def GetAngles(mol):
"""Determine bond angle atom triplets from bond graph and get parameters.
Search bond graph for bond angle triplets, and parameter tables for mm
parameters. Use to create a new Angle object and append to Molecule.
Count as angle if ij and jk are bonded in triplet ijk.
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 i in mol.bond_graph[j].keys():
at1 = mol.atoms[i]
r_ij = mol.bond_graph[i][j]
for k in mol.bond_graph[j].keys():
if i >= k:
continue
at3 = mol.atoms[k]
r_jk = mol.bond_graph[j][k]
a_ijk = geomcalc.GetAijk(at1.coords, at2.coords, at3.coords,
r_ij, r_jk)
k_a, a_eq = param.GetAngleParam(at1.type_, at2.type_,
at3.type_)
if k_a > 0.0:
mol.angles.append(molecule.Angle(i, j, k, a_ijk, a_eq,
k_a))
mol.angles = sorted(mol.angles, key=lambda a: a.at3)
mol.angles = sorted(mol.angles, key=lambda a: a.at2)
mol.angles = sorted(mol.angles, key=lambda a: a.at1)
mol.n_angles = len(mol.angles)
def GetAngles(atoms, bond_graph):
"""Determine bond angle atom triplets from bond graph and get parameters.
Search bond graph for bond angle triplets, and parameter tables for mm
parameters. Use to create a new Angle object and append to Molecule.
Count as angle if ij and jk are bonded in triplet ijk.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int:float)): Dictionary of bond connectivity.
Returns:
angles (mmlib.molecule.Angle*): Array of molecule's Angle objects.
"""
angles = []
for j, at2 in enumerate(atoms):
for i, k in itertools.combinations(bond_graph[j], 2):
if i > k:
continue
at1, at3 = atoms[i], atoms[k]
a_ijk = geomcalc.GetAijk(at1.coords, at2.coords, at3.coords)
k_a, a_eq = param.GetAngleParam(at1.type_, at2.type_, at3.type_)
if k_a:
angles.append(molecule.Angle(i, j, k, k_a, a_eq, a_ijk))
angles.sort(key=lambda a: (a.at1, a.at2, a.at3))
return angles
def GetAngleFromPrm(row):
"""Parses angle row into an Angle object.
Args:
row (str*): Array of strings from line of prm file.
Returns:
angle (mmlib.molecule.Angle): Angle object with attributes from row.
Raises:
IndexError: If insufficient number of fields.
ValueError: If incorrect data type of any field.
"""
if len(row) < 6:
raise IndexError('Insufficient columns to parse prm file row into Angle '
'object: %s' % ' '.join(row))
at1, at2, at3, k_a, a_eq = row[1:6]
if not _IsType(int, at1) or not int(at1) > 0:
raise ValueError('Angle atom1 index must be positive integer: %s' % at1)
if not _IsType(int, at2) or not int(at2) > 0:
raise ValueError('Angle atom2 index must be positive integer: %s' % at2)
if not _IsType(int, at3) or not int(at3) > 0:
raise ValueError('Angle atom3 index must be positive integer: %s' % at3)
if not _IsType(float, k_a) or not float(k_a) > 0.0:
raise ValueError(
'Angle spring constant must be positive numeric value: %s' % k_a)
if not _IsType(float, a_eq) or not 0.0 <= float(a_eq) <= 180.0:
raise ValueError(
'Equilibrium bond angle must be between 0.0 and 180.0: %s' % a_eq)
return molecule.Angle(
int(at1)-1, int(at2)-1, int(at3)-1, float(k_a), float(a_eq))
def GetAngleFromPrm(record, atoms):
"""Parses angle record into an Angle object.
Args:
record (str*): Array of strings from line of prm file.
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
angle (mmlib.molecule.Angle): Angle object with attributes from record.
"""
at1, at2, at3 = (x - 1 for x in (map(int, record[1:4])))
k_a, a_eq = tuple(map(float, record[4:6]))
c1, c2, c3 = (atoms[i].coords for i in (at1, at2, at3))
a_ijk = geomcalc.GetAijk(c1, c2, c3)
return molecule.Angle(at1, at2, at3, a_ijk, a_eq, k_a)
def _GetAngle(mol, record):
"""Parse angle record into an angle object and append to molecule.
Appends mmlib.molecule.Angle object to mmlib.molecule.Molecule object.
Contents of angle object include (int) 3 atomic indices, (float) spring
constant [kcal/(mol*radian^2)], (float) equilibrium bond angle [degrees], and
(float) bond angle [degrees].
Args:
mol (mmlib.molecule.Molecule): Molecule to append angle.
record (str*): Array of strings from line of prm file.
"""
at1, at2, at3 = [x-1 for x in list(map(int, record[1:4]))]
k_a, a_eq = list(map(float, record[4:6]))
c1, c2, c3 = [mol.atoms[i].coords for i in [at1, at2, at3]]
a_ijk = geomcalc.GetAijk(c1, c2, c3)
angle = molecule.Angle(at1, at2, at3, a_ijk, a_eq, k_a)
mol.angles.append(angle)
def get_angle(mol, record):
"""Parse angle record into an angle object and append to molecule.
Appends mmlib.molecule.Angle object to mmlib.molecule.Molecule
object. Contents of angle object include (int) 3 atomic indices,
(float) spring constant [kcal/(mol*radian^2)], (float) equilibrium
bond angle [degrees], and (float) bond angle [degrees].
Args:
mol (mmlib.molecule.Molecule): Molecule to append angle.
record (str*): Array of strings from line of prm file.
"""
at1, at2, at3 = int(record[1])-1, int(record[2])-1, int(record[3])-1
k_a, a_eq = float(record[4]), float(record[5])
c1, c2, c3 = (mol.atoms[at1].coords, mol.atoms[at2].coords,
mol.atoms[at3].coords)
a_ijk = geomcalc.get_a_ijk(c1, c2, c3)
angle = molecule.Angle(at1, at2, at3, a_ijk, a_eq, k_a)
mol.angles.append(angle)
def GetAngles(records, atoms):
"""Parses angle records into an array of Angle objects.
Args:
records (str**): 2d array of strings from lines of prm file.
atom (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
angles (mmlib.molecule.Angle): Array of Angle objects with parameters from
records.
"""
angles = []
for record in records:
if not record[0].upper() == 'ANGLE':
continue
at1, at2, at3 = [x - 1 for x in list(map(int, record[1:4]))]
k_a, a_eq = list(map(float, record[4:6]))
c1, c2, c3 = [atoms[i].coords for i in [at1, at2, at3]]
a_ijk = geomcalc.GetAijk(c1, c2, c3)
angles.append(molecule.Angle(at1, at2, at3, a_ijk, a_eq, k_a))
return angles
def testArbitrary(self):
"""Asserts correct Angle object for arbitrary input parameters."""
param = ['ANGLE', '62', '64', '67', '179.838', '17.76']
test.assertObjectEqual(self, fileio.GetAngleFromPrm(param),
molecule.Angle(61, 63, 66, 179.838, 17.76))
def testSmallestValues(self):
"""Asserts correct Angle object for smallest allowed values."""
param = ['ANGLE', '1', '2', '3', '0.000001', '0.000001']
test.assertObjectEqual(self, fileio.GetAngleFromPrm(param),
molecule.Angle(0, 1, 2, 0.000001, 0.000001))
