def GetTorsions(atoms, bond_graph):
"""Determine torsion angle atom quartets and parameters from bond graph.
Search bond graph for torsion angle quartets, and parameter tables for mm
parameters. Use to create a new Torsion object and append to Molecule. Count
as torsion if ij and jk and kl are bonded in quartet ijkl.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int:float)): Dictionary of bond connectivity.
Returns:
torsions (mmlib.molecule.Torsion*): Array of molecule's Torsion objects.
"""
torsions = []
for j, at2 in enumerate(atoms):
for i, k in itertools.permutations(bond_graph[j], 2):
if j > k:
continue
at1, at3 = atoms[i], atoms[k]
for l in bond_graph[k]:
if l == i or l == j:
continue
at4 = atoms[l]
t_ijkl = geomcalc.GetTijkl(at1.coords, at2.coords, at3.coords,
at4.coords)
params = param.GetTorsionParam(at1.type_, at2.type_, at3.type_,
at4.type_)
for v_n, gamma, nfold, paths in params:
if v_n:
torsions.append(
molecule.Torsion(i, j, k, l, v_n, gamma, nfold,
paths, t_ijkl))
torsions.sort(key=lambda t: (t.at1, t.at2, t.at3, t.at4))
return torsions
def testBadInput(self):
"""Asserts raise of ValueError for missing string input."""
with self.assertRaises(ValueError) as e:
param.GetTorsionParam('AA', 'BB', 'CC', 'DD')
self.assertEqual(
str(e.exception),
'No torsion parameters found for central atom pair: BB, CC')
def testEmptyInput(self):
"""Asserts raise of ValueError for empty string input."""
with self.assertRaises(ValueError) as e:
param.GetTorsionParam('', '', '', '')
self.assertEqual(
str(e.exception),
'No torsion parameters found for central atom pair: , ')
def GetTorsions(mol):
"""Determine torsion angle atom quartets and parameters from bond graph.
Search bond graph for torsion angle quartets, and parameter tables for mm
parameters. Use to create a new Torsion object and append to Molecule. Count
as torsion if ij and jk and kl are bonded in quartet ijkl.
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 k in mol.bond_graph[j].keys():
if j >= k:
continue
at3 = mol.atoms[k]
r_jk = mol.bond_graph[j][k]
for i in mol.bond_graph[j].keys():
if i == j or i == k:
continue
at1 = mol.atoms[i]
r_ij = mol.bond_graph[i][j]
for l in mol.bond_graph[k].keys():
if i == l or j == l or k == l:
continue
at4 = mol.atoms[l]
r_kl = mol.bond_graph[k][l]
t_ijkl = geomcalc.GetTijkl(at1.coords, at2.coords,
at3.coords, at4.coords, r_ij,
r_jk, r_kl)
params = param.GetTorsionParam(at1.type_, at2.type_,
at3.type_, at4.type_)
for p in range(len(params)):
v_n, gamma, nfold, paths = params[p]
if v_n > 0.0:
mol.torsions.append(
molecule.Torsion(i, j, k, l, t_ijkl, v_n,
gamma, nfold, paths))
mol.torsions = sorted(mol.torsions, key=lambda t: t.at4)
mol.torsions = sorted(mol.torsions, key=lambda t: t.at3)
mol.torsions = sorted(mol.torsions, key=lambda t: t.at2)
mol.torsions = sorted(mol.torsions, key=lambda t: t.at1)
mol.n_torsions = len(mol.torsions)
def testFourAtomReversed(self):
"""Asserts correct parameters for given reversed atom quartet."""
self.assertEqual(param.GetTorsionParam('C', 'N', 'CT', 'CT'),
_CT_CT_N_C_TORSION_PARAMS)
def testCentralReversed(self):
"""Asserts correct parameters for given reversed central atom pair."""
self.assertEqual(param.GetTorsionParam('X', 'CA', 'C', 'X'),
[(14.50, 180.0, 2, 4)])