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_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 get_g_angle(a_ijk, a_eq, k_a):
"""Calculate energy gradient magnitude of angle bend.
Args:
a_ijk (float): Angle [degrees] between atoms i, j, and k.
a_eq (float): Equilibrium bond angle [degrees] of angle ijk.
k_a (float): Spring constant [kcal/(mol*rad^2)] of angle ijk.
Returns:
g_angle (float): Magnitude of energy gradient [kcal/(mol*A)].
"""
g_angle = 2.0 * k_a * (geomcalc.deg2rad() * (a_ijk - a_eq))
return g_angle
def get_g_outofplane(o_ijkl, v_n):
"""Calculate energy gradient magnitude of outofplane bend.
Args:
o_ijkl (float): Outofplane angle [degrees] between atoms
i, j, k, and l.
v_n (float): Half-barrier height [kcal/mol] of outofplane ijkl.
Returns:
g_outofplane (float): Magnitude of energy gradient [kcal/(mol*A)].
"""
g_outofplane = (-v_n * 2.0 * math.sin(geomcalc.deg2rad() *
(2.0 * o_ijkl - 180.0)))
return g_outofplane
def get_g_torsion(t_ijkl, v_n, gamma, n_fold, paths):
"""Calculate energy gradient magnitude of torsion strain.
Args:
t_ijkl (float): Torsion [degrees] between atoms i, j, k, and l.
v_n (float): Half-barrier height [kcal/mol] of torsion ijkl.
gamma (float): Barrier offset [degrees] of torsion ijkl.
n_fold (int): Barrier frequency of torsion ijkl.
paths (int): Number of distinct paths in torsion ijkl.
Returns:
g_torsion (float): Magnitude of energy gradient [kcal/(mol*A)].
"""
g_torsion = (-v_n * n_fold * math.sin(geomcalc.deg2rad() *
(n_fold * t_ijkl - gamma)) / paths)
return g_torsion