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Dice.py

# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.

import re
import warnings
from Bio.PDB.PDBIO import PDBIO


_hydrogen=re.compile("[123 ]*H.*")


00014 class ChainSelector:
    """
    Only accepts residues with right chainid
    and between start and end. Remove hydrogens, waters and ligands.
    Only use model 0 by default.
    """
    def __init__(self, chain_id, start, end, model_id=0):
        self.chain_id=chain_id
        self.start=start
        self.end=end
        self.model_id=0

    def accept_model(self, model):
        # model - only keep model 0
        if model.get_id()==self.model_id:
            return 1
        return 0

    def accept_chain(self, chain):
        if chain.get_id()==self.chain_id:
            return 1
        return 0

    def accept_residue(self, residue):
        # residue - between start and end
        hetatm_flag, resseq, icode=residue.get_id()
        if hetatm_flag!=" ":
            # skip HETATMS
            return 0
        if icode!=" ":
            warnings.warn("WARNING: Icode at %s" % residue.get_id(),
                          RuntimeWarning)
        if self.start<=resseq<=self.end:
            return 1
        return 0

    def accept_atom(self, atom):
        # atoms - get rid of hydrogens
        name=atom.get_id()
        if _hydrogen.match(name):
            return 0
        else:
            return 1


def extract(structure, chain_id, start, end, filename):
    """
    Write out selected portion to filename.
    """
    sel=ChainSelector(chain_id, start, end)
    io=PDBIO()
    io.set_structure(structure)
    io.save(filename, sel)



if __name__=="__main__":

    from Bio.PDB.PDBParser import PDBParser

    import sys

    p=PDBParser()
    s=p.get_structure("scr", sys.argv[1])

    extract(s, " ", 1, 100, "out.pdb")
    

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