def GetAngles(mol):
"""Determine bond angle atom triplets from bond graph and get parameters.
Search bond graph for bond angle triplets, and parameter tables for mm
parameters. Use to create a new Angle object and append to Molecule.
Count as angle if ij and jk are bonded in triplet ijk.
Args:
mol (mmlib.molecule.Molecule): Molecule object with bond graph of
atom pairs within covalent radius cutoff threshold.
"""
for j in range(mol.n_atoms):
at2 = mol.atoms[j]
for i in mol.bond_graph[j].keys():
at1 = mol.atoms[i]
r_ij = mol.bond_graph[i][j]
for k in mol.bond_graph[j].keys():
if i >= k:
continue
at3 = mol.atoms[k]
r_jk = mol.bond_graph[j][k]
a_ijk = geomcalc.GetAijk(at1.coords, at2.coords, at3.coords,
r_ij, r_jk)
k_a, a_eq = param.GetAngleParam(at1.type_, at2.type_,
at3.type_)
if k_a > 0.0:
mol.angles.append(molecule.Angle(i, j, k, a_ijk, a_eq,
k_a))
mol.angles = sorted(mol.angles, key=lambda a: a.at3)
mol.angles = sorted(mol.angles, key=lambda a: a.at2)
mol.angles = sorted(mol.angles, key=lambda a: a.at1)
mol.n_angles = len(mol.angles)
def GetAngles(atoms, bond_graph):
"""Determine bond angle atom triplets from bond graph and get parameters.
Search bond graph for bond angle triplets, and parameter tables for mm
parameters. Use to create a new Angle object and append to Molecule.
Count as angle if ij and jk are bonded in triplet ijk.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int:float)): Dictionary of bond connectivity.
Returns:
angles (mmlib.molecule.Angle*): Array of molecule's Angle objects.
"""
angles = []
for j, at2 in enumerate(atoms):
for i, k in itertools.combinations(bond_graph[j], 2):
if i > k:
continue
at1, at3 = atoms[i], atoms[k]
a_ijk = geomcalc.GetAijk(at1.coords, at2.coords, at3.coords)
k_a, a_eq = param.GetAngleParam(at1.type_, at2.type_, at3.type_)
if k_a:
angles.append(molecule.Angle(i, j, k, k_a, a_eq, a_ijk))
angles.sort(key=lambda a: (a.at1, a.at2, a.at3))
return angles
def testBadInput(self):
"""Asserts raise of ValueError for missing string input."""
with self.assertRaises(ValueError) as e:
param.GetAngleParam('AA', 'BB', 'CC')
self.assertEqual(
str(e.exception),
'No angle parameters found for atom type triplet: AA, BB, CC')
def testEmptyInput(self):
"""Asserts raise of ValueError for empty string input."""
with self.assertRaises(ValueError) as e:
param.GetAngleParam('', '', '')
self.assertEqual(
str(e.exception),
'No angle parameters found for atom type triplet: , , ')
def testCCHBenzene(self):
"""Asserts correct mass for heaviest present atom."""
self.assertEqual(param.GetAngleParam('HA', 'CA', 'CA'), (35.0, 120.0))
def testHOHWater(self):
"""Asserts correct mass for hydrogen atom."""
self.assertEqual(param.GetAngleParam('HW', 'OW', 'HW'),
(100.0, 104.52))
def testDummyInput(self):
"""Asserts zero mass for dummy atom input."""
self.assertEqual(param.GetAngleParam('X', 'X', 'X'), (0.0, 0.0))
