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 _GetTorsion(mol, record):
"""Parse torsion record into a torsion object and append to molecule.
Appends mmlib.molecule.Torsion object to mmlib.molecule.Molecule object.
Contents of torsion object include (int) 4 atomic indices, (float)
half-barrier height [kcal/mol], (float) barrier offset [degrees], (int)
barrier frequency, (int) barrier paths, and (float) torsion angle [degrees].
Args:
mol (mmlib.molecule.Molecule): Molecule to append torsion.
record (str*): Array of strings from line of prm file.
"""
at1, at2, at3, at4 = [x-1 for x in list(map(int, record[1:5]))]
v_n, gamma = list(map(float, record[5:7]))
nfold, paths = list(map(int, record[7:9]))
c1, c2, c3, c4 = [mol.atoms[i].coords for i in [at1, at2, at3, at4]]
t_ijkl = geomcalc.GetTijkl(c1, c2, c3, c4)
tors = molecule.Torsion(at1, at2, at3, at4, t_ijkl, v_n, gamma, nfold, paths)
mol.torsions.append(tors)
def GetTorsions(records, atoms):
"""Parses torsion records into an array of Torsion objects.
Args:
records (str**): 2d array of strings from lines of prm file.
atom (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
torsions (mmlib.molecule.Torsion*): Array of Torsion objects with parameters
from record.
"""
torsions = []
for record in records:
if not record[0].upper() == 'TORSION':
continue
at1, at2, at3, at4 = [x - 1 for x in list(map(int, record[1:5]))]
v_n, gamma = list(map(float, record[5:7]))
nfold, paths = list(map(int, record[7:9]))
c1, c2, c3, c4 = [atoms[i].coords for i in [at1, at2, at3, at4]]
t_ijkl = geomcalc.GetTijkl(c1, c2, c3, c4)
torsions.append(
molecule.Torsion(at1, at2, at3, at4, t_ijkl, v_n, gamma, nfold,
paths))
return torsions
def testReflixe(self):
"""Asserts same value when inverting the order of points."""
params = ARBITRARY_XYZ5, ARBITRARY_XYZ4, ARBITRARY_XYZ3, ARBITRARY_XYZ2
self.assertAlmostEqual(geomcalc.GetTijkl(*params), 37.31802340)
def testArbitraryPositive(self):
"""Asserts correct negative value between arbitrary 3d points."""
params = ARBITRARY_XYZ2, ARBITRARY_XYZ3, ARBITRARY_XYZ4, ARBITRARY_XYZ5
self.assertAlmostEqual(geomcalc.GetTijkl(*params), 37.31802340)
def testArbitraryNegative(self):
"""Asserts correct negative value between arbitrary 3d points."""
params = ARBITRARY_XYZ1, ARBITRARY_XYZ2, ARBITRARY_XYZ3, ARBITRARY_XYZ4
self.assertAlmostEqual(geomcalc.GetTijkl(*params), -92.01024227)
def testPositiveRightTorsion(self):
"""Asserts positive ninety degree torsion combination."""
params = POSITIVE_UNIT_X, ORIGIN, POSITIVE_UNIT_Y, ARBITRARY_UNIT_XY4
self.assertAlmostEqual(geomcalc.GetTijkl(*params), 180.0)
def testNegativeRightTorsion(self):
"""Asserts negative ninety degree torsion combination."""
params = POSITIVE_UNIT_X, ORIGIN, POSITIVE_UNIT_Y, POSITIVE_UNIT_Z
self.assertAlmostEqual(geomcalc.GetTijkl(*params), -90.0)
def testZeroTorsion(self):
"""Asserts zero torsion within the xy-plane."""
params = POSITIVE_UNIT_X, ORIGIN, POSITIVE_UNIT_Y, ARBITRARY_UNIT_XY1
self.assertAlmostEqual(geomcalc.GetTijkl(*params), 0.0)
