def test_generates_correct_connected_shells_level1(self):
from e3fp.fingerprint import fprinter
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
bonds_dict = {0: {1, 2}, 1: {0}, 2: {0}}
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45 * atom])
expected_shells_dict = {
0: Shell(0, {1}),
1: Shell(1, {0}),
2: Shell(2, {})
}
with mock.patch('e3fp.fingerprint.fprinter.bound_atoms_from_mol',
return_value=bonds_dict):
shells_gen = fprinter.ShellsGenerator(conf,
atoms,
radius_multiplier=0.5,
include_disconnected=False)
for i in range(2):
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict)
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_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_shells_diff_center_same_atoms_nonequal(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
shell1 = Shell(atoms[0], atoms[2:])
shell2 = Shell(atoms[1], atoms[2:])
self.assertNotEqual(shell1, shell2)
def test_creation_with_atoms_or_ids_equivalent(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
atom_ids = [x.GetIdx() for x in atoms]
self.assertEqual(Shell(atoms[0], atoms[1:]),
Shell(atom_ids[0], atom_ids[1:]))
def test_shell_creation_from_substruct_without_center_fails(self):
from e3fp.fingerprint.structs import Shell, Substruct, FormatError
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
substruct = Substruct(None, atoms[:2])
with self.assertRaises(FormatError):
Shell.from_substruct(substruct)
def test_equal_shells_hash_to_same_value(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
center_atom = atoms[0]
shell1 = Shell(center_atom, atoms[1:])
shell2 = Shell(center_atom, atoms[1:])
self.assertEqual(hash(shell1), hash(shell2))
def test_creation_with_atoms_or_shells_equal(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
shells = list(map(Shell, atoms))
center_atom = atoms[0]
shell1 = Shell(center_atom, atoms[1:])
shell2 = Shell(center_atom, shells[1:])
self.assertEqual(shell1, shell2)
def test_generates_correct_disconnected_shells_level0(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
expected_shells_dict = {0: Shell(0), 1: Shell(1), 2: Shell(2)}
shells_gen = ShellsGenerator(conf, atoms)
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict)
def test_recursive_atom_shells_correct(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
shell1 = Shell(atoms[5], atoms[6:8])
shell2 = Shell(atoms[2], atoms[3:5])
shell = Shell(atoms[0], (shell1, shell2))
self.assertEqual(shell.atoms,
{x.GetIdx()
for x in (atoms[0], atoms[2], atoms[5])})
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_recursive_shell_substruct_correct2(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
shell1 = Shell(atoms[1], atoms[2:5])
shell2 = Shell(atoms[5], {shell1})
shell3 = Shell(atoms[6], atoms[7:10])
shell4 = Shell(atoms[10], {shell3})
shell = Shell(atoms[0], (shell2, shell4))
self.assertEqual(shell.substruct.atoms,
{x.GetIdx()
for x in atoms[:11]})
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)
def test_create_shell_no_shell(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
center_atom = atoms[0]
Shell(center_atom)
def test_generates_correct_disconnected_shells_level1(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45*atom])
expected_shells_dict = {0: Shell(0, {1}), 1: Shell(1, {0, 2}),
2: Shell(2, {1})}
shells_gen = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
for i in range(2):
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict)
def test_error_when_shells_has_non_shell(self):
from e3fp.fingerprint.structs import Shell
atom = 0
shells = [None]
with self.assertRaises(TypeError):
Shell(atom, shells)
def test_substruct_creation_from_shell(self):
from e3fp.fingerprint.structs import Shell, Substruct
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
shell = Shell(atoms[0], atoms[1:])
substruct = Substruct.from_shell(shell)
self.assertEqual(shell.substruct, substruct)
def test_create_shell_with_same_center_fails(self):
from e3fp.fingerprint.structs import Shell, FormatError
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
center_atom = atoms[0]
with self.assertRaises(FormatError):
Shell(center_atom, atoms)
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_atoms_converted_to_shells(self):
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
atoms = list(mol.GetAtoms())
center_atom = atoms[0]
shell = Shell(center_atom, atoms[1:])
for s in shell.shells:
self.assertIsInstance(s, Shell)
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_error_when_center_not_atom(self):
from e3fp.fingerprint.structs import Shell
with self.assertRaises(TypeError):
Shell(None)
