def test_stereo_sets_correct_transform_matrix(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.array_ops import project_to_plane, \
make_transform_matrix, \
transform_array
from e3fp.fingerprint.structs import Shell
shell = Shell(0, {1, 2})
atom_coords = np.asarray([[0, 0, 0.],
[0, 2., 0.], # -> y
[0, 0, 3.]], # -> z
dtype=np.float)
atom_tuples = [(1, 1, Shell(1)), # -> y
(5, 5, Shell(2))] # -> z
for i in range(20):
rand_trans = np.random.uniform(size=3)*100
rand_y = np.random.uniform(size=3)*10
rand_v = np.random.uniform(size=3)*20
rand_z = project_to_plane(rand_v, rand_y)*30
rand_transform_mat = make_transform_matrix(np.zeros(3), rand_y,
rand_z)
trans_mat = np.identity(4, dtype=np.float)
trans_mat[:3, 3] = rand_trans
rand_transform_mat = np.dot(trans_mat, rand_transform_mat)
new_coords = transform_array(rand_transform_mat, atom_coords)
reverse_trans_mat = np.linalg.inv(rand_transform_mat)
np.testing.assert_almost_equal(
atom_coords, transform_array(reverse_trans_mat, new_coords))
atom_coords_dict = dict(list(zip(list(range(3)), new_coords)))
stereo_indicators_from_shell(shell, atom_tuples, atom_coords_dict)
np.testing.assert_almost_equal(shell.transform_matrix,
reverse_trans_mat)
def test_no_neighbors_transform_matrix_is_translate(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.structs import Shell
shell = Shell(0)
center_coord = np.random.uniform(3)
stereo_indicators_from_shell(shell, [], {0: center_coord})
np.testing.assert_almost_equal(shell.transform_matrix[:3, 3],
-center_coord)
def test_stereo_indicators_for_frame(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.array_ops import project_to_plane,\
make_transform_matrix,\
transform_array
from e3fp.fingerprint.structs import Shell
shell = Shell(0, {1, 2, 3})
atom_coords = np.asarray([[0, 0, 0.],
[1, -0.5, 0.],
[0, 2., 0.], # -> y
[0, 0, 3.]], # -> z
dtype=np.float)
atom_tuples = [(1, 1, Shell(2)), # -> y
(2, 1, Shell(1)),
(5, 5, Shell(3))] # -> z
for i in range(20):
rand_trans = np.random.uniform(size=3)*100
rand_y = np.random.uniform(size=3)*10
rand_v = np.random.uniform(size=3)*20
rand_z = project_to_plane(rand_v, rand_y)*30
rand_transform_mat = make_transform_matrix(np.zeros(3), rand_y,
rand_z)
new_coords = transform_array(rand_transform_mat, atom_coords)
np.testing.assert_almost_equal(
atom_coords, transform_array(
np.linalg.inv(rand_transform_mat), new_coords))
new_coords += rand_trans
atom_coords_dict = dict(list(zip(list(range(4)), new_coords)))
stereo_ind = stereo_indicators_from_shell(shell, atom_tuples,
atom_coords_dict)
# 2 is chosen for y, 3 for z
expect_stereo_ind = [1, -5, 2]
self.assertEqual(stereo_ind, expect_stereo_ind)
def test_empty_tuples_returns_empty(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.structs import Shell
shell = Shell(0, {})
atom_coords_dict = {0: np.random.uniform(size=3)}
atom_tuples = []
stereo_ind = stereo_indicators_from_shell(shell, atom_tuples,
atom_coords_dict)
self.assertEqual(len(stereo_ind), 0)
def test_no_unique_y_two_evenly_spaced_correct(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.structs import Shell
shell = Shell(0, {1, 2})
atom_coords_dict = {0: [0, 0, 0], 1: [0, 1, 0], 2: [0, 0, 1]}
atom_tuples = [(1, 1, Shell(1)), (1, 1, Shell(2))]
stereo_ind = stereo_indicators_from_shell(shell, atom_tuples,
atom_coords_dict)
# mean should be between 1 and 2, so z cannot be picked, so all 0.
expect_stereo_ind = [1, 2]
self.assertEqual(stereo_ind, expect_stereo_ind)
def test_no_unique_y_along_poles_correct(self):
from e3fp.fingerprint.fprinter import stereo_indicators_from_shell
from e3fp.fingerprint.structs import Shell
shell = Shell(0, {1, 2, 3})
atom_coords_dict = {0: [0, 0, 0], 1: [0, 1, 0], 2: [0, -5, 0],
3: [0, -10, 0]}
atom_tuples = [(1, 1, Shell(1)),
(1, 1, Shell(2)),
(1, 1, Shell(3))]
stereo_ind = stereo_indicators_from_shell(shell, atom_tuples,
atom_coords_dict)
# mean should be along atom 2/3, so z not be picked, but all at poles.
expect_stereo_ind = [-1, 1, 1]
self.assertEqual(stereo_ind, expect_stereo_ind)
