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Chain.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.  

# Python stuff
from types import IntType

# My Stuff
from Entity import Entity

__doc__="Chain class, used in Structure objects."


00015 class Chain(Entity):
    def __init__(self, id):
        self.level="C"
        Entity.__init__(self, id)

    # Private methods

00022     def _sort(self, r1, r2):
        """Sort function for residues in a chain

        Residues are first sorted according to their hetatm records.
        Protein and nucleic acid residues first, hetatm residues next, 
        and waters last. Within each group, the residues are sorted according
        to their resseq's (sequence identifiers). Finally, residues with the
        same resseq's are sorted according to icode.

        Arguments:
        o r1, r2 - Residue objects
        """
        hetflag1, resseq1, icode1=r1.id
        hetflag2, resseq2, icode2=r2.id
        if hetflag1!=hetflag2:
            return cmp(hetflag1[0], hetflag2[0])
        elif resseq1!=resseq2:
            return cmp(resseq1, resseq2)
        return cmp(icode1, icode2)

00042     def _translate_id(self, id):
        """
        A residue id is normally a tuple (hetero flag, sequence identifier, 
        insertion code). Since for most residues the hetero flag and the 
        insertion code are blank (i.e. " "), you can just use the sequence 
        identifier to index a residue in a chain. The _translate_id method
        translates the sequence identifier to the (" ", sequence identifier,
        " ") tuple. 

        Arguments:
        o id - int, residue resseq 
        """
        if type(id)==IntType:
            id=(' ', id, ' ')
        return id
            
    # Special methods   

00060     def __getitem__(self, id):
        """Return the residue with given id.

        The id of a residue is (hetero flag, sequence identifier, insertion code). 
        If id is an int, it is translated to (" ", id, " ") by the _translate_id
        method. 

        Arguments:
        o id - (string, int, string) or int
        """
        id=self._translate_id(id)
        return Entity.__getitem__(self, id)

00073     def __delitem__(self, id):
        """
        Arguments:
        o id - (string, int, string) or int
        """
        id=self._translate_id(id)
        return Entity.__delitem__(self, id)

    def __repr__(self):
        return "<Chain id=%s>" % self.get_id()

    # Public methods

00086     def get_unpacked_list(self):
        """Return a list of undisordered residues.

        Some Residue objects hide several disordered residues
        (DisorderedResidue objects). This method unpacks them, 
        ie. it returns a list of simple Residue objects.
        """
        unpacked_list=[]
        for residue in self.get_list():
            if residue.is_disordered()==2:
                for dresidue in residue.disordered_get_list():
                    unpacked_list.append(dresidue)
            else:
                unpacked_list.append(residue)
        return unpacked_list

00102     def has_id(self, id):
        """Return 1 if a residue with given id is present.

        The id of a residue is (hetero flag, sequence identifier, insertion code).
                If id is an int, it is translated to (" ", id, " ") by the _translate_id
        method.

        Arguments:
        o id - (string, int, string) or int
        """
        id=self._translate_id(id)
        return Entity.has_id(self, id)


    # Public

    def get_atoms(self):
        for r in self:
            for a in r:
                yield a


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