Abstract Classes#

pydantic model pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies[source]#

Bases: ABC, AbstractSpeciesDataclass

Due to inheritance and type-checking issues, the dataclass has to be mixed in.

Show JSON schema
{
   "title": "AbstractSpecies",
   "description": "Due to inheritance and type-checking issues, the dataclass has to be mixed in.",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "meta_id": {
         "title": "Meta Id",
         "type": "string"
      },
      "id": {
         "title": "Id",
         "type": "string"
      },
      "vessel_id": {
         "title": "Vessel Id",
         "type": "string"
      },
      "init_conc": {
         "title": "Init Conc",
         "type": "number"
      },
      "constant": {
         "title": "Constant",
         "type": "boolean"
      },
      "boundary": {
         "title": "Boundary",
         "type": "boolean"
      },
      "unit": {
         "title": "Unit",
         "type": "string"
      },
      "ontology": {
         "$ref": "#/definitions/SBOTerm"
      },
      "uri": {
         "title": "Uri",
         "type": "string"
      },
      "creator_id": {
         "title": "Creator Id",
         "type": "string"
      }
   },
   "required": [
      "name",
      "vessel_id",
      "constant",
      "boundary",
      "ontology"
   ],
   "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"
      }
   }
}

Fields
Validators
field boundary: bool [Required]#
field constant: bool [Required]#
field creator_id: Optional[str] = None#
field id: Optional[str] = None#
Validated by
field init_conc: Optional[float] = None#
field meta_id: Optional[str] = None#
field name: str [Required]#
field ontology: SBOTerm [Required]#
field unit: Optional[str] = None#
field uri: Optional[str] = None#
field vessel_id: str [Required]#
validator set_meta_id  »  id[source]#

Sets the meta ID when an ID is provided

unitdef()[source]#

Returns the appropriate unitdef if an enzmldoc is given

pydantic model pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass[source]#

Bases: BaseModel

Abstract dataclass to describe an EnzymeML/SBML species.

Show JSON schema
{
   "title": "AbstractSpeciesDataclass",
   "description": "Abstract dataclass to describe an EnzymeML/SBML species.",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "meta_id": {
         "title": "Meta Id",
         "type": "string"
      },
      "id": {
         "title": "Id",
         "type": "string"
      },
      "vessel_id": {
         "title": "Vessel Id",
         "type": "string"
      },
      "init_conc": {
         "title": "Init Conc",
         "type": "number"
      },
      "constant": {
         "title": "Constant",
         "type": "boolean"
      },
      "boundary": {
         "title": "Boundary",
         "type": "boolean"
      },
      "unit": {
         "title": "Unit",
         "type": "string"
      },
      "ontology": {
         "$ref": "#/definitions/SBOTerm"
      },
      "uri": {
         "title": "Uri",
         "type": "string"
      },
      "creator_id": {
         "title": "Creator Id",
         "type": "string"
      }
   },
   "required": [
      "name",
      "vessel_id",
      "constant",
      "boundary",
      "ontology"
   ],
   "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"
      }
   }
}

Fields
field boundary: bool [Required]#
field constant: bool [Required]#
field creator_id: Optional[str] = None#
field id: Optional[str] = None#
field init_conc: Optional[float] = None#
field meta_id: Optional[str] = None#
field name: str [Required]#
field ontology: SBOTerm [Required]#
field unit: Optional[str] = None#
field uri: Optional[str] = None#
field vessel_id: str [Required]#
class pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory[source]#

Bases: ABC

Factory that returns a specific species instance.

enzymeml_part: str#
abstract get_species(**kwargs) → AbstractSpecies[source]#

Return a new species object