def calcDihedralForce(self, dihedral):
if dihedral.get_conformation() is None:
return
cosdelta = 1.0
if dihedral.get_conformation() == 'cis':
cosdelta = -1.0
atom1 = dihedral.get_a_1()
atom2 = dihedral.get_a_2()
atom3 = dihedral.get_a_3()
atom4 = dihedral.get_a_4()
rij = vectorFromAtoms(dihedral.get_a_1(),dihedral.get_a_2())
rkj = vectorFromAtoms(dihedral.get_a_3(),dihedral.get_a_2())
rkl = vectorFromAtoms(dihedral.get_a_3(),dihedral.get_a_4())
k = 33.5
#rmj = np.cross(rij,rkj)
#rnk = np.cross(rkj,rkl)
dkj2 = np.linalg.norm(rkj)*np.linalg.norm(rkj)
frim = np.dot(rij,rkj) / dkj2
frln = np.dot(rkl,rkj) / dkj2
rim = np.array(rij) - frim * np.array(rkj)
rln = frln * np.array(rkj) - np.array(rkl)
dim = math.sqrt(np.linalg.norm(rim)*np.linalg.norm(rim))
dln = math.sqrt(np.linalg.norm(rln)*np.linalg.norm(rln))
ip = np.dot(rim,rln)
cosphi = ip / (dim * dln)
cosphi2 = cosphi*cosphi
cosphi3 = cosphi2*cosphi
cosphi4 = cosphi3*cosphi
cosmphi = cosphi
dcosmphi = 1
ki = -k * cosdelta * dcosmphi / dim
kl = -k * cosdelta * dcosmphi / dln
kj1 = frim - 1.0
kj2 = frln
fi = ki * (np.array(rln) / dln - np.array(rim) / dim * cosphi)
fl = kl * (np.array(rim) / dim - np.array(rln) / dln * cosphi)
fj = kj1 * np.array(fi) - kj2 * np.array(fl)
fk = -1.0 * (np.array(fi) + np.array(fl) + np.array(fj))
self.forces[int(atom1.get_nr()) - 1] += fi
self.forces[int(atom2.get_nr()) - 1] += fj
self.forces[int(atom3.get_nr()) - 1] += fk
self.forces[int(atom4.get_nr()) - 1] += fl
def calcMediaTeta(self):
media = 0.0
for angle in self.top.get_angle_list():
atom1 = angle.get_a_1()
atom2 = angle.get_a_2()
atom3 = angle.get_a_3()
vecAB = vectorFromAtoms(atom2, atom1)
vecAB = unit_vector(vecAB)
vecBC = vectorFromAtoms(atom2, atom3)
vecBC = unit_vector(vecBC)
teta = self.angle_between(vecAB, vecBC)
media += teta
def calcMediaAngle(self):
media = 0.0
for angle in self.top.get_angle_list():
atom1 = angle.get_a_1()
atom2 = angle.get_a_2()
atom3 = angle.get_a_3()
vecAB = vectorFromAtoms(atom2, atom1)
vecAB = unit_vector(vecAB)
vecBC = vectorFromAtoms(atom2, atom3)
vecBC = unit_vector(vecBC)
teta = self.cosine_similarity(vecAB, vecBC)
media += teta
def calcAngledForce(self, angle, ff_angles):
k = 1000
cost0 = -0.5 # 120 degree
atom1 = angle.get_a_1()
atom2 = angle.get_a_2()
atom3 = angle.get_a_3()
# Overwrite the hardcoded params
if ff_angles is not None:
t0 = ff_angles[angle.get_param()][0]
cost0 = np.cos(t0 * (np.pi / 180))
# k = ff_angles[angle.get_param()][1]
vecAB = self.vectorFromAtoms(atom1, atom2)
vecAB = unit_vector(vecAB)
vecCB = vectorFromAtoms(atom3, atom2)
vecCB = unit_vector(vecCB)
costeta = self.cosine_2unit_v(vecAB, vecCB)
df = -k * (costeta - cost0)
forceA = df * (vecCB - vecAB * costeta)
forceC = df * (vecAB - vecCB * costeta)
forceB = -1 * forceA - forceC
self.forces[int(atom1.get_nr()) - 1] += forceA
self.forces[int(atom2.get_nr()) - 1] += forceB
self.forces[int(atom3.get_nr()) - 1] += forceC
self.totalAngles[0] += self.calcVectorModule(forceA)
self.totalAngles[1] += self.calcVectorModule(forceB)
self.totalAngles[2] += self.calcVectorModule(forceC)
def calcDihedralEnergy(self, dihedral, ff_dihedrals):
if dihedral.get_conformation() is None:
return 0
cosdelta = 1.0
if dihedral.get_conformation() == 'cis':
cosdelta = -1.0
rij = vectorFromAtoms(dihedral.get_a_1(), dihedral.get_a_2())
rkj = vectorFromAtoms(dihedral.get_a_3(), dihedral.get_a_2())
rkl = vectorFromAtoms(dihedral.get_a_3(), dihedral.get_a_4())
# Overwrite the hardcoded params
if ff_dihedrals is not None:
delta = ff_dihedrals[dihedral.get_param()][0]
cosdelta = np.cos(delta * (np.pi / 180))
k = 33.5
dkj2 = np.linalg.norm(rkj) * np.linalg.norm(rkj)
frim = np.dot(rij, rkj) / dkj2
frln = np.dot(rkl, rkj) / dkj2
rim = np.array(rij) - frim * np.array(rkj)
rln = frln * np.array(rkj) - np.array(rkl)
dim = math.sqrt(np.linalg.norm(rim) * np.linalg.norm(rim))
dln = math.sqrt(np.linalg.norm(rln) * np.linalg.norm(rln))
ip = np.dot(rim, rln)
cosphi = ip / (dim * dln)
# This is a simplified formula considering only multiplicity 2
cosmphi = cosphi
energy = k * (1 + cosdelta * cosmphi)
return energy
def calcAngledForce(self, angle):
k = 1000
cost0 = -0.5 # 120 degree
atom1 = angle.get_a_1()
atom2 = angle.get_a_2()
atom3 = angle.get_a_3()
vecAB = self.vectorFromAtoms(atom1, atom2)
vecAB = unit_vector(vecAB)
vecCB = vectorFromAtoms(atom3, atom2)
vecCB = unit_vector(vecCB)
costeta = self.cosine_2unit_v(vecAB, vecCB)
df = -k * (costeta - cost0)
forceA = df * (vecCB - vecAB * costeta)
forceC = df * (vecAB - vecCB * costeta)
forceB = -1 * forceA - forceC
self.forces[int(atom1.get_nr()) - 1] += forceA
self.forces[int(atom2.get_nr()) - 1] += forceB
self.forces[int(atom3.get_nr()) - 1] += forceC
def calcAngleEnergy(self, angle, ff_angles):
k = 1000
cost0 = -0.5 # 120 degree
atom1 = angle.get_a_1()
atom2 = angle.get_a_2()
atom3 = angle.get_a_3()
#Overwrite the hardcoded params
if ff_angles is not None:
t0 = ff_angles[angle.get_param()][0]
cost0 = np.cos(t0 * (np.pi / 180))
k = ff_angles[angle.get_param()][1]
vecAB = self.vectorFromAtoms(atom1, atom2)
vecAB = unit_vector(vecAB)
vecCB = vectorFromAtoms(atom3, atom2)
vecCB = unit_vector(vecCB)
costeta = self.cosine_2unit_v(vecAB, vecCB)
energy = 0.5 * k * (costeta - cost0)**2
return energy
def setPositionNeighbor(self, neighbor, atom, count, insertedNeighbors,
previousAtom):
bond = 0.10 if ((neighbor.get_atomtype() == 'H') or
(neighbor.get_atomtype() == 'HC')) else 0.15
if previousAtom == atom:
if count == 0:
# print ("COUNT 0 - level 0")
neighbor.setposition(atom.get_x() + bond, atom.get_y(),
atom.get_z())
return
if count == 1:
# print ("COUNT 1 - level 0!!!")
z = 1
cos = -0.5
sin = 0.866
x = atom.get_x() + bond * cos
y = atom.get_y() + bond * sin
neighbor.setposition(x, y, z)
return
if count == 2:
# print("COUNT 2 - level 0!!!")
v1 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v2 = unit_vector(vectorFromAtoms(insertedNeighbors[1], atom))
v3 = unit_vector(np.array(v1) + np.array(v2))
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) - bond * np.array(v3)
neighbor.setposition(position[0], position[1], position[2])
return
if count == 3:
neighbor.setposition(
atom.get_x(), atom.get_y(),
atom.get_z() - 0.1 + random.uniform(0, 0.05))
return
if count == 0:
dihedral = self.find_dihedral(previousAtom, atom)
if dihedral != None:
# print("COUNT 0a - level 1!!!")
otherAtom = None
if dihedral.get_a_1() == neighbor:
otherAtom = dihedral.get_a_4()
if dihedral.get_a_4() == neighbor:
otherAtom = dihedral.get_a_1()
v1 = unit_vector(vectorFromAtoms(otherAtom, previousAtom))
v2 = unit_vector(vectorFromAtoms(previousAtom, atom))
v4 = unit_vector(np.cross(v1, v2))
if dihedral.get_conformation() is not None:
v5 = unit_vector(np.cross(v2, v4))
if dihedral.get_conformation() == 'cis':
v6 = bond * -0.5 * v2 - bond * 0.866 * -v5
else:
v6 = bond * -0.5 * v2 - bond * 0.866 * v5
position = np.array([
atom.get_x(), atom.get_y(),
atom.get_z()
]) + v6
neighbor.setposition(position[0], position[1], position[2])
return
v5 = unit_vector(np.cross(
v2, v4)) + (0, 0, random.uniform(-0.5, 0.5))
v6 = bond * -0.5 * v2 - bond * 0.866 * unit_vector(v5)
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) + v6
neighbor.setposition(position[0], position[1], position[2])
return
if dihedral is None:
# print("COUNT 0b - level 1!!!")
cos = -0.5
sin = 0.866
x = atom.get_x() + bond * cos
y = atom.get_y() + bond * sin
z = atom.get_z()
neighbor.setposition(x, y, z)
return
if count == 1:
# print("COUNT 1 - level 1!!!")
sp3angle = math.radians(109.5)
v2 = unit_vector(vectorFromAtoms(previousAtom, atom))
v3 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v4 = unit_vector(-(v2 + v3))
v5 = np.cross(v2, v3)
position = np.array([atom.get_x(
), atom.get_y(), atom.get_z()]) + bond * math.sin(
0.5 * sp3angle) * v5 + bond * math.cos(0.5 * sp3angle) * v4
neighbor.setposition(position[0], position[1], position[2])
return
if count == 2:
# print("COUNT 2 - level 1!!!")
v1 = unit_vector(vectorFromAtoms(previousAtom, atom))
v2 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v3 = unit_vector(vectorFromAtoms(insertedNeighbors[1], atom))
v4 = v1 + v2 + v3
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) - bond * np.array(v4)
neighbor.setposition(position[0], position[1], position[2])
return
def setPositionNeighbor(self, neighbor, atom, count, insertedNeighbors,
previousAtom):
bond = 0.10 if ((neighbor.get_atomtype() == 'H') or
(neighbor.get_atomtype() == 'HC')) else 0.15
if previousAtom == atom:
if count == 0:
neighbor.setposition(atom.get_x() + bond, atom.get_y(),
atom.get_z())
return
if count == 1:
z = 1
cos = -0.5
sin = 0.866
x = atom.get_x() + bond * cos
y = atom.get_y() + bond * sin
neighbor.setposition(x, y, z)
return
if count == 2:
v1 = unit_vector(vectorFromAtoms(previousAtom, atom))
v2 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v3 = unit_vector(np.array(v1) + np.array(v2))
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) - bond * np.array(v3)
neighbor.setposition(position[0], position[1], position[2])
return
if count == 3:
neighbor.setposition(
atom.get_x(), atom.get_y(),
atom.get_z() - 0.1 + random.uniform(0, 0.05))
return
if count == 0:
dihedral = self.find_dihedral(previousAtom, atom)
otherAtom = None
if dihedral.get_a_1() == neighbor: otherAtom = dihedral.get_a_4()
if dihedral.get_a_4() == neighbor: otherAtom = dihedral.get_a_1()
v1 = unit_vector(vectorFromAtoms(otherAtom, previousAtom))
v2 = unit_vector(vectorFromAtoms(previousAtom, atom))
v4 = unit_vector(np.cross(v1, v2))
if dihedral.get_conformation() is not None:
v5 = unit_vector(np.cross(v2, v4))
if dihedral.get_conformation() == 'cis':
v6 = bond * -0.5 * v2 - bond * 0.866 * -v5
else:
v6 = bond * -0.5 * v2 - bond * 0.866 * v5
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) + v6
neighbor.setposition(position[0], position[1], position[2])
return
v5 = unit_vector(np.cross(v2,
v4)) + (0, 0, random.uniform(-0.5, 0.5))
v6 = bond * -0.5 * v2 - bond * 0.866 * unit_vector(v5)
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) + v6
neighbor.setposition(position[0], position[1], position[2])
return
if count == 1:
v1 = unit_vector(vectorFromAtoms(previousAtom, atom))
v2 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v3 = unit_vector(np.array(v1) + np.array(v2))
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) - bond * np.array(v3)
neighbor.setposition(position[0], position[1], position[2])
return
if count == 2:
v1 = unit_vector(vectorFromAtoms(previousAtom, atom))
v2 = unit_vector(vectorFromAtoms(insertedNeighbors[0], atom))
v3 = unit_vector(vectorFromAtoms(insertedNeighbors[1], atom))
v4 = unit_vector(np.cross(v1, v2))
position = np.array([atom.get_x(),
atom.get_y(),
atom.get_z()]) - bond * np.array(v4)
neighbor.setposition(position[0], position[1], position[2])
return
