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 standard_orientation(self, nuclei_array, rotation_symmetry,
reflection_symmetry):
vector_i = vector_j = (0.0, 0.0, 0.0)
if len(rotation_symmetry) > 1:
highest_n_folds = heapq.nlargest(
2, [rotation.fold for rotation in rotation_symmetry])
for rotation in rotation_symmetry:
if rotation.fold == highest_n_folds[0]:
vector_i = rotation.vector
break
for rotation in rotation_symmetry:
if rotation.fold == highest_n_folds[
1] and rotation.vector != vector_i:
vector_j = rotation.vector
break
if len(rotation_symmetry) == 1:
vector_i = rotation_symmetry[0].vector
for reflection in reflection_symmetry:
if phi(reflection.vector) > self.error:
vector_j = reflection.vector
break
if len(rotation_symmetry) == 0 and len(reflection_symmetry) > 1:
vector_i = reflection_symmetry[0].vector
vector_j = reflection_symmetry[1].vector
if rho(nuclei_array[0].coordinates) > 1e-3:
i = 0
else:
i = 1
if len(rotation_symmetry) == 0 and len(reflection_symmetry) == 1:
vector_i = reflection_symmetry[0].vector
vector_j = nuclei_array[i].coordinates
if len(rotation_symmetry) == 0 and len(reflection_symmetry) == 0:
vector_i = nuclei_array[i].coordinates
vector_j = nuclei_array[i + 1].coordinates
if rho(vector_i) <= self.error:
vector_i = (1.0, 0.0, 0.0)
quaternion_i = create_quaternion((-vector_i[1], vector_i[0], 0.0),
-theta(vector_i))
quaternion_j = create_quaternion((0.0, 0.0, 1.0), -phi(vector_j))
quaternion = quaternion_multi(quaternion_j, quaternion_i)
for rotation in rotation_symmetry:
rotation.vector = quaternion_rotation(quaternion, rotation.vector)
for reflection in reflection_symmetry:
reflection.vector = quaternion_rotation(quaternion,
reflection.vector)
for nuclei in nuclei_array:
nuclei.coordinates = quaternion_rotation(quaternion,
nuclei.coordinates)
return nuclei_array, rotation_symmetry, reflection_symmetry
def test_create_quaternion_returns_quaternion_for_45_degree_rotation_around_x_axis(
self):
axis_of_rotation = (1.0, 0.0, 0.0)
theta = pi / 4
quaternion = create_quaternion(axis_of_rotation, theta)
testing.assert_array_almost_equal(quaternion,
(0.923880, 0.382683, 0.0, 0.0), 6)
def test_create_quaternion_returns_quaternion_for_90_degree_rotation_around_y_axis(
self):
axis_of_rotation = (0.0, 1.0, 0.0)
theta = pi / 2
quaternion = create_quaternion(axis_of_rotation, theta)
testing.assert_array_almost_equal(quaternion,
(0.707107, 0.0, 0.707107, 0.0), 6)
def test_rotation_of_unit_y_vector_with_axis_of_rotation_y_by_90_degrees(
self):
theta = pi / 2
axis_of_rotation = (0, 1, 0)
x_vector = (1, 0, 0)
quaternion = create_quaternion(axis_of_rotation, theta)
rotated_vector = quaternion_rotation(quaternion, x_vector)
testing.assert_array_almost_equal(rotated_vector, (0, 0, -1), 6)
def test_rotation_of_unit_z_vector_with_axis_of_rotation_x_by_45_degrees(
self):
theta = pi / 4
axis_of_rotation = (1, 0, 0)
z_vector = (0, 0, -1)
quaternion = create_quaternion(axis_of_rotation, theta)
rotated_vector = quaternion_rotation(quaternion, z_vector)
testing.assert_array_almost_equal(rotated_vector,
(0, 0.707107, -0.707107), 6)
def brute_force_reflection_symmetry(self, nuclei_array, rotation_symmetry,
vertices, cross_vertices_vertices,
cross_edge_vertices):
# rotate all orthogonal vectors by principal axis by half it's n-fold angle
vector_cross = self.remove_duplicate(vertices +
cross_vertices_vertices +
cross_edge_vertices)
vectors_cross_rotated = []
if len(rotation_symmetry) > 0:
highest_symmetries = []
highest_n_fold = max(
[rotation.fold for rotation in rotation_symmetry])
for rotation in rotation_symmetry:
if rotation.fold == highest_n_fold:
highest_symmetries.append(rotation)
for highest_symmetry in highest_symmetries:
quaternion_list = []
vector = highest_symmetry.vector
for i in range(1, highest_symmetry.fold):
theta_i = pi * i / highest_symmetry.fold
quaternion = create_quaternion(vector, theta_i)
quaternion_list.append(quaternion)
for quaternion in quaternion_list:
for orthogonal_vector_i in vector_cross:
orthogonal_vector_j = quaternion_rotation(
quaternion, orthogonal_vector_i)
vectors_cross_rotated.append(orthogonal_vector_j)
reflection_planes = []
if len(vector_cross) > 0:
total_vectors_cross = cross_vertices_vertices + vectors_cross_rotated
vectors_reflection_plane = self.remove_duplicate(
total_vectors_cross)
planes_of_reflection = []
for planes in vectors_reflection_plane:
householder_matrix = ReflectionSymmetry(planes)
planes_of_reflection.append(householder_matrix)
# check each reflection
for plane_of_reflection in planes_of_reflection:
if self.check_symmetry_operation(nuclei_array,
plane_of_reflection):
reflection_planes.append(plane_of_reflection)
return reflection_planes
def operate(self, coordinate):
"""Rotates a point around the axis of rotation for a angle of 2 * pi / self.fold
Parameters
----------
coordinate : Tuple[float, float, float]
Returns
-------
: Tuple[float, float, float]
"""
angle = 2 * pi / self.fold
quaternion = create_quaternion(self.vector, angle)
return quaternion_rotation(quaternion, coordinate)
def operate(self, coordinate):
"""Rotates a point around the axis of rotation for a angle of 2 * pi / self.fold and then inverts.
Parameters
----------
coordinate : Tuple[float, float, float]
Returns
-------
: Tuple[float, float, float]
"""
angle = 2 * pi / self.fold
quaternion = create_quaternion(self.vector, angle)
householder_matrix = create_householder_matrix(self.vector)
x, y, z = householder_matrix_reflection(
quaternion_rotation(quaternion, coordinate), householder_matrix)
return x, y, z
def int_operate(self, coordinate):
"""Returns the rotation symmetry operation on a coordinate but returns a tuple of ints.
This method is useful for seeing how the symmetry operation affects the sign of a gaussian functions integral
exponents.
Parameters
----------
coordinate : Tuple[float, float, float]
Returns
-------
: Tuple[int, int, int]
"""
angle = 2 * pi / self.fold
quaternion = create_quaternion(self.vector, angle)
x, y, z = quaternion_rotation(quaternion, coordinate)
return int(round(x, 1)), int(round(y, 1)), int(round(z, 1))