated by simulation.", "default": false, "type": "boolean" }, "uri": { "title": "Uri", "description": "URI of the protein.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" } }, "required": [ "id", "species_id", "data_unit", "time_unit" ] }, "MeasurementData": { "title": "MeasurementData", "description": "Helper class to organize elements", "type": "object", "properties": { "init_conc": { "title": "Init Conc", "description": "Initial concentration of the measurement data.", "type": "number" }, "unit": { "title": "Unit", "description": "The unit of the measurement data.", "type": "string" }, "measurement_id": { "title": "Measurement Id", "description": "Unique measurement identifier this dataset belongs to.", "type": "string" }, "reactant_id": { "title": "Reactant Id", "description": "The identifier for the described reactant.", "type": "string" }, "protein_id": { "title": "Protein Id", "description": "The identifier for the described protein.", "type": "string" }, "replicates": { "title": "Replicates", "description": "A list of replicate objects holding raw data of the measurement.", "type": "array", "items": { "$ref": "#/definitions/Replicate" } } }, "required": [ "init_conc", "unit" ] }, "Measurement": { "title": "Measurement", "type": "object", "properties": { "name": { "title": "Name", "description": "Name of the measurement", "type": "string" }, "temperature": { "title": "Temperature", "description": "Numeric value of the temperature of the reaction.", "template_alias": "Temperature value", "type": "number" }, "temperature_unit": { "title": "Temperature Unit", "description": "Unit of the temperature of the reaction.", "pattern": "kelvin|Kelvin|k|K|celsius|Celsius|C|c", "type": "string" }, "ph": { "title": "Ph", "description": "PH value of the reaction.", "inclusiveMinimum": 0, "inclusiveMaximum": 14, "type": "number" }, "species_dict": { "title": "Species Dict", "description": "Species of the measurement.", "default": { "proteins": {}, "reactants": {} }, "type": "object", "additionalProperties": { "type": "object", "additionalProperties": { "$ref": "#/definitions/MeasurementData" } } }, "global_time": { "title": "Global Time", "description": "Global time of the measurement all replicates agree on.", "type": "array", "items": { "type": "number" } }, "global_time_unit": { "title": "Global Time Unit", "description": "Unit of the global time.", "type": "string" }, "id": { "title": "Id", "description": "Unique identifier of the measurement.", "pattern": "m[\\d]+", "type": "string" }, "uri": { "title": "Uri", "description": "URI of the reaction.", "type": "string" }, "creator_id": { "title": "Creator Id", "description": "Unique identifier of the author.", "type": "string" } }, "required": [ "name" ] } } }
- Config
validate_all: bool = True
validate_assignment: bool = True
- Fields
complex_dict (Dict[str, pyenzyme.enzymeml.core.complex.Complex])
creator_dict (Dict[str, pyenzyme.enzymeml.core.creator.Creator])
global_parameters (Dict[str, pyenzyme.enzymeml.models.kineticmodel.KineticParameter])
measurement_dict (Dict[str, pyenzyme.enzymeml.core.measurement.Measurement])
protein_dict (Dict[str, pyenzyme.enzymeml.core.protein.Protein])
reactant_dict (Dict[str, pyenzyme.enzymeml.core.reactant.Reactant])
reaction_dict (Dict[str, pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction])
unit_dict (Dict[str, pyenzyme.enzymeml.core.unitdef.UnitDef])
vessel_dict (Dict[str, pyenzyme.enzymeml.core.vessel.Vessel])
- Validators
- field complex_dict: Dict[str, pyenzyme.enzymeml.core.complex.Complex] [Required] (alias 'complexes')
Dictionary mapping from complex IDs to complex describing objects.
- field created: Optional[str] = None
Date the EnzymeML document was created.
- field creator_dict: Dict[str, pyenzyme.enzymeml.core.creator.Creator] [Required] (alias 'creators')
Dictionary mapping from creator IDs to creator describing objects.
- field doi: Optional[str] = None
Digital Object Identifier of the referenced publication or the EnzymeML document.
- field file_dict: Dict[str, dict] [Required] (alias 'files')
Dictionary mapping from protein IDs to protein describing objects.
- field global_parameters: Dict[str, pyenzyme.enzymeml.models.kineticmodel.KineticParameter] [Required]
Dictionary mapping from parameter IDs to global kinetic parameter describing objects.
- field level: int = 3
SBML evel of the EnzymeML XML.
- Constraints
inclusiveMinimum = 1
inclusiveMaximum = 3
- field log: str = ''
- Validated by
- field measurement_dict: Dict[str, pyenzyme.enzymeml.core.measurement.Measurement] [Required] (alias 'measurements')
Dictionary mapping from measurement IDs to measurement describing objects.
- field modified: Optional[str] = None
Date the EnzymeML document was modified.
- field name: str [Required]
Title of the EnzymeML Document.
- field protein_dict: Dict[str, pyenzyme.enzymeml.core.protein.Protein] [Required] (alias 'proteins')
Dictionary mapping from protein IDs to protein describing objects.
- field pubmedid: Optional[str] = None
Pubmed ID reference.
- Validated by
- field reactant_dict: Dict[str, pyenzyme.enzymeml.core.reactant.Reactant] [Required] (alias 'reactants')
Dictionary mapping from reactant IDs to reactant describing objects.
- field reaction_dict: Dict[str, pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction] [Required] (alias 'reactions')
Dictionary mapping from reaction IDs to reaction describing objects.
- field unit_dict: Dict[str, pyenzyme.enzymeml.core.unitdef.UnitDef] [Required] (alias 'units')
Dictionary mapping from unit IDs to unit describing objects.
- field url: Optional[str] = None
Arbitrary type of URL that is related to the EnzymeML document.
- field version: int = 2
SBML version of the EnzymeML XML.
- field vessel_dict: Dict[str, pyenzyme.enzymeml.core.vessel.Vessel] [Required] (alias 'vessels')
Dictionary mapping from vessel IDs to vessel describing objects.
- addComplex(name: str, participants: List[str], vessel_id: str, init_conc: Optional[float] = None, unit: Optional[str] = None)[source]
- addCreator(creator: pyenzyme.enzymeml.core.creator.Creator, log: bool = True) str [source]
Adds a creator object to the EnzymeML document.
- Parameters
creator (Creator) – Creator object to be added to the document.
- Returns
Unique internal identifier of the creator.
- Return type
str
- addFile(filepath=None, file_handle=None, description='Undefined') str [source]
Adds any arbitrary file to the document. Please note, that if a filepath is given, any file_handle will be ignored.
- Parameters
filepath (str, optional) – Path to the file that is added to the document. Defaults to None.
file_handle (io.BufferedReader, optional) – File handle that will be read to a bytes string. Defaults to None.
- Returns
Internal identifier for the file.
- Return type
str
- addGlobalParameter(name: str, value: Optional[float] = None, initial_value: Optional[float] = None, unit: Optional[str] = None, constant: bool = False, upper: Optional[float] = None, lower: Optional[float] = None, stdev: Optional[float] = None, ontology: Optional[pyenzyme.enzymeml.core.ontology.SBOTerm] = None)[source]
Adds a global parameter to the model that will be referred by KineticModel objects in reaction models.
- Parameters
name (str) – Name of the estimated parameter.
value (Optional[float], optional) – Numerical value of the estimated parameter. Defaults to None.
initial_value (Optional[float], optional) – Initial value that was used for the parameter estimation. Defaults to None.
unit (Optional[str], optional) – Unit of the estimated parameter. Defaults to None.
stdev (Optional[float], optional) – Standard deviation of the estimated parameter. Defaults to None.
ontology (Optional[SBOTerm], optional) – Type of the estimated parameter. Defaults to None.
- Returns
Name of the parameter that has been added.
- Return type
str
- addMeasurement(measurement: pyenzyme.enzymeml.core.measurement.Measurement) str [source]
Adds a measurement to an EnzymeMLDocument and validates consistency with already defined elements of the document.
- Parameters
measurement (Measurement) – Collection of data and initial concentrations per reaction
- Returns
Assigned measurement identifier.
- Return type
measurement_id (String)
- addProtein(protein: pyenzyme.enzymeml.core.protein.Protein, use_parser: bool = True) str [source]
Adds a Protein object to the EnzymeML document.
- Parameters
protein (Protein) – Protein object to be added to the document.
use_parser (bool, optional) – Whether to user the unit parser or not. Defaults to True.
- Returns
Unique internal identifier of the protein.
- Return type
str
- addReactant(reactant: pyenzyme.enzymeml.core.reactant.Reactant, use_parser: bool = True) str [source]
Adds a Reactant object to the EnzymeML document.
- Parameters
reactant (Reactant) – Reactant object to be added to the document.
use_parser (bool, optional) – Whether to user the unit parser or not. Defaults to True.
- Returns
Unique internal identifier of the reactant.
- Return type
str
- addReaction(reaction: pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction, use_parser: bool = True) str [source]
Adds EnzymeReaction object to EnzymeMLDocument object. Automatically assigns ID and converts units.
- Parameters
reaction (EnzymeReaction) – Object describing reaction
use_parser (bool, optional) – If set True, will use internal unit parser. Defaults to True.
- Returns
Internal identifier for the reaction. Use it for other objects!
- Return type
string
- addReactions(reactions: List[pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction])[source]
Adds multiple reactions to an EnzymeML document.
- Parameters
reactions (List[EnzymeReaction]) – List of EnzymeReaction objects
- addVessel(vessel: pyenzyme.enzymeml.core.vessel.Vessel, use_parser: bool = True) str [source]
Adds a Vessel object to the EnzymeML document.
- Parameters
vessel (Vessel) – Vessel object to be added to the document.
use_parser (bool, optional) – Whether to user the unit parser or not. Defaults to True.
- Returns
Unique internal identifier of the reactant.
- Return type
str
- validator add_identifier » pubmedid[source]
Adds an identifiers.org link in front of the pubmed ID if not given
- applyModelInitialization(path: str, to_values: bool = False) None [source]
Adds initial values per reaction to the model from a YAML config file.
This method loads a YAML that previously generated from the function ‘generateInitialValueTemplate’ and was filled with values. These are then used to populate the ‘initial_value’ fields of KineticParameter objects.
- Parameters
path (str) – Path to the YAML file containing the initial values.
- checkUnitConsistency(strict: bool = False, return_report: bool = True)[source]
Validates unit consistency in an EnzymeMLDocument.
This method will check whether all (initial) concentration units of a species are consistent throughout the document. Default mode only requires measurements and replicates to comply to the species unit.
This can also be set to ‘strict’, where any species, measurement, replicate and parameter has to comply in a global fashion. To summarise, strict mode checks on:
Consistent usage of time
Consistent concentration units for ALL concentrations
Consistent volumetric unit including vessels
Strict mode is of greates importance for kinetic modeling, differing scales can lead to wrong results. However, the code will still run and only warnings will be given.
- Parameters
strict (bool, optional) – Enables strict mode. Defaults to False.
return_report (bool, optional) – Whether a report should be returned. Defaults to False.
- Returns
Report on which units are inconsistent Bool: Whether the document is consistent in units
- Return type
Dict
- exportKineticParameters(exclude_constant: bool = False, as_dataframe: bool = True)[source]
Exports all kinetic parameters found in the EnzymeMLDocument
- Parameters
reactions (List[str]) – Reactions from which the parameters are to be exported.
- Returns
Mapping from parameter name to estimated value
- Return type
Dict
- exportMeasurementData(measurement_ids: Union[str, List[str]] = 'all', species_ids: Union[str, List[str]] = 'all', proteins: bool = True, reactants: bool = True) Dict[str, Dict[str, Union[Tuple, pandas.core.frame.DataFrame]]] [source]
Exports either all replicates present in any measurement or the ones specified via ‘species_ids’ or ‘measurement_ids’
- Parameters
measurement_ids (Union[str, List[str]], optional) – The measurements from which to export the data. Defaults to “all”.
species_ids (Union[str, List[str]], optional) – The species from which to export the data. Defaults to “all”.
- Returns
The data corresponding to the specified options. The dictionary will still distinguish between meassuremnts.
- Return type
Dict[str, Dict[str, Union[tuple, pd.DataFrame]]]
- static fromFile(path: str)[source]
Initializes an EnzymeMLDocument from an OMEX container.”
- Parameters
path (Path) – Path to the OMEX container.
- Returns
The intialized EnzymeML document.
- Return type
- classmethod fromTemplate(path: str)[source]
Reads an EnzymeML spreadsheet template to an EnzymeMLDocument object.
- Parameters
path (str) – Path to the EnzymeML spreadsheet template.
- Returns
Resulting EnzymeML document.
- Return type
- generateInitialValueTemplate(dir: str = '.') None [source]
Generates an initial value template as a YAML file, which can be used for modeling.
- Parameters
dir (str, optional) – Dirpath to the output file. Defaults to “.”.
- getAny(id: str) pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies [source]
Returns anything associated with the given ID.
- Parameters
id (str) – Unique internal ID of the object.
- Raises
SpeciesNotFoundError – Raised when the requested object is not found.
- Returns
The corresponding file object.
- Return type
Dict[str, dict]
- getFile(id: str, by_id: bool = True) dict [source]
Returns the file associated with the given ID.
- Parameters
id (str) – Unique internal ID of the file.
- Raises
SpeciesNotFoundError – Raised when the requested file is not found.
- Returns
The corresponding file object.
- Return type
Dict[str, dict]
- getFilesList()[source]
Returns a list of all files in the EnzymeML document.”
- Returns
List of all files in the EnzymeML document.
- Return type
List[dict]
- getMeasurement(id: str) pyenzyme.enzymeml.core.measurement.Measurement [source]
Returns the measurement associated with the given ID.
- Parameters
id (str) – Unique internal ID of the measurement.
- Raises
SpeciesNotFoundError – Raised when the requested measurement is not found.
- Returns
The corresponding measurement object.
- Return type
- getProtein(id: str) pyenzyme.enzymeml.core.protein.Protein [source]
Returns the protein associated with the given ID.
- Parameters
id (str) – Unique internal ID of the protein.
- Raises
SpeciesNotFoundError – Raised when the requested protein is not found.
- Returns
The corresponding protein object.
- Return type
- getProteinList() List[pyenzyme.enzymeml.core.protein.Protein] [source]
Returns a list of all proteins in the EnzymeML document.”
- Returns
List of all proteins in the EnzymeML document.
- Return type
List[Protein]
- getReactant(id: str) pyenzyme.enzymeml.core.reactant.Reactant [source]
Returns the reactant associated with the given ID.
- Parameters
id (str) – Unique internal ID of the reactant.
- Raises
SpeciesNotFoundError – Raised when the requested reactant is not found.
- Returns
The corresponding reactant object.
- Return type
- getReactantList() List[pyenzyme.enzymeml.core.reactant.Reactant] [source]
Returns a list of all reactants in the EnzymeML document.”
- Returns
List of all reactants in the EnzymeML document.
- Return type
List[Reactant]
- getReaction(id: str) pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction [source]
Returns the reaction associated with the given ID.
- Parameters
id (str) – Unique internal ID of the reaction.
- Raises
SpeciesNotFoundError – Raised when the requested reaction is not found.
- Returns
The corresponding reaction object.
- Return type
- getReactionList() List[pyenzyme.enzymeml.core.enzymereaction.EnzymeReaction] [source]
Returns a list of all reactions in the EnzymeML document.”
- Returns
List of all reactions in the EnzymeML document.
- Return type
List[EnzymeReaction]
- getUnitDef(id: str) pyenzyme.enzymeml.core.unitdef.UnitDef [source]
Returns the unit associated with the given ID.
- Parameters
id (str) – Unique internal ID of the unit.
- Raises
SpeciesNotFoundError – Raised when the requested unit is not found.
- Returns
The corresponding unit object.
- Return type
- getUnitString(unit_id: Optional[str]) str [source]
Return the unit name corresponding to the given unit ID.
- Parameters
unit_id (str) – Unique internal ID of the unit.
- Raises
SpeciesNotFoundError – Raised when the requested unit is not found.
- Returns
String representation of the unit.
- Return type
str
- getVessel(id: str) pyenzyme.enzymeml.core.vessel.Vessel [source]
Returns the vessel associated with the given ID.
- Parameters
id (str) – Unique internal ID of the vessel.
- Raises
SpeciesNotFoundError – Raised when the requested vessel is not found.
- Returns
The corresponding unit object.
- Return type
- printDocument(measurements: bool = False, units: bool = False, stdout: bool = True) Optional[str] [source]
Prints the document’s content
- printReactionSchemes(by_name: bool = True)[source]
Prints all reaction equations to inspect the content
- toDataFrame(measurement_ids: List[str] = ['all'], use_names: bool = False) pandas.core.frame.DataFrame [source]
Transforms exported measurement data to a single DataFrame
- Parameters
measurement_ids (List[str], optional) – Measurements to include or all of them. Defaults to [“all”].
use_names (bool, optional) – Wether names or IDs should be used. Defaults to False.
- Returns
Transformed measurement data.
- Return type
pd.DataFrame
- toFile(path: str, name: Optional[str] = None)[source]
Saves an EnzymeML document to an OMEX container at the specified path
- Parameters
path (Path) – Path where the document should be saved.
verbose (PositiveInt, optional) – Level of verbosity, in order to print a message and the resulting path. Defaults to 1.
- unifyMeasurementUnits(kind: str, scale: int, measurement_ids: Union[str, List[str]] = 'all') None [source]
Rescales and unifies the units of either all measurements or those that are provided to the given kind and scale.
- Parameters
kind (str) – The unit kind from which to rescale. Currently supported: ‘mole’, ‘gram’, ‘litre’.
scale (int) – Decade scale to which the values will be rescaled.
measurement_ids (Union[str, List[str]], optional) – Measurements that will be rescaled. Defaults to “all”.
- uploadToDataverse(dataverse_name: str, base_url: Optional[str] = None, api_token: Optional[str] = None)[source]
Uploads an EnzymeML document to a Dataverse installation of choice.
It should be noted, that the environment variables ‘DATAVERSE_URL’ and ‘DATAVERSE_API_TOKEN’ should be given approriately before the upload. If not, tje upload cant be done.
- Parameters
dataverse_name (str) – Name of the dataverse to upload the EnzymeML document. You can find the name in the link of your dataverse (e.g. https://dataverse.installation/dataverse/{dataverseName})
base_url (str) – Base URL of the dataverse to upload. Defaults to None. If None the URL will be drawn from env vars.
api_token (str) – API Token of the dataverse to upload. Defaults to None. If None the API Token will be drawn from env vars.
- validate(yaml_path: str) Tuple[Dict, bool] [source]
Validates an EnzymeML based on a given YAML file.
The YAML file should be compliant with PyEnzymes template found on Github or generated via the EnzymeMLValidator instance. Ultimately, it can also be derived from a spreadsheet template, which can also be generated via the EnzymeMLValidator instance.
- Parameters
yaml_path (str) – Path to the Validation YAML file
- Returns
Report on which fields are incompatible Bool: Whether or not the document is valid to the given YAML
- Return type
Dict
- visualize(measurement_ids: List[str] = ['all'], interactive: bool = False, use_names: bool = False, sharey: bool = True, col_wrap: int = 4, trendline: bool = False, width: int = 1000, height: int = 500, hovermode: str = 'closest', **kwargs)[source]
Visualizes either all or selected measurements found in the EnzymeML document as FacetGrid or interactive.
In order to use this method correctly, make sure to pass nothing to ‘measurement_ids’ when all meassurements should be visualised. Otherwise pass a list or string for multiple or single measurements respectively.
- Parameters
measurement_ids (List[str], optional) – List of measurements that should be plotted or all. Defaults to [“all”].
interactive (bool, optional) – [description]. Whether to return an interatcive or static plot. Defaults to to False.
use_names (bool, optional) – Whether names or IDs should be used. Defaults to False.
sharey (bool, optional) – Whether all plots in FacetGrid should share the y-axis. Defaults to True.
col_wrap (int, optional) – Specifies in FacetGrid at which number of cols to create a new row. Defaults to 4.
trendline (bool, optional) – Whether the plot should include a trendline. Defaults to False.
width (int, optional) – Interactive plot width. Defaults to 1000.
height (int, optional) – Interactive plot height. Defaults to 500.
hovermode (str, optional) – Changes behaviour of hovering. Following options are available [‘closest’, ‘x unified’, ‘x’, ‘y’, ‘y unified’]. Defaults to ‘closest’.
- Returns
[description]
- Return type
[type]