# 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.

"""Model class, used in Structure objects."""

from Bio.PDB.Entity import Entity


class Model(Entity):
    """
    The object representing a model in a structure. In a structure
    derived from an X-ray crystallography experiment, only a single
    model will be present (with some exceptions). NMR structures
    normally contain many different models.
    """

    def __init__(self, id, serial_num=None):
        """
        Arguments:
        o id - int
        o serial_num - int
        """
        self.level = "M"
        if serial_num is None:
            self.serial_num = id
        else:
            self.serial_num = serial_num

        Entity.__init__(self, id)

    # Private methods

    def _sort(self, c1, c2):
        """Sort the Chains instances in the Model instance.

        Chain instances are sorted alphabetically according to
        their chain id. Blank chains come last, as they often consist
        of waters.

        Arguments:
        o c1, c2 - Chain objects
        """
        id1 = c1.get_id()
        id2 = c2.get_id()
        # make sure blank chains come last (often waters)
        if id1 == " " and not id2 == " ":
            return 1
        elif id2 == " " and not id1 == " ":
            return -1
        return cmp(id1, id2)

    # Special methods

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

    # Public

    def get_chains(self):
        for c in self:
            yield c

    def get_residues(self):
        for c in self.get_chains():
            for r in c:
                yield r

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