.venv_haddock/lib/python3.12/site-packages/Bio/SCOP/Residues.py

# Copyright 2000 by Jeffrey Chang.  All rights reserved.
# Revisions copyright 2001 by Gavin E. Crooks. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""A collection of residues from a PDB structure."""

import re

_pdbid_re = re.compile(r"^(\w\w\w\w)(?:$|\s+|_)(.*)")
_fragment_re = re.compile(r"\(?(\w:)?(-?\w*)-?(-?\w*)\)?(.*)")


class Residues:
    """A collection of residues from a PDB structure.

    This class provides code to work with SCOP domain definitions. These
    are concisely expressed as one or more chain fragments. For example,
    "(1bba A:10-20,B:)" indicates residue 10 through 20 (inclusive) of
    chain A, and every residue of chain B in the pdb structure 1bba. The pdb
    id and brackets are optional. In addition "-" indicates every residue of
    a pbd structure with one unnamed chain.

    Start and end residue ids consist of the residue sequence number and an
    optional single letter insertion code. e.g. "12", "-1", "1a", "1000"


    pdbid -- An optional PDB id, e.g. "1bba"

    fragments -- A sequence of tuples (chainID, startResID, endResID)

    """

    def __init__(self, str=None):
        """Initialize the class."""
        self.pdbid = ""
        self.fragments = ()
        if str is not None:
            self._parse(str)

    def _parse(self, str):
        str = str.strip()

        # Is there a pdbid at the front? e.g. 1bba A:1-100
        m = _pdbid_re.match(str)
        if m is not None:
            self.pdbid = m.group(1)
            str = m.group(2)  # Everything else

        if str == "" or str == "-" or str == "(-)":  # no fragments, whole sequence
            return

        fragments = []
        for fragment in str.split(","):
            m = _fragment_re.match(fragment)
            if m is None:
                raise ValueError(f"I don't understand the format of {fragment}")
            chain, start, end, postfix = m.groups()

            if postfix != "":
                raise ValueError(f"I don't understand the format of {fragment}")

            if chain:
                if chain[-1] != ":":
                    raise ValueError(f"I don't understand the chain in {fragment}")
                chain = chain[:-1]  # chop off the ':'
            else:
                chain = ""

            fragments.append((chain, start, end))
        self.fragments = tuple(fragments)

    def __str__(self):
        """Represent the SCOP residues record as a string."""
        prefix = ""
        if self.pdbid:
            prefix = self.pdbid + " "

        if not self.fragments:
            return prefix + "-"
        strs = []
        for chain, start, end in self.fragments:
            s = []
            if chain:
                s.append(f"{chain}:")
            if start:
                s.append(f"{start}-{end}")
            strs.append("".join(s))
        return prefix + ",".join(strs)