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 GetTorsionFromPrm(record, atoms):
"""Parses torsion record into an Torsion object.
Args:
record (str*): Array of strings from line of prm file.
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
torsion (mmlib.molecule.Torsion): Torsion object.
"""
at1, at2, at3, at4 = (x - 1 for x in map(int, record[1:5]))
v_n, gamma = tuple(map(float, record[5:7]))
nfold, paths = tuple(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)
return molecule.Torsion(at1, at2, at3, at4, t_ijkl, v_n, gamma, nfold,
paths)
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 GetTorsionFromPrm(row):
"""Parses torsion row into an Torsion object.
Args:
row (str*): Array of strings from line of prm file.
Returns:
torsion (mmlib.molecule.Torsion): Torsion object.
Raises:
IndexError: If insufficient number of fields.
ValueError: If incorrect data type of any field.
"""
if len(row) < 9:
raise IndexError('Insufficient columns to parse prm file row into Torsion '
'object: %s' % ' '.join(row))
at1, at2, at3, at4, v_n, gamma, nfold, paths = row[1:9]
if not _IsType(int, at1) or not int(at1) > 0:
raise ValueError('Torsion atom1 index must be positive integer: %s' % at1)
if not _IsType(int, at2) or not int(at2) > 0:
raise ValueError('Torsion atom2 index must be positive integer: %s' % at2)
if not _IsType(int, at3) or not int(at3) > 0:
raise ValueError('Torsion atom3 index must be positive integer: %s' % at3)
if not _IsType(int, at4) or not int(at4) > 0:
raise ValueError('Torsion atom4 index must be positive integer: %s' % at4)
if not _IsType(float, v_n) or not float(v_n) > 0.0:
raise ValueError(
'Torsion half-barrier must be positive numeric value: %s' % v_n)
if not _IsType(float, gamma) or not -180.0 <= float(gamma) <= 180.0:
raise ValueError(
'Torsion offset angle must be between -180.0 and 180.0: %s' % gamma)
if not nfold.isdigit() or not int(nfold) > 0:
raise ValueError(
'Torsion barrier frequency must be positive integer: %s' % nfold)
if not paths.isdigit() or not int(paths) > 0:
raise ValueError(
'Torsion path number must be positive integer: %s' % paths)
return molecule.Torsion(
int(at1)-1, int(at2)-1, int(at3)-1, int(at4)-1, float(v_n), float(gamma),
int(nfold), int(paths))
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 get_torsion(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 = (int(record[1])-1, int(record[2])-1,
int(record[3])-1, int(record[4])-1)
v_n, gamma, nfold, paths = (float(record[5]), float(record[6]),
int(record[7]), int(record[8]))
c1, c2, c3, c4 = (mol.atoms[at1].coords, mol.atoms[at2].coords,
mol.atoms[at3].coords, mol.atoms[at4].coords)
t_ijkl = geomcalc.get_t_ijkl(c1, c2, c3, c4)
torsion = molecule.Torsion(at1, at2, at3, at4, t_ijkl,
v_n, gamma, nfold, paths)
mol.torsions.append(torsion)
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 testArbitrary(self):
"""Asserts correct Torsion object for arbitrary input parameters."""
param = ['ANGLE', '62', '64', '67', '51', '10.0', '90.0', '3', '9']
test.assertObjectEqual(
self, fileio.GetTorsionFromPrm(param),
molecule.Torsion(61, 63, 66, 50, 10.0, 90.0, 3, 9))
def testSmallestValues(self):
"""Asserts correct Torsion object for smallest allowed values."""
param = ['TORSION', '1', '2', '3', '4', '0.000001', '-180.0', '1', '1']
test.assertObjectEqual(
self, fileio.GetTorsionFromPrm(param),
molecule.Torsion(0, 1, 2, 3, 0.000001, -180.0, 1, 1))
