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.

addReplicate(replicate: Replicate) None[source]#
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.

getUnit() str[source]#

Deprecated since version Use: the attribute unit instead.

get_id() str[source]#

Internal usage to get IDs from objects without ID attribute

setMeasurementIDs(id: str) None[source]#
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.

unitdef()[source]#

Returns the appropriate unitdef if an enzmldoc is given