Protein#
- pydantic model pyenzyme.enzymeml.core.protein.Protein[source]#
Bases:
EnzymeMLBase
,AbstractSpecies
Show JSON schema
{ "title": "Protein", "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 protein", "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": "p[\\d]+", "template_alias": "ID", "type": "string" }, "vessel_id": { "title": "Vessel Id", "description": "Identifier of the vessel in which the protein was stored.", "pattern": "v[\\d.]+", "template_alias": "Vessel", "type": "string" }, "init_conc": { "title": "Init Conc", "description": "Initial concentration of the protein.", "type": "number" }, "constant": { "title": "Constant", "description": "Whether the proteins concentration remains constant or not.", "default": true, "template_alias": "Constant", "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:0000252", "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" }, "sequence": { "title": "Sequence", "description": "Amino acid sequence of the protein", "template_alias": "Sequence", "type": "string" }, "ecnumber": { "title": "Ecnumber", "description": "EC number of the protein.", "pattern": "(\\d+.)(\\d+.)(\\d+.)(\\d+)", "template_alias": "EC Number", "type": "string" }, "organism": { "title": "Organism", "description": "Organism the protein was expressed in.", "template_alias": "Source organism", "type": "string" }, "organism_tax_id": { "title": "Organism Tax Id", "description": "Taxonomy identifier of the expression host.", "type": "string" }, "uniprotid": { "title": "Uniprotid", "description": "Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database.", "template_alias": "UniProt ID", "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 protein is under any boundary conditions (SBML Technicality, better leave it to default)
- field constant: bool = True#
Whether the proteins concentration remains constant or not.
- field creator_id: Optional[str] = None#
Unique identifier of the author.
- field ecnumber: Optional[str] = None#
EC number of the protein.
- Constraints
pattern = (d+.)(d+.)(d+.)(d+)
- field id: Optional[str] = None#
Unique identifier of the protein.
- Constraints
pattern = p[d]+
- Validated by
- 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: Optional[str] = None#
Name of the protein
- field organism: Optional[str] = None#
Organism the protein was expressed in.
- field organism_tax_id: Optional[str] = None#
Taxonomy identifier of the expression host.
- field sequence: Optional[str] = None#
Amino acid sequence of the protein
- Validated by
- field uniprotid: Optional[str] = None#
Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database.
- 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 clean_sequence » sequence[source]#
Cleans a sequence from whitespaces as well as newlines and transforms uppercase
- classmethod fromUniProtID(uniprotid: str, vessel_id: str, init_conc: Optional[float] = None, unit: Optional[str] = None, constant: bool = False) Protein [source]#
Initializes a protein based on the UniProt database.
- Raises
UniProtIdentifierError – Raised when the UniProt identifier is invalid.
- Returns
The initialiized Protein object.
- Return type