Reactant#

pydantic model pyenzyme.enzymeml.core.reactant.Reactant[source]#

Bases: EnzymeMLBase, AbstractSpecies

Show JSON schema
{
   "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"
   ],
   "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
Validators
field boundary: bool = False#

Whether the reactant is under any boundary conditions (SBML Technicality, better leave it to default)

field chebi_id: Optional[str] = None#

Unique identifier of the CHEBI database. Use this identifier to initialize the object from the CHEBI database.

field constant: bool = False#

Whether the reactants 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 = s[d]+

Validated by
field inchi: Optional[str] = None#

International Chemical Identifier (InChI) encoding of the reactant.

field init_conc: Optional[float] = None#

Initial concentration of the reactant.

field meta_id: Optional[str] = None#

Unique meta identifier of the protein.

field name: Optional[str] = None#

Name of the reactant.

field ontology: SBOTerm = SBOTerm.SMALL_MOLECULE#

Ontology describing the characteristic of the reactant.

field smiles: Optional[str] = None#

Simplified Molecular Input Line Entry System (SMILES) encoding of the reactant.

field unit: Optional[str] = None#

Unit of the reactant intial concentration.

field uri: Optional[str] = None#

URI of the protein.

field vessel_id: str [Required]#

Identifier of the vessel in which the reactant was stored.

classmethod fromChebiID(chebi_id: str, vessel_id: str, constant: bool = False, init_conc: Optional[float] = None, unit: Optional[str] = None) Reactant[source]#

Initializes a reactant based

Raises

ChEBIIdentifierError – [description]

Returns

[description]

Return type

[type]

getBoundary()[source]#

Deprecated since version Use: the attribute boundary instead.

getConstant()[source]#

Deprecated since version Use: the attribute constant instead.

getId()[source]#

Deprecated since version Use: the attribute id instead.

getInchi()[source]#

Deprecated since version Use: the attribute inchi instead.

getInitConc()[source]#

Deprecated since version Use: the attribute init_conc instead.

getMetaid()[source]#

Deprecated since version Use: the attribute meta_id instead.

getName()[source]#

Deprecated since version Use: the attribute name instead.

getSboterm()[source]#

Deprecated since version Use: the attribute ontology instead.

getSmiles()[source]#

Deprecated since version Use: the attribute smiles instead.

getSubstanceUnits()[source]#

Deprecated since version Use: the attribute unit instead.

getVessel()[source]#

Deprecated since version Use: the attribute vessel_id instead.