def get_gdir_angle(coords1, coords2, coords3, r_21=None, r_23=None):
"""Calculate direction of energy gradients between bond angle 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.
r_21 (float): Distance between atom2 and atom1 (default None).
r_23 (float): Distance between atom2 and atom3 (default None).
Returns:
gdir1 (float*), gdir2 (float*), gdir3 (float*): vectors in the
direction of max increasing bond angle.
"""
if (not r_21):
r_21 = geomcalc.get_r_ij(coords2, coords1)
if (not r_23):
r_23 = geomcalc.get_r_ij(coords2, coords3)
u_21 = geomcalc.get_u_ij(coords2, coords1, r_21)
u_23 = geomcalc.get_u_ij(coords2, coords3, r_23)
cp = geomcalc.get_ucp(u_21, u_23)
gdir1 = geomcalc.get_ucp(u_21, cp) / r_21
gdir3 = geomcalc.get_ucp(cp, u_23) / r_23
gdir2 = -1.0 * (gdir1 + gdir3)
return gdir1, gdir2, gdir3
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_g_nonbonded(mol):
"""Calculate vdw and elst energy gradients for all nonbonded atom pairs.
Args:
mol (mmlib.molecule.Molecule): Molecule object with associated
Atom objects with geometry and parameter data.
"""
mol.g_nonbonded.fill(0.0)
mol.g_vdw.fill(0.0)
mol.g_elst.fill(0.0)
for i in range(mol.n_atoms):
at1 = mol.atoms[i]
for j in range(i + 1, mol.n_atoms):
if (not j in mol.nonints[i]):
at2 = mol.atoms[j]
r_ij = geomcalc.get_r_ij(at1.coords, at2.coords)
dir1, dir2 = get_gdir_inter(at1.coords, at2.coords, r_ij)
eps_ij = at1.sreps * at2.sreps
ro_ij = at1.ro + at2.ro
g_elst = get_g_elst_ij(r_ij, at1.charge, at2.charge,
mol.dielectric)
g_vdw = get_g_vdw_ij(r_ij, eps_ij, ro_ij)
mol.g_vdw[i] += g_vdw * dir1
mol.g_vdw[j] += g_vdw * dir2
mol.g_elst[i] += g_elst * dir1
mol.g_elst[j] += g_elst * dir2
def get_g_bound_i(k_box, bound, coord, origin, boundtype):
"""Calculate energy gradient magnitude of boundary energy.
Args:
k_box (float): Spring constant [kcal/(mol*A^2)] of boundary.
bound (float): Distance from origin [Angstrom] of boundary.
coords (float*): Array of cartesian coordinates [Angstrom]
of atom.
origin (float*): Array of cartesian coordiantes [Angstrom]
of origin of simulation.
boundtype (str): `cube` or `sphere`, type of boundary condition.
Returns:
g_bound_i (float): Magnitude of energy gradient [kcal/(mol*A)].
"""
g_bound_i = numpy.zeros(3)
if (boundtype == 'cube'):
for j in range(3):
sign = 1.0 if ((coord[j] - origin[j]) <= 0.0) else -1.0
scale = 1.0 if (abs(coord[j] - origin[j]) >= bound) else 0.0
g_bound_i[j] = (-2.0 * sign * scale * k_box *
(abs(coord[j]) - bound))
elif (boundtype == 'sphere'):
r_io = geomcalc.get_r_ij(origin, coord)
u_io = geomcalc.get_u_ij(origin, coord)
scale = 1.0 if (r_io >= bound) else 0.0
g_bound_i = 2.0 * scale * k_box * (r_io - bound) * u_io
return g_bound_i
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_bonds(mol):
"""Update all bond lengths [Angstrom] within a molecule object.
Args:
mol (mmlib.molecule.Molecule): Molecule object with bond data.
"""
for p in range(mol.n_bonds):
b = mol.bonds[p]
c1 = mol.atoms[b.at1].coords
c2 = mol.atoms[b.at2].coords
b.r_ij = geomcalc.get_r_ij(c1, c2)
mol.bond_graph[b.at1][b.at2] = b.r_ij
mol.bond_graph[b.at2][b.at1] = b.r_ij
def get_bond(mol, record):
"""Parse bond record into a bond object and append to molecule.
Appends mmlib.molecule.Bond object to mmlib.molecule.Molecule
object. Contents of bond object include (int) 2 atomic indices,
(float) spring constant [kcal/(mol*A^2)], (float) equilibrium bond
length [Angstrom], (float) bond length [Angstrom].
Args:
mol (mmlib.molecule.Molecule): Molecule to append bond.
record (str*): Array of strings from line of prm file.
"""
at1, at2 = int(record[1])-1, int(record[2])-1
k_b, r_eq = float(record[3]), float(record[4])
c1, c2 = mol.atoms[at1].coords, mol.atoms[at2].coords
r_ij = geomcalc.get_r_ij(c1, c2)
bond = molecule.Bond(at1, at2, r_ij, r_eq, k_b)
mol.bonds.append(bond)
mol.bond_graph[at1][at2] = r_ij
mol.bond_graph[at2][at1] = r_ij