def testEmptyInput(self):
"""Asserts raise of ValueError for empty string input."""
with self.assertRaises(ValueError) as e:
param.GetBondParam('', '')
self.assertEqual(str(e.exception),
'No bond parameters found for atom type pair: , ')
def GetBonds(atoms, bond_graph):
"""Determine covalently bonded atoms from bond graph and get parameters.
Search bond graph for bonded atom pairs, and parameter tables for mm
parameters. Use to create a new Bond object and append to Molecule.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int: float)): Dictionary of bond connectivity.
Returns:
bonds (mmlib.molecule.Bond*): Array of molecule's Bond objects.
"""
bonds = []
for i, at1 in enumerate(atoms):
for j in bond_graph[i]:
if i > j:
continue
at2 = atoms[j]
r_ij = bond_graph[i][j]
k_b, r_eq = param.GetBondParam(at1.type_, at2.type_)
if k_b:
bonds.append(molecule.Bond(i, j, k_b, r_eq, r_ij))
bonds.sort(key=lambda b: (b.at1, b.at2))
return bonds
def testBadInput(self):
"""Asserts raise of ValueError for missing atom types input."""
with self.assertRaises(ValueError) as e:
param.GetBondParam('AA', 'BB')
self.assertEqual(
str(e.exception),
'No bond parameters found for atom type pair: AA, BB')
def GetBonds(mol):
"""Determine covalently bonded atoms from bond graph and get parameters.
Search bond graph for bonded atom pairs, and parameter tables for mm
parameters. Use to create a new Bond object and append to Molecule.
Args:
mol (mmlib.molecule.Molecule): Molecule object with bond graph of atom pairs
within covalent radius cutoff threshold.
"""
for i in range(mol.n_atoms):
at1 = mol.atoms[i]
for j in mol.bond_graph[i].keys():
at2 = mol.atoms[j]
if i >= j:
r_ij = mol.bond_graph[i][j]
k_b, r_eq = param.GetBondParam(at1.type_, at2.type_)
if k_b > 0.0:
mol.bonds.append(molecule.Bond(i, j, r_ij, r_eq, k_b))
mol.bonds = sorted(mol.bonds, key=lambda b: b.at2)
mol.bonds = sorted(mol.bonds, key=lambda b: b.at1)
mol.n_bonds = len(mol.bonds)
def testCarbonHydrogenReversedBond(self):
"""Asserts correct parameters for aromatic reversed carbon-hydrogen bond."""
self.assertEqual(param.GetBondParam('HA', 'CA'), (367.0, 1.080))
def testOxygenHydrogenBond(self):
"""Asserts correct parameters for water hydrogen-oxygen bond."""
self.assertEqual(param.GetBondParam('OW', 'HW'), (553.0, 0.9572))
def testDummyInput(self):
"""Asserts zero parameters for dummy atom types input."""
self.assertEqual(param.GetBondParam('X', 'X'), (0.0, 0.0))