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Residues.py

# 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 

import re

"""A collection of residues from a PDB structure."""

_pdbid_re = re.compile(r"^(\w\w\w\w)(?:$|\s+|_)(.*)")
_fragment_re = re.compile(r"\(?(\w:)?(-?\w*)-?(-?\w*)\)?(.*)")

00016 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 a 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 SyntaxError, "I don't understand the format of %s" % l
            chain, start, end, postfix = m.groups()

            if postfix != "" :
                 raise SyntaxError, "I don't understand the format of %s" % l

            if chain:
                if chain[-1] != ':':
                    raise SyntaxError, "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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