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77 lines
2.4 KiB
Python
77 lines
2.4 KiB
Python
# Copyright 2000 by Jeffrey Chang. All rights reserved.
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# Revisions copyright 2001 by Gavin E. Crooks. All rights reserved.
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Handle the SCOP DOMain file.
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The DOM file has been officially deprecated. For more information see
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the SCOP"release notes.":http://scop.berkeley.edu/release-notes-1.55.html
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The DOM files for older releases can be found
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"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
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"""
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from .Residues import Residues
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class Record:
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"""Holds information for one SCOP domain.
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Attributes:
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- sid - The SCOP ID of the entry, e.g. d1anu1
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- residues - The domain definition as a Residues object
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- hierarchy - A string specifying where this domain is in the hierarchy.
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"""
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def __init__(self, line=None):
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"""Initialize the class."""
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self.sid = ""
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self.residues = []
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self.hierarchy = ""
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if line:
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self._process(line)
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def _process(self, line):
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"""Parse DOM records (PRIVATE).
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Records consist of 4 tab deliminated fields;
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sid, pdbid, residues, hierarchy
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"""
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# For example ::
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#
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# d1sctg_ 1sct g: 1.001.001.001.001.001
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# d1scth_ 1sct h: 1.001.001.001.001.001
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# d1flp__ 1flp - 1.001.001.001.001.002
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# d1moh__ 1moh - 1.001.001.001.001.002
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line = line.rstrip() # no trailing whitespace
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columns = line.split("\t") # separate the tab-delineated cols
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if len(columns) != 4:
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raise ValueError(f"I don't understand the format of {line}")
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self.sid, pdbid, res, self.hierarchy = columns
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self.residues = Residues(res)
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self.residues.pdbid = pdbid
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def __str__(self):
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"""Represent the SCOP domain record as a tab-separated string."""
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s = []
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s.append(self.sid)
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s.append(str(self.residues).replace(" ", "\t"))
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s.append(self.hierarchy)
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return "\t".join(s) + "\n"
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def parse(handle):
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"""Iterate over a DOM file as a Dom record for each line.
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Arguments:
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- handle -- file-like object.
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"""
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for line in handle:
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if line.startswith("#"):
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continue
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yield Record(line)
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