Source code for pyenzyme.enzymeml.core.protein

# File:
# Project: core
# Author: Jan Range
# License: BSD-2 clause
# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart

import re

from pydantic import validator, Field
from typing import Dict, Optional, TYPE_CHECKING, Any
from dataclasses import dataclass

from pyenzyme.enzymeml.core.ontology import SBOTerm
from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
from pyenzyme.enzymeml.core.exceptions import UniProtIdentifierError
from pyenzyme.enzymeml.core.abstract_classes import AbstractSpecies
from pyenzyme.enzymeml.core.utils import type_checking, deprecated_getter

if TYPE_CHECKING:  # pragma: no cover
    static_check_init_args = dataclass
    static_check_init_args = type_checking

[docs]@static_check_init_args class Protein(EnzymeMLBase, AbstractSpecies): name: Optional[str] = Field( None, description="Name of the protein", template_alias="Name" ) sequence: Optional[str] = Field( None, description="Amino acid sequence of the protein", template_alias="Sequence", ) vessel_id: str = Field( ..., description="Identifier of the vessel in which the protein was stored.", template_alias="Vessel", regex=r"v[\d.]+", ) init_conc: Optional[float] = Field( default=None, description="Initial concentration of the protein.", ) unit: Optional[str] = Field( None, description="Unit of the proteins intial concentration.", ) constant: bool = Field( True, description="Whether the proteins concentration remains constant or not.", template_alias="Constant", ) id: Optional[str] = Field( None, description="Unique identifier of the protein.", template_alias="ID", regex=r"p[\d]+", ) meta_id: Optional[str] = Field( None, description="Unique meta identifier of the protein.", ) ecnumber: Optional[str] = Field( None, description="EC number of the protein.", template_alias="EC Number", regex=r"(\d+.)(\d+.)(\d+.)(\d+)", ) organism: Optional[str] = Field( None, description="Organism the protein was expressed in.", template_alias="Source organism", ) organism_tax_id: Optional[str] = Field( None, description="Taxonomy identifier of the expression host.", ) boundary: bool = Field( False, description="Whether the protein is under any boundary conditions (SBML Technicality, better leave it to default)", ) ontology: SBOTerm = Field( SBOTerm.PROTEIN, description="Ontology describing the characteristic of the protein.", ) uri: Optional[str] = Field( None, description="URI of the protein.", ) creator_id: Optional[str] = Field( None, description="Unique identifier of the author.", ) uniprotid: Optional[str] = Field( None, description="Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database.", template_alias="UniProt ID", ) # ! Validators
[docs] @validator("id") def set_meta_id(cls, id: Optional[str], values: dict): """Sets the meta ID when an ID is provided""" if id: # Set Meta ID with ID values["meta_id"] = f"METAID_{id.upper()}" return id
[docs] @validator("sequence") def clean_sequence(cls, sequence): """Cleans a sequence from whitespaces as well as newlines and transforms uppercase""" if sequence: return re.sub(r"\s+", "", sequence).upper() else: return sequence
# ! Initializers
[docs] @classmethod def fromUniProtID( cls, uniprotid: str, vessel_id: str, init_conc: Optional[float] = None, unit: Optional[str] = None, constant: bool = False, ) -> "Protein": """Initializes a protein based on the UniProt database. Raises: UniProtIdentifierError: Raised when the UniProt identifier is invalid. Returns: Protein: The initialiized Protein object. """ # Get UniProt Parameters parameters = cls._getUniProtParameters(uniprotid=uniprotid) return cls( init_conc=init_conc, unit=unit, vessel_id=vessel_id, constant=constant, uniprotid=uniprotid, **parameters, )
@staticmethod def _getUniProtParameters(uniprotid: str) -> Dict[str, Any]: import requests import xml.etree.ElementTree as ET # Send request to CHEBI database endpoint = f"{uniprotid}.xml" # Fetch data response = requests.get(endpoint) # Check if the UniProt ID is correct if response.status_code == 404: raise UniProtIdentifierError(uniprotid=uniprotid) # Create XML Tree tree = ET.ElementTree(ET.fromstring(response.text)) # Set prefix to match tag prefix = r"{}" # Define mapping for the used attributes attribute_mapping = { prefix + "sequence": "sequence", prefix + "fullName": "name", prefix + "ecNumber": "ecnumber", } # Collect parameters parameters = {} for elem in tree.iter(): if elem.tag in attribute_mapping and parameters.get(elem.tag) is None: parameters[attribute_mapping[elem.tag]] = elem.text return parameters # ! Getters
[docs] @deprecated_getter("organism_tax_id") def getOrganismTaxId(self): return self.organism_tax_id
[docs] @deprecated_getter("ecnumber") def getEcnumber(self): return self.ecnumber
[docs] @deprecated_getter("uniprotid") def getUniprotID(self): return self.uniprotid
[docs] @deprecated_getter("organism") def getOrganism(self): return self.organism
[docs] @deprecated_getter("init_conc") def getInitConc(self): return self.init_conc
[docs] @deprecated_getter("name") def getName(self): return
[docs] @deprecated_getter("id") def getId(self): return
[docs] @deprecated_getter("meta_id") def getMetaid(self): return self.meta_id
[docs] @deprecated_getter("sequence") def getSequence(self): return self.sequence
[docs] @deprecated_getter("ontology") def getSboterm(self): return self.ontology
[docs] @deprecated_getter("vessel_id") def getVessel(self): return self.vessel_id
[docs] @deprecated_getter("unit") def getSubstanceUnits(self): return self.unit
[docs] @deprecated_getter("boundary") def getBoundary(self): return self.boundary
[docs] @deprecated_getter("constant") def getConstant(self): return self.constant