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 check_n_two_fold_perpendicular_to_n_fold(self, rotation_symmetry):
principal_axis = self.return_principal_axis(rotation_symmetry)
axis_of_rotation = []
for rotation in rotation_symmetry:
if principal_axis != rotation and rotation.fold == 2 and (
theta(rotation.vector) - pi / 2 <= self.error):
axis_of_rotation.append(rotation.vector)
if len(axis_of_rotation) == principal_axis.fold:
return True
else:
return False
def return_principal_axis(self, rotation_symmetry):
for rotation in rotation_symmetry:
if theta(rotation.vector) % pi <= self.error:
return rotation
def check_linear(self, nuclei_array):
for nuclei in nuclei_array:
if theta(nuclei.coordinates) % pi > self.error:
return False
return True
def check_sigma_h(self, reflection_symmetry):
for reflection in reflection_symmetry:
if theta(reflection.vector) % pi <= self.error:
return True
return False
