def get_angles(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.get_a_ijk(at1.coords, at2.coords, at3.coords,
r_ij, r_jk)
k_a, a_eq = param.get_angle_param(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 get_gdir_torsion(coords1,
coords2,
coords3,
coords4,
r_12=None,
r_23=None,
r_34=None):
"""Calculate direction of energy gradients between torsion atoms.
Args:
coords1 (float*): 3 cartesian coordinates [Angstrom] of atom1.
coords2 (float*): 3 cartesian coordinates [Angstrom] of atom2.
coords3 (float*): 3 cartesian coordinates [Angstrom] of atom3.
coords4 (float*): 3 cartesian coordinates [Angstrom] of atom4.
r_12 (float): Distance between atom1 and atom2 (default None).
r_23 (float): Distance between atom2 and atom3 (default None).
r_34 (float): Distance between atom3 and atom4 (default None).
Returns:
gdir1 (float*), gdir2 (float*), gdir3 (float*), gdir4 (float*):
vectors in the direction of max increasing torsion angle.
"""
if (not r_12):
r_12 = geomcalc.get_r_ij(coords1, coords2)
if (not r_23):
r_23 = geomcalc.get_r_ij(coords2, coords3)
if (not r_34):
r_34 = geomcalc.get_r_ij(coords3, coords4)
u_21 = geomcalc.get_u_ij(coords2, coords1, r_12)
u_34 = geomcalc.get_u_ij(coords3, coords4, r_34)
u_23 = geomcalc.get_u_ij(coords2, coords3, r_23)
u_32 = -1.0 * u_23
a_123 = geomcalc.get_a_ijk(coords1, coords2, coords3, r_12, r_23)
a_432 = geomcalc.get_a_ijk(coords4, coords3, coords2, r_34, r_23)
s_123 = math.sin(geomcalc.deg2rad() * a_123)
s_432 = math.sin(geomcalc.deg2rad() * a_432)
c_123 = math.cos(geomcalc.deg2rad() * a_123)
c_432 = math.cos(geomcalc.deg2rad() * a_432)
gdir1 = geomcalc.get_ucp(u_21, u_23) / (r_12 * s_123)
gdir4 = geomcalc.get_ucp(u_34, u_32) / (r_34 * s_432)
gdir2 = (r_12 / r_23 * c_123 - 1.0) * gdir1 - (r_34 / r_23 * c_432) * gdir4
gdir3 = (r_34 / r_23 * c_432 - 1.0) * gdir4 - (r_12 / r_23 * c_123) * gdir1
return gdir1, gdir2, gdir3, gdir4
def update_angles(mol):
"""Update all bond angles [degrees] within a molecule object.
Args:
mol (mmlib.molecule.Molecule): Molecule object with angle data.
"""
for p in range(mol.n_angles):
a = mol.angles[p]
r12 = mol.bond_graph[a.at1][a.at2]
r23 = mol.bond_graph[a.at2][a.at3]
c1 = mol.atoms[a.at1].coords
c2 = mol.atoms[a.at2].coords
c3 = mol.atoms[a.at3].coords
a.a_ijk = geomcalc.get_a_ijk(c1, c2, c3, r12, r23)
def get_gdir_outofplane(coords1,
coords2,
coords3,
coords4,
oop,
r_31=None,
r_32=None,
r_34=None):
"""Calculate direction of energy gradients between outofplane atoms.
Args:
coords1 (float*): 3 cartesian coordinates [Angstrom] of atom1.
coords2 (float*): 3 cartesian coordinates [Angstrom] of atom2.
coords3 (float*): 3 cartesian coordinates [Angstrom] of atom3.
coords4 (float*): 3 cartesian coordinates [Angstrom] of atom4.
oop (float): Out-of-plane angles bewteen atoms 1, 2, 3, and 4.
r_31 (float): Distance between atom3 and atom1 (default None).
r_32 (float): Distance between atom3 and atom2 (default None).
r_34 (float): Distance between atom3 and atom4 (default None).
Returns:
gdir1 (float*), gdir2 (float*), gdir3 (float*), gdir4 (float*):
vectors in the direction of max increasing outofplane angle.
"""
if (not r_31):
r_31 = geomcalc.get_r_ij(coords3, coords1)
if (not r_32):
r_32 = geomcalc.get_r_ij(coords3, coords2)
if (not r_34):
r_34 = geomcalc.get_r_ij(coords3, coords4)
u_31 = geomcalc.get_u_ij(coords3, coords1, r_31)
u_32 = geomcalc.get_u_ij(coords3, coords2, r_32)
u_34 = geomcalc.get_u_ij(coords3, coords4, r_34)
cp_3234 = geomcalc.get_cp(u_32, u_34)
cp_3431 = geomcalc.get_cp(u_34, u_31)
cp_3132 = geomcalc.get_cp(u_31, u_32)
a_132 = geomcalc.get_a_ijk(coords1, coords3, coords2)
s_132 = math.sin(geomcalc.deg2rad() * a_132)
c_132 = math.cos(geomcalc.deg2rad() * a_132)
c_oop = math.cos(geomcalc.deg2rad() * oop)
t_oop = math.tan(geomcalc.deg2rad() * oop)
gdir1 = ((1.0 / r_31) * (cp_3234 / (c_oop * s_132) - (t_oop / s_132**2) *
(u_31 - c_132 * u_32)))
gdir2 = ((1.0 / r_32) * (cp_3431 / (c_oop * s_132) - (t_oop / s_132**2) *
(u_32 - c_132 * u_31)))
gdir4 = ((1.0 / r_34) * (cp_3132 / (c_oop * s_132) - (t_oop * u_34)))
gdir3 = -1.0 * (gdir1 + gdir2 + gdir4)
return gdir1, gdir2, gdir3, gdir4
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)