def GetOutofplanes(atoms, bond_graph):
"""Determine outofplane atom quartets and parameters from bond graph.
Search bond graph for outofplane angle quartets, and parameter tables for mm
parameters. Use to create a new Outofplane object and append to Molecule.
Count as outofplane if il and jl and kl are bonded in quartet ijkl.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int:foat)): Dictionary of bond connectivity.
Returns:
outofplanes (mmlib.molecule.Outofplane*): Array of molecule's Outofplane
objects.
"""
outofplanes = []
for k, at3 in enumerate(atoms):
for i, j, l in itertools.combinations(bond_graph[k], 3):
at1, at2, at4 = atoms[i], atoms[j], atoms[l]
# Three unique oop angles with this central atom (k) and atom quartet
combos = [(min(i, j), max(i, j), k, l), (min(j, l), max(j,
l), k, i),
(min(l, i), max(l, i), k, j)]
for combo in combos:
o_ijkl = geomcalc.GetOijkl(*[atoms[x].coords for x in combo])
v_n = param.GetOutofplaneParam(
*[atoms[x].type_ for x in combo])
if v_n:
outofplanes.append(molecule.Outofplane(
*combo, v_n, o_ijkl))
outofplanes.sort(key=lambda o: (o.at1, o.at2, o.at3, o.at4))
return outofplanes
def GetOutofplanes(mol):
"""Determine outofplane atom quartets and parameters from bond graph.
Search bond graph for outofplane angle quartets, and parameter tables for mm
parameters. Use to create a new Outofplane object and append to Molecule.
Count as outofplane if il and jl 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 k in range(mol.n_atoms):
at3 = mol.atoms[k]
for l in mol.bond_graph[k].keys():
if k == l:
continue
at4 = mol.atoms[l]
r34 = mol.bond_graph[k][l]
for i in mol.bond_graph[k].keys():
if i == k or i == l:
continue
at1 = mol.atoms[i]
r31 = mol.bond_graph[k][i]
for j in mol.bond_graph[k].keys():
if j >= i or j == k or j == l:
continue
at2 = mol.atoms[j]
r32 = mol.bond_graph[k][j]
o_ijkl = geomcalc.GetOijkl(at1.coords, at2.coords,
at3.coords, at4.coords, r31,
r32, r34)
v_n = param.GetOutofplaneParam(at1.type_, at2.type_,
at3.type_, at4.type_)
if v_n > 0.0:
mol.outofplanes.append(
molecule.Outofplane(i, j, k, l, o_ijkl, v_n))
mol.outofplanes = sorted(mol.outofplanes, key=lambda o: o.at4)
mol.outofplanes = sorted(mol.outofplanes, key=lambda o: o.at3)
mol.outofplanes = sorted(mol.outofplanes, key=lambda o: o.at2)
mol.outofplanes = sorted(mol.outofplanes, key=lambda o: o.at1)
mol.n_outofplanes = len(mol.outofplanes)
def test1234(self):
"""Asserts correct paramter for complete atom quartet."""
self.assertEqual(param.GetOutofplaneParam('CA', 'CA', 'C', 'OH'), 1.1)
def test234(self):
"""Asserts correct parameter for ending atom triplet."""
self.assertEqual(param.GetOutofplaneParam('', 'CT', 'N', 'CT'), 1.0)
def test34(self):
"""Asserts correct parameter for ending atom pair."""
self.assertEqual(param.GetOutofplaneParam('', '', 'C', 'O'), 10.5)
def testEmptyInput(self):
"""Asserts zero value for empty string input."""
self.assertEqual(param.GetOutofplaneParam('', '', '', ''), 0.0)