def __calc_ab(model, bonds, angles):
y0 = []
for i1 in range(0, len(bonds), 2):
i2 = i1 + 1
x = model.coords[i1*3] - model.coords[i2*3]
y = model.coords[i1*3+1] - model.coords[i2*3+1]
z = model.coords[i1*3+2] - model.coords[i2*3+2]
y0.append(sqrt(x*x+y*y+z*z))
for i1 in range(0, len(angles), 3):
i2 = i1 + 1
i3 = i2 + 2
v1 = XYZ(model.coords[i1*3], model.coords[i1*3+1], model.coords[i1*3+2])
v2 = XYZ(model.coords[i2*3], model.coords[i2*3+1], model.coords[i2*3+2])
v3 = XYZ(model.coords[i3*3], model.coords[i3*3+1], model.coords[i3*3+2])
y0.append(angle(v1, v2, v3))
return y0
def alpha(self):
return angle(self.vb, self.vc)
