Source code for MMTK.Bonds

# 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.
#
[docs]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__
[docs] 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
[docs] 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 #
[docs]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` +')'
[docs] 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 #
[docs]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 #
[docs]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]
[docs] 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 #
[docs]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