Source code for pestifer.objs.cfusion

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
"""
CFusions are user-specified modifications which fuse residues from a
named residue range of a named protein chain of a named input coordinate
file to the C-terminus of a named segment of base molecule.
"""
import logging
logger=logging.getLogger(__name__)

from pydantic import Field
from typing import ClassVar

from ..core.baseobj import BaseObj, BaseObjList
from .resid import ResID



class Cfusion(BaseObj):
    """
    A class for handling fusions of residues represented by an existing 
    coordinate file to the C-termini of base-molecule segments
    """

    _required_fields = {'sourcefile', 'sourceseg', 'resid1', 'resid2', 'chainID'}
    _optional_fields = {'insertion1', 'insertion2', 'obj_id'}

    sourcefile: str = Field(..., description="Path to the source coordinate file containing the residues to be fused")
    sourceseg: str = Field(..., description="Segment in the source file from which residues are taken")
    resid1: ResID = Field(..., description="Residue information for the N-terminal residue")
    resid2: ResID = Field(..., description="Residue information for the C-terminal residue")
    chainID: str = Field(..., description="Chain ID of the segment in the base molecule to which the fusion is applied")
    obj_id: int = Field(0, description="Unique identifier for the Cfusion object")

    _yaml_header: ClassVar[str] = 'Cfusions'
    _objcat: ClassVar[str] = 'seq'
    _counter: ClassVar[int] = 0  # Class variable to keep track of Cfusion instances

    _segfile: str = None  # Internal attribute to store the segment file name

    @classmethod
    def _adapt(cls, *args, **kwargs) -> dict:
        """
        Override the _adapt classmethod to handle initialization from a shortcode.
        """
        if args and isinstance(args[0], str):
            input_dict = Cfusion._from_shortcode(args[0])
            input_dict['obj_id'] = Cfusion._counter
            Cfusion._counter += 1
            return input_dict
        return super()._adapt(*args, **kwargs)

    @staticmethod
    def _from_shortcode(raw: str) -> dict:
        """
        Converts a shortcode string to a dictionary of parameters for Cfusion.
        The shortcode format is: filename:C:nnn-ccc,S
        where:
        - filename is the source coordinate file
        - C is the source segment
        - nnn is the N-terminal residue number of the fusion sequence
        - ccc is the C-terminal residue number of the fusion sequence
        - S is the chain ID of the segment in the base molecule to which the fusion is applied
        """
        sourcefile, sourceseg, seq_range_chainID = raw.split(":")
        seq_range, chainID = seq_range_chainID.split(",")
        resrange = seq_range.split("-")
        resid1 = ResID(resrange[0])
        resid2 = ResID(resrange[1])
        base_dict = {
            'sourcefile': sourcefile,
            'sourceseg': sourceseg,
            'resid1': resid1,
            'resid2': resid2,
            'chainID': chainID
        }
        return base_dict



    def shortcode(self) -> str:
        return f"{self.sourcefile}:{self.sourceseg}:{self.resid1.resid}-{self.resid2.resid},{self.chainID}"






class CfusionList(BaseObjList[Cfusion]):


    def describe(self) -> str:
        return f"<CfusionList with {len(self)} items>"