def reorient_molecule(self, nuclei_list):
first_nuclei = nuclei_list.pop(0)
coordinates = first_nuclei.coordinates
first_nuclei.coordinates = (0, 0, 0)
for nuclei in nuclei_list:
x = nuclei.coordinates[0] - coordinates[0]
y = nuclei.coordinates[1] - coordinates[1]
z = nuclei.coordinates[2] - coordinates[2]
nuclei.coordinates = (x, y, z)
if len(nuclei_list) >= 1:
second_nuclei = nuclei_list[0]
coordinates = normalize(second_nuclei.coordinates)
quaternion = create_quaternion(
(-coordinates[1], coordinates[0], 0.0), -theta(coordinates))
for nuclei in nuclei_list:
nuclei.coordinates = quaternion_rotation(
quaternion, nuclei.coordinates)
if len(nuclei_list) >= 2:
third_nuclei = nuclei_list[1]
coordinates = normalize(third_nuclei.coordinates)
quaternion = create_quaternion((0.0, 0.0, 1.0),
-phi(coordinates) + np.pi / 2)
for nuclei in nuclei_list:
nuclei.coordinates = quaternion_rotation(
quaternion, nuclei.coordinates)
return [first_nuclei], nuclei_list
def cross_products(self, vector_i, vector_j):
cross_products = []
for axis_i, axis_j in itertools.product(vector_i, vector_j):
if axis_i is not axis_j:
axis_cross = cross_product(axis_i, axis_j)
if rho(axis_cross) > self.error:
axis_cross = normalize(axis_cross)
cross_products.append(axis_cross)
return cross_products
def center_two_vertices(self, nuclei_array):
center_of_edge = []
for nuclei_i, nuclei_j in itertools.combinations(nuclei_array, 2):
axis_i = nuclei_i.coordinates
axis_j = nuclei_j.coordinates
axis_edge = vector_add(axis_i, axis_j)
if rho(axis_edge) > self.error:
axis_edge = normalize(axis_edge)
center_of_edge.append(axis_edge)
return center_of_edge
def vertices(self, nuclei_array):
corner = []
for nuclei in nuclei_array:
coordinates = normalize(nuclei.coordinates)
corner.append(coordinates)
return corner