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# 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)
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