Protein#

pydantic model pyenzyme.enzymeml.core.complex.Complex[source]#

Bases: EnzymeMLBase, AbstractSpecies

Show JSON schema

{
   "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"
   ],
   "definitions": {
      "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"
      }
   }
}

Config

validate_all: bool = True
validate_assignment: bool = True

Fields

boundary (bool)
constant (bool)
creator_id (Optional[str])
id (Optional[str])
init_conc (Optional[float])
meta_id (Optional[str])
name (str)
ontology (pyenzyme.enzymeml.core.ontology.SBOTerm)
participants (List[str])
unit (Optional[str])
uri (Optional[str])
vessel_id (str)

Validators

check_reactant_ids » participants
set_meta_id » id

field boundary: bool = False#: Whether the protein is under any boundary conditions (SBML Technicality, better leave it to default)

field constant: bool = False#: Whether the proteins concentration remains constant or not.

field creator_id: Optional[str] = None#: Unique identifier of the author.

field id: Optional[str] = None#

Unique identifier of the protein.

Constraints

pattern = c[d]+

Validated by

set_meta_id

field init_conc: Optional[float] = None#: Initial concentration of the protein.

field meta_id: Optional[str] = None#: Unique meta identifier of the protein.

field name: str [Required]#: Name of the complex

field ontology: SBOTerm = SBOTerm.MACROMOLECULAR_COMPLEX#: Ontology describing the characteristic of the protein.

field participants: List[str] [Optional]#

Array of IDs the complex contains

Validated by

check_reactant_ids

field unit: Optional[str] = None#: Unit of the proteins intial concentration.

field uri: Optional[str] = None#: URI of the protein.

field vessel_id: str [Required]#

Identifier of the vessel in which the protein was stored.

Constraints

pattern = v[d]+

validator check_reactant_ids » participants[source]#: Checks ID consistency for reactants

validator set_meta_id » id [source]#: Sets the meta ID when an ID is provided