def angles(xyz):
angleLabel = []
angle = []
atomLabel = op.atom_label(xyz[0])
xCoord = xyz[1]
yCoord = xyz[2]
zCoord = xyz[3]
for i in range(0,len(atomLabel)-1):
for j in range(i, len(atomLabel)):
for k in range(0, len(atomLabel)):
if i is j:
continue
elif i is k:
continue
elif j is k:
continue
else:
ex_ki = float(xCoord[k]) - float(xCoord[i])
ex_kj = float(xCoord[k]) - float(xCoord[j])
ey_ki = float(yCoord[k]) - float(yCoord[i])
ey_kj = float(yCoord[k]) - float(yCoord[j])
ez_ki = float(zCoord[k]) - float(zCoord[i])
ez_kj = float(zCoord[k]) - float(zCoord[j])
rki = math.sqrt(ex_ki**2.0 + ey_ki**2.0 + ez_ki **2.0)
rkj = math.sqrt(ex_kj**2.0 + ey_kj**2.0 + ez_kj **2.0)
ex_ki = ex_ki/rki
ey_ki = ey_ki/rki
ez_ki = ez_ki/rki
ex_kj = ex_kj/rkj
ey_kj = ey_kj/rkj
ez_kj = ez_kj/rkj
angle.append(180.0/math.pi*math.acos(ex_ki*ex_kj + ey_ki*ey_kj + ez_ki*ez_kj))
angleLabel.append(atomLabel[i] + str(i+1) + "-" + atomLabel[k] + str(k+1) + "-" + atomLabel[j] + str(j+1))
return(angleLabel,angle)
def bonddistance(xyz):
bondLabel = []
bondDistance = []
atomLabel = op.atom_label(xyz[0])
xCoord = xyz[1]
yCoord = xyz[2]
zCoord = xyz[3]
for i in range(0,len(atomLabel)-1):
for j in range(i,len(atomLabel)):
if i is not j:
bondLabel.append(atomLabel[i] + str(i+1) + "-" + atomLabel[j] + str(j+1))
bondDistance.append(math.sqrt((float(xCoord[i])-float(xCoord[j]))**2 + (float(yCoord[i])-float(yCoord[j]))**2 + (float(zCoord[i])-float(zCoord[j]))**2))
return(bondLabel,bondDistance)
