def test_normalisation(self):
r = np.random.rand(100,3)
n = norm_vect(r)
d = dot_product(n,n)
ones = np.ones((100))
assert_almost_equal(d, ones, 8, err_msg="Your vectors don't normalise too well")
def dihedral_calc(r1, r2, r3, r4):
"""
This function calculates the angle made by the vectors normal
to the planes made by r1, r2, r3 and r2, r3, r4.
Each of the positions is assumed to be a 3 by n array for
n lists of dihedral sets
r1
\
\
r2---r3
\
\
r4
The angle for dihedral will go between +180 and -180 degrees
"""
r12 = vect_calc(r1, r2)
r23 = vect_calc(r2, r3)
r34 = vect_calc(r3, r4)
r123 = np.cross(r12[:], r23[:])
r234 = np.cross(r23[:], r34[:])
n123 = norm_vect(r123)
n234 = norm_vect(r234)
axis_2 = np.cross(n123[:], r23[:])
axis_2_norm = norm_vect(axis_2)
x = dot_product(n123[:], n234[:])
y = dot_product(axis_2_norm[:], n234[:])
dih_angle = np.arctan2(y, x)
return dih_angle