# This module implements classes that represent lists of bonds,
# bond angles, and dihedral angles.
#
# Written by Konrad Hinsen
#

"""
Bonds, bond lists, bond angle lists, and dihedral angle lists

The classes in this module are normally not used directly from
client code. They are used by the classes in ChemicalObjects and
ForceField.
"""

__docformat__ = 'restructuredtext'

from MMTK import Database, Utility
from copy import copy

#
# Bonds
#
# Bond objects are created from the specifications in the data base.
#
class Bond(object):

    """
    Chemical bond

    A bond links two atoms (attributes a1 and a2)
    """

    def __init__(self, blueprint, memo = None):
        if type(blueprint) is type(()):
            self.a1 = blueprint[0]
            self.a2 = blueprint[1]
        else:
            self.a1 = Database.instantiate(blueprint.a1, memo)
            self.a2 = Database.instantiate(blueprint.a2, memo)
        if Utility.uniqueID(self.a2) < Utility.uniqueID(self.a1):
            self.a1, self.a2 = self.a2, self.a1
        Utility.uniqueID.registerObject(self)

    blueprintclass = Database.BlueprintBond

    __safe_for_unpickling__ = 1
    __had_initargs__ = 1

    def __repr__(self):
        return 'Bond(' + `self.a1` + ', ' + `self.a2` + ')'
    __str__ = __repr__

    def hasAtom(self, a):
        """
        :param a: an atom
        :type a: :class:`~MMTK.ChemicalObjects.Atom`
        :returns: True if a participates in the bond
        """
        return a is self.a1 or a is self.a2

    def otherAtom(self, a):
        """
        :param a: an atom involved in the bond
        :type a: :class:`~MMTK.ChemicalObjects.Atom`
        :returns: the atom at the other end of the bond
        :rtype: :class:`~MMTK.ChemicalObjects.Atom`
        :raises ValueError: if a does not belong to the bond
        """
        if a is self.a1:
            return self.a2
        elif a is self.a2:
            return self.a1
        else:
            raise ValueError('atom not in bond')

    def _graphics(self, conf, distance_fn, model, module, options):
        objects = []
        if model == 'ball_and_stick' or model == 'vdw_and_stick':
            radius = options.get('stick_radius', 0.01)
        elif model == 'wireframe':
            radius = None
        else:
            return []
        p1 = self.a1.position(conf)
        p2 = self.a2.position(conf)
        if p1 is not None and p2 is not None:
            bond_vector = 0.5*distance_fn(self.a1, self.a2, conf)
            cut = bond_vector != 0.5*(p2-p1)
            color1 = self.a1._atomColor(self.a1, options)
            color2 = self.a2._atomColor(self.a2, options)
            material1 = module.EmissiveMaterial(color1)
            material2 = module.EmissiveMaterial(color2)
            if color1 == color2 and not cut:
                if radius is None:
                    objects.append(module.Line(p1, p2, material = material1))
                else:
                    objects.append(module.Cylinder(p1, p2, radius,
                                                   material = material1))
            else:
                if radius is None:
                    objects.append(module.Line(p1, p1+bond_vector,
                                               material = material1))
                    objects.append(module.Line(p2, p2-bond_vector,
                                               material = material2))
                else:
                    objects.append(module.Cylinder(p1, p1+bond_vector, radius,
                                                   material = material1))
                    objects.append(module.Cylinder(p2, p2-bond_vector, radius,
                                                   material = material2))
        return objects

Database.registerInstanceClass(Bond.blueprintclass, Bond)

#
# Bond angles
#
class BondAngle(object):

    """
    Bond angle
    
    A bond angle is the angle between two bonds that share a common atom.
    It is defined by two bond objects (attributes b1 and b2) and an atom
    object (the common atom, attribute ca).
    """

    def __init__(self, b1, b2, ca):
        self.b1 = b1 # bond 1
        self.b2 = b2 # bond 2
        self.ca = ca # common atom
        if Utility.uniqueID(self.b2) < Utility.uniqueID(self.b1):
            self.b1, self.b2 = self.b2, self.b1
        self.a1 = b1.otherAtom(ca)
        self.a2 = b2.otherAtom(ca)
        Utility.uniqueID.registerObject(self)

    def __repr__(self):
        return 'BondAngle(' + `self.a1` +',' + `self.ca` +','+ `self.a2` +')'

    def otherBond(self, bond):
        """
        :param bond: a bond involved in the angle
        :type bond: :class:`~MMTK.Bonds.Bond`
        :returns: the other bond involved in the angle
        :rtype: :class:`~MMTK.Bonds.Bond`
        :raises ValueError: if bond does not belong to the angle
        """
        if bond is self.b1:
            return self.b2
        elif bond is self.b2:
            return self.b1
        else:
            raise ValueError('bond not in bond angle')

#
# Dihedral angles
#
class DihedralAngle(object):

    """
    Dihedral angle
    
    A dihedral angle is the angle between two planes that are defined by
    BondAngle objects (attributes ba1 and ba2) and their common bond
    (attribute cb).

    There are proper dihedrals (four atoms linked by three bonds in
    sequence) and improper dihedrals (a central atom linked to three
    surrounding atoms by three bonds). The boolean attribute improper
    indicates whether a dihedral is an improper one.    
    """

    def __init__(self, ba1, ba2, cb):
        self.ba1 = ba1 # bond angle 1
        self.ba2 = ba2 # bond angle 2
        # cb is the common bond, i.e. the central bond for a proper dihedral
        if Utility.uniqueID(self.ba2) < Utility.uniqueID(self.ba1):
            self.ba1, self.ba2 = self.ba2, self.ba1
        self.improper = (self.ba1.ca is self.ba2.ca)
        if self.improper:
            self.b1 = self.ba1.otherBond(cb)
            self.b2 = cb
            self.b3 = self.ba2.otherBond(cb)
            self.a1 = self.ba1.ca # central atom
            self.a2 = self.b1.otherAtom(self.ba1.ca)
            self.a3 = cb.otherAtom(self.ba1.ca)
            self.a4 = self.b3.otherAtom(self.ba2.ca)
            # each improper dihedral will come in three versions;
            # identify an arbitrary unique one for constructing the list
            self.normalized = Utility.uniqueID(cb) < Utility.uniqueID(self.b1)\
                              and Utility.uniqueID(cb) < \
                                  Utility.uniqueID(self.b3)
        else:
            self.b1 = self.ba1.otherBond(cb)
            self.b2 = cb
            self.b3 = self.ba2.otherBond(cb)
            self.a1 = self.b1.otherAtom(self.ba1.ca)
            self.a2 = self.ba1.ca # these two are
            self.a3 = self.ba2.ca #   on the common bond
            self.a4 = self.b3.otherAtom(self.ba2.ca)
            self.normalized = self.a1 is not self.a4

    def __repr__(self):
        if self.improper:
            return 'ImproperDihedral(' + `self.a1` +','+ `self.a2` +','+ \
                   `self.a3` +','+ `self.a4` +')'
        else:
            return 'Dihedral(' + `self.a1` +','+ `self.a2` +','+ \
                   `self.a3` +','+ `self.a4` +')'

#
# Bond lists
#
# Bond lists can create bond angle and dihedral angle lists
# for themselves. These are cached for efficiency. The cached
# copy is deleted whenever the bond list is modified.
#
class BondList(list):

    def __init__(self, initlist=None):
        list.__init__(self, initlist)
        self._clearCache()

    __safe_for_unpickling__ = 1

    def _clearCache(self):
        self.bond_angles = None
        self.dihedral_angles = None

    def __getinitargs__(self):
        return (None,)

    def __getstate__(self):
        self._clearCache()
        return self.__dict__

    def __setitem__(self, i, item):
        list.__setitem__(self, i, item)
        self._clearCache()

    def __setslice__(self, i, j, data):
        list.__setslice__(self, i, j, data)
        self._clearCache()

    def __delslice__(self, i, j):
        list.__delslice__(self, i, j)
        self._clearCache()

    def append(self, item):
        list.append(self, item)
        self._clearCache()

    def extend(self, data):
        list.extend(self, data)
        self._clearCache()

    def insert(self, i, item):
        list.insert(i, item)
        self._clearCache()

    def remove(self, item):
        list.remove(self, item)
        self._clearCache()

    def bondAngles(self):
        """
        :returns: a list of all bond angles that can be formed from the
                  bonds in the list
        :rtype: :class:`~MMTK.Bonds.BondAngleList`
        """
        if self.bond_angles is None:
            # find all atoms that are involved in more than one bond
            bonds = {}
            atom_list = []
            for bond in self:
                try:
                    bl = bonds[bond.a1]
                except KeyError:
                    bl = []
                    bonds[bond.a1] = bl
                    atom_list.append(bond.a1)
                bl.append(bond)
                try:
                    bl = bonds[bond.a2]
                except KeyError:
                    bl = []
                    bonds[bond.a2] = bl
                    atom_list.append(bond.a2)
                bl.append(bond)
            angles = []
            for atom in atom_list:
                # each pair of bonds at the same atom defines a bond angle
                for p in Utility.pairs(bonds[atom]):
                    angles.append(BondAngle(p[0], p[1], atom))
            self.bond_angles = BondAngleList(angles)
        return self.bond_angles

    def dihedralAngles(self):
        """
        :returns: a list of all dihedral angles that can be formed from the
                  bonds in the list
        :rtype: :class:`~MMTK.Bonds.DihedralAngleList`
        """
        if self.dihedral_angles is None:
            self.dihedral_angles = self.bondAngles().dihedralAngles()
        return self.dihedral_angles

    def bondedTo(self, atom):
        """
        :param atom: an atom
        :type atom: :class:`~MMTK.ChemicalObjects.Atom`
        :returns: a list of all atoms to which the given atom is bound
        :rtype: list
        """
        return [b.otherAtom(atom) for b in self if b.hasAtom(atom)]

    def bondsOf(self, atom):
        """
        :param atom: an atom
        :type atom: :class:`~MMTK.ChemicalObjects.Atom`
        :returns: a list of all bonds in which the given atom is involved
        :rtype: list
        """
        return [b for b in self if b.hasAtom(atom)]

    def setBondAttributes(self):
        """
        Create an attribute in all atoms of all bonds that points to the
        bonded atom.

        :note: Bond attributes are only set temporarily for optimization
               purposes.
        """
        for b in self:
            b.a1.setBondAttribute(b.a2)
            b.a2.setBondAttribute(b.a1)

#
# Bond angle lists
#
class BondAngleList(object):

    """
    Bond angle list
    """

    def __init__(self, angles):
        self.data = angles

    def __repr__(self):
        return repr(self.data)
    def __len__(self):
        return len(self.data)
    def __getitem__(self, i):
        return self.data[i]

    def dihedralAngles(self):
        """
        :returns: a list of all dihedral angles that can be formed from the
                  bond angles in the list
        :rtype: :class:`~MMTK.Bonds.DihedralAngleList`
        """
        # find all bonds that are involved in more than one bond angle
        angles = {}
        bond_list = []
        for angle in self.data:
            try:
                al = angles[angle.b1]
            except KeyError:
                al = []
                angles[angle.b1] = al
                bond_list.append(angle.b1)
            al.append(angle)
            try:
                al = angles[angle.b2]
            except KeyError:
                al = []
                angles[angle.b2] = al
                bond_list.append(angle.b2)
            al.append(angle)
        dihedrals = []
        for bond in bond_list:
            # each pair of bond angles with a common bond defines a dihedral
            for p in Utility.pairs(angles[bond]):
                d = DihedralAngle(p[0], p[1], bond)
                if d.normalized:
                    dihedrals.append(d)
        return DihedralAngleList(dihedrals)

#
# Dihedral angle lists
#
class DihedralAngleList(object):

    """
    Dihedral angle list
    """

    def __init__(self, dihedrals):
        self.data = dihedrals

    def __repr__(self):
        return repr(self.data)
    def __len__(self):
        return len(self.data)
    def __getitem__(self, i):
        return self.data[i]

#
# Dummy bond length database, for constraints without a force field
#
class DummyBondLengthDatabase(object):

    def __init__(self, universe):
        pass

    def bondLength(self, bond):
        return None

    def bondAngle(self, angle):
        return None