# 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.

"""Residue class, used by Structure objects."""

# My Stuff
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.Entity import Entity, DisorderedEntityWrapper

_atom_name_dict = {}
_atom_name_dict["N"] = 1
_atom_name_dict["CA"] = 2
_atom_name_dict["C"] = 3
_atom_name_dict["O"] = 4


class Residue(Entity):
    """
    Represents a residue. A Residue object stores atoms.
    """
    def __init__(self, id, resname, segid):
        self.level = "R"
        self.disordered = 0
        self.resname = resname
        self.segid = segid
        Entity.__init__(self, id)

    # Special methods

    def __repr__(self):
        resname = self.get_resname()
        hetflag, resseq, icode = self.get_id()
        full_id = (resname, hetflag, resseq, icode)
        return "<Residue %s het=%s resseq=%s icode=%s>" % full_id

    # Private methods

    def _sort(self, a1, a2):
        """Sort the Atom objects.

        Atoms are sorted alphabetically according to their name,
        but N, CA, C, O always come first.

        Arguments:
        o a1, a2 - Atom objects
        """
        name1 = a1.get_name()
        name2 = a2.get_name()
        if name1 == name2:
            return(cmp(a1.get_altloc(), a2.get_altloc()))
        if name1 in _atom_name_dict:
            index1 = _atom_name_dict[name1]
        else:
            index1 = None
        if name2 in _atom_name_dict:
            index2 = _atom_name_dict[name2]
        else:
            index2 = None
        if index1 and index2:
            return cmp(index1, index2)
        if index1:
            return -1
        if index2:
            return 1
        return cmp(name1, name2)

    # Public methods

    def add(self, atom):
        """Add an Atom object.

        Checks for adding duplicate atoms, and raises a
        PDBConstructionException if so.
        """
        atom_id = atom.get_id()
        if self.has_id(atom_id):
            raise PDBConstructionException(
                "Atom %s defined twice in residue %s" % (atom_id, self))
        Entity.add(self, atom)

    def sort(self):
        self.child_list.sort(self._sort)

    def flag_disordered(self):
        "Set the disordered flag."
        self.disordered = 1

    def is_disordered(self):
        "Return 1 if the residue contains disordered atoms."
        return self.disordered

    def get_resname(self):
        return self.resname

    def get_unpacked_list(self):
        """
        Returns the list of all atoms, unpack DisorderedAtoms."
        """
        atom_list = self.get_list()
        undisordered_atom_list = []
        for atom in atom_list:
            if atom.is_disordered():
                undisordered_atom_list = (undisordered_atom_list + atom.disordered_get_list())
            else:
                undisordered_atom_list.append(atom)
        return undisordered_atom_list

    def get_segid(self):
        return self.segid

    def get_atom(self):
        for a in self:
            yield a


class DisorderedResidue(DisorderedEntityWrapper):
    """
    DisorderedResidue is a wrapper around two or more Residue objects. It is
    used to represent point mutations (e.g. there is a Ser 60 and a Cys 60 residue,
    each with 50 % occupancy).
    """
    def __init__(self, id):
        DisorderedEntityWrapper.__init__(self, id)

    def __repr__(self):
        resname = self.get_resname()
        hetflag, resseq, icode = self.get_id()
        full_id = (resname, hetflag, resseq, icode)
        return "<DisorderedResidue %s het=%s resseq=%i icode=%s>" % full_id

    def add(self, atom):
        residue = self.disordered_get()
        if not atom.is_disordered() == 2:
            # Atoms in disordered residues should have non-blank
            # altlocs, and are thus represented by DisorderedAtom objects.
            resname = residue.get_resname()
            het, resseq, icode = residue.get_id()
            # add atom anyway, if PDBParser ignores exception the atom will be part of the residue
            residue.add(atom)
            raise PDBConstructionException(
                "Blank altlocs in duplicate residue %s (%s, %i, %s)"
                % (resname, het, resseq, icode))
        residue.add(atom)

    def sort(self):
        "Sort the atoms in the child Residue objects."
        for residue in self.disordered_get_list():
            residue.sort()

    def disordered_add(self, residue):
        """Add a residue object and use its resname as key.

        Arguments:
        o residue - Residue object
        """
        resname = residue.get_resname()
        # add chain parent to residue
        chain = self.get_parent()
        residue.set_parent(chain)
        assert(not self.disordered_has_id(resname))
        self[resname] = residue
        self.disordered_select(resname)
