MeasurementData#
- pydantic model pyenzyme.enzymeml.core.measurementData.MeasurementData[source]#
Bases:
EnzymeMLBase
Helper class to organize elements
Show JSON schema
{ "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": { "$ref": "#/definitions/Replicate" } } }, "required": [ "init_conc", "unit" ], "definitions": { "DataTypes": { "title": "DataTypes", "description": "String enumeration used to assign replicate type ontologies", "enum": [ "conc", "abs", "feed", "biomass", "conversion", "peak-area" ], "type": "string" }, "Replicate": { "title": "Replicate", "type": "object", "properties": { "id": { "title": "Id", "description": "Unique identifier of the replicate", "type": "string" }, "species_id": { "title": "Species Id", "description": "Unique identifier of the species that has been measured.", "pattern": "[s|r|p][\\d]+", "type": "string" }, "measurement_id": { "title": "Measurement Id", "description": "Unique identifier of the measurement that the replicate is part of.", "pattern": "m[\\d]+", "type": "string" }, "data_type": { "description": "Type of data that was measured (e.g. concentration)", "default": "conc", "allOf": [ { "$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" ] } } }
- Config
validate_all: bool = True
validate_assignment: bool = True
- Fields
- Validators
- field init_conc: float [Required]#
Initial concentration of the measurement data.
- field measurement_id: Optional[str] = None#
Unique measurement identifier this dataset belongs to.
- field protein_id: Optional[str] = None#
The identifier for the described protein.
- Validated by
- field reactant_id: Optional[str] = None#
The identifier for the described reactant.
- field replicates: List[Replicate] [Optional]#
A list of replicate objects holding raw data of the measurement.
- field unit: str [Required]#
The unit of the measurement data.
- validator check_id_occurences » protein_id[source]#
- getInitConc() PositiveFloat [source]#
Deprecated since version Use: the attribute init_conc instead.
- getProteinID() Optional[str] [source]#
Deprecated since version Use: the attribute protein_id instead.
- getReactantID() Optional[str] [source]#
Deprecated since version Use: the attribute reactant_id instead.
- getReplicates() List[Replicate] [source]#
Deprecated since version Use: the attribute replicates instead.
- unifyUnits(kind: str, scale: int, enzmldoc) Optional[str] [source]#
Rescales all replicates data_unit to match the desired scale.
- Parameters
replicate (Replicate) – Replicate object containing time course data.
kind (str) – The kind of unit that will be rescaled.
scale (int) – The scale to whih the data will be transformed.
enzmldoc ([type]) – The EnzymeML document to which the new unit will be added.