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# 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.
"""Handle the SCOP DEScription file.
The file format is described in the scop
"release notes.":http://scop.berkeley.edu/release-notes-1.55.html
The latest DES file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
"Release 1.55":http://scop.berkeley.edu/parse/des.cla.scop.txt_1.55 (July 2001)
"""
class Record:
"""Holds information for one node in the SCOP hierarchy.
Attributes:
- sunid - SCOP unique identifiers
- nodetype - One of 'cl' (class), 'cf' (fold), 'sf' (superfamily),
'fa' (family), 'dm' (protein), 'sp' (species), 'px' (domain).
Additional node types may be added.
- sccs - SCOP concise classification strings. e.g. b.1.2.1
- name - The SCOP ID (sid) for domains (e.g. d1anu1), currently empty for other node types
- description - e.g. "All beta proteins","Fibronectin type III",
"""
def __init__(self, line=None):
"""Initialize the class."""
self.sunid = ""
self.nodetype = ""
self.sccs = ""
self.name = ""
self.description = ""
if line:
self._process(line)
def _process(self, line):
"""Parse DES records (PRIVATE).
Records consist of 5 tab deliminated fields,
sunid, node type, sccs, node name, node description.
"""
# For example ::
#
# 21953 px b.1.2.1 d1dan.1 1dan T:,U:91-106
# 48724 cl b - All beta proteins
# 48725 cf b.1 - Immunoglobulin-like beta-sandwich
# 49265 sf b.1.2 - Fibronectin type III
# 49266 fa b.1.2.1 - Fibronectin type III
line = line.rstrip() # no trailing whitespace
columns = line.split("\t") # separate the tab-delineated cols
if len(columns) != 5:
raise ValueError(f"I don't understand the format of {line}")
sunid, self.nodetype, self.sccs, self.name, self.description = columns
if self.name == "-":
self.name = ""
self.sunid = int(sunid)
def __str__(self):
"""Represent the SCOP description record as a tab-separated string."""
s = []
s.append(self.sunid)
s.append(self.nodetype)
s.append(self.sccs)
if self.name:
s.append(self.name)
else:
s.append("-")
s.append(self.description)
return "\t".join(map(str, s)) + "\n"
def parse(handle):
"""Iterate over a DES file as a Des record for each line.
Arguments:
- handle - file-like object
"""
for line in handle:
if line.startswith("#"):
continue
yield Record(line)
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