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# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Gavin E. Crooks 2001-11-03
# Minor extensions, some bug fixes, and major changes to the interface
"""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(object):
"""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):
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 l in str.split(","):
m = _fragment_re.match(l)
if m is None:
raise ValueError("I don't understand the format of %s" % l)
chain, start, end, postfix = m.groups()
if postfix != "":
raise ValueError("I don't understand the format of %s" % l)
if chain:
if chain[-1] != ':':
raise ValueError("I don't understand the chain in %s" % l)
chain = chain[:-1] # chop off the ':'
else:
chain = ""
fragments.append((chain, start, end))
self.fragments = tuple(fragments)
def __str__(self):
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("%s:" % chain)
if start:
s.append("%s-%s" % (start, end))
strs.append("".join(s))
return prefix + ",".join(strs)
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