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

# Copyright 2001 by Gavin E. Crooks.  All rights reserved.
# Revisions copyright 2010 Jeffrey Finkelstein. 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.
"""Handle the SCOP CLAssification file, which describes SCOP domains.

The file format is described in the scop
"release notes.":http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html
The latest CLA file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/

"Release 1.73": http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.73
(July 2008)

"""

from . import Residues


class Record:
    """Holds information for one SCOP domain.

    Attributes:
     - sid - SCOP identifier. e.g. d1danl2
     - residues - The domain definition as a Residues object
     - sccs - SCOP concise classification strings.  e.g. b.1.2.1
     - sunid - SCOP unique identifier for this domain
     - hierarchy - A dictionary, keys are nodetype, values are sunid,
       describing the location of this domain in the SCOP hierarchy. See
       the Scop module for a description of nodetypes. This used to be a
       list of (key,value) tuples in older versions of Biopython (see
       Bug 3109).

    """

    def __init__(self, line=None):
        """Initialize the class."""
        self.sid = ""
        self.residues = None
        self.sccs = ""
        self.sunid = ""
        self.hierarchy = {}
        if line:
            self._process(line)

    def _process(self, line):
        line = line.rstrip()  # no trailing whitespace
        columns = line.split("\t")  # separate the tab-delineated cols
        if len(columns) != 6:
            raise ValueError(f"I don't understand the format of {line}")

        self.sid, pdbid, residues, self.sccs, self.sunid, hierarchy = columns
        self.residues = Residues.Residues(residues)
        self.residues.pdbid = pdbid
        self.sunid = int(self.sunid)

        for ht in hierarchy.split(","):
            key, value = ht.split("=")
            self.hierarchy[key] = int(value)

    def __str__(self):
        """Represent the SCOP classification record as a tab-separated string."""
        s = []
        s.append(self.sid)
        s += str(self.residues).split(" ")
        s.append(self.sccs)
        s.append(self.sunid)

        s.append(
            ",".join(
                "=".join((key, str(value))) for key, value in self.hierarchy.items()
            )
        )

        return "\t".join(map(str, s)) + "\n"


def parse(handle):
    """Iterate over a CLA file as Cla records for each line.

    Arguments:
     - handle - file-like object.

    """
    for line in handle:
        if line.startswith("#"):
            continue
        yield Record(line)


class Index(dict):
    """A CLA file indexed by SCOP identifiers for rapid random access."""

    def __init__(self, filename):
        """Create CLA index.

        Arguments:
         - filename - The file to index

        """
        dict.__init__(self)
        self.filename = filename
        with open(self.filename) as f:
            position = 0
            while True:
                line = f.readline()
                if not line:
                    break
                if line.startswith("#"):
                    continue
                record = Record(line)
                key = record.sid
                if key is not None:
                    self[key] = position
                position = f.tell()

    def __getitem__(self, key):
        """Return an item from the indexed file."""
        position = dict.__getitem__(self, key)

        with open(self.filename) as f:
            f.seek(position)
            line = f.readline()
            record = Record(line)
        return record