def test_neighbor_list_shape(self):
"""
Simple test that Neighbor Lists have right shape.
"""
nblist_featurizer = NeighborListAtomicCoordinates()
N = self.mol.GetNumAtoms()
coords = get_coords(self.mol)
x_bins, y_bins, z_bins = get_cells(coords,
nblist_featurizer.neighbor_cutoff)
nblist_featurizer = NeighborListAtomicCoordinates()
nblist = nblist_featurizer._featurize(self.mol)[1]
assert isinstance(nblist, dict)
assert len(nblist.keys()) == N
for (atom, neighbors) in nblist.items():
assert isinstance(atom, int)
assert isinstance(neighbors, list)
assert len(neighbors) <= N
# Do a manual distance computation and make
for i in range(N):
for j in range(N):
dist = np.linalg.norm(coords[i] - coords[j])
print("Distance(%d, %d) = %f" % (i, j, dist))
if dist < nblist_featurizer.neighbor_cutoff and i != j:
assert j in nblist[i]
else:
assert j not in nblist[i]
def test_neighbor_list_shape(self):
"""
Simple test that Neighbor Lists have right shape.
"""
nblist_featurizer = NeighborListAtomicCoordinates()
N = self.mol.GetNumAtoms()
coords = get_coords(self.mol)
x_bins, y_bins, z_bins = get_cells(coords, nblist_featurizer.neighbor_cutoff)
nblist_featurizer = NeighborListAtomicCoordinates()
nblist = nblist_featurizer._featurize(self.mol)[1]
assert isinstance(nblist, dict)
assert len(nblist.keys()) == N
for (atom, neighbors) in nblist.items():
assert isinstance(atom, int)
assert isinstance(neighbors, list)
assert len(neighbors) <= N
# Do a manual distance computation and make
for i in range(N):
for j in range(N):
dist = np.linalg.norm(coords[i] - coords[j])
print("Distance(%d, %d) = %f" % (i, j, dist))
if dist < nblist_featurizer.neighbor_cutoff and i != j:
assert j in nblist[i]
else:
assert j not in nblist[i]
def test_put_atoms_in_cells(self):
"""
Test that atoms are placed into correct cells.
"""
# As in previous example, coordinates span size-2 cube on (-1, 1)
coords = np.array(
[[1., 1., 1.],
[-1., -1., -1.]])
# Set cell size (neighbor_cutoff) at 1 angstrom.
neighbor_cutoff = 1
# We should get 2 bins in each dimension
x_bins, y_bins, z_bins = get_cells(coords, neighbor_cutoff)
cell_to_atoms, atom_to_cell = put_atoms_in_cells(
coords, x_bins, y_bins, z_bins)
# Both cell_to_atoms and atom_to_cell are dictionaries
assert isinstance(cell_to_atoms, dict)
assert isinstance(atom_to_cell, dict)
# atom_to_cell should be of len 2 since 2 atoms
assert len(atom_to_cell) == 2
# cell_to_atoms should be of len 8 since 8 cells total.
assert len(cell_to_atoms) == 8
# We have two atoms. The first is in highest corner (1,1,1)
# Second atom should be in lowest corner (0, 0, 0)
assert atom_to_cell[0] == (1, 1, 1)
assert atom_to_cell[1] == (0, 0, 0)
# (1,1,1) should contain atom 0. (0, 0, 0) should contain atom 1.
# Everything else should be an empty list
for cell, atoms in cell_to_atoms.items():
if cell == (1, 1, 1):
assert atoms == [0]
elif cell == (0, 0, 0):
assert atoms == [1]
else:
assert atoms == []
def test_get_cells(self):
"""
Test that coordinates are split into cell appropriately.
"""
# The coordinates span the cube of side-length 2 set on (-1, 1)
coords = np.array([[1., 1., 1.], [-1., -1., -1.]])
# Set cell size (neighbor_cutoff) at 1 angstrom.
neighbor_cutoff = 1
# We should get 2 bins in each dimension
x_bins, y_bins, z_bins = get_cells(coords, neighbor_cutoff)
# Check bins are lists
assert isinstance(x_bins, list)
assert isinstance(y_bins, list)
assert isinstance(z_bins, list)
assert len(x_bins) == 2
assert x_bins == [(-1.0, 0.0), (0.0, 1.0)]
assert len(y_bins) == 2
assert y_bins == [(-1.0, 0.0), (0.0, 1.0)]
assert len(z_bins) == 2
assert z_bins == [(-1.0, 0.0), (0.0, 1.0)]
def test_put_atoms_in_cells(self):
"""
Test that atoms are placed into correct cells.
"""
# As in previous example, coordinates span size-2 cube on (-1, 1)
coords = np.array([[1., 1., 1.], [-1., -1., -1.]])
# Set cell size (neighbor_cutoff) at 1 angstrom.
neighbor_cutoff = 1
# We should get 2 bins in each dimension
x_bins, y_bins, z_bins = get_cells(coords, neighbor_cutoff)
cell_to_atoms, atom_to_cell = put_atoms_in_cells(
coords, x_bins, y_bins, z_bins)
# Both cell_to_atoms and atom_to_cell are dictionaries
assert isinstance(cell_to_atoms, dict)
assert isinstance(atom_to_cell, dict)
# atom_to_cell should be of len 2 since 2 atoms
assert len(atom_to_cell) == 2
# cell_to_atoms should be of len 8 since 8 cells total.
assert len(cell_to_atoms) == 8
# We have two atoms. The first is in highest corner (1,1,1)
# Second atom should be in lowest corner (0, 0, 0)
assert atom_to_cell[0] == (1, 1, 1)
assert atom_to_cell[1] == (0, 0, 0)
# (1,1,1) should contain atom 0. (0, 0, 0) should contain atom 1.
# Everything else should be an empty list
for cell, atoms in cell_to_atoms.items():
if cell == (1, 1, 1):
assert atoms == [0]
elif cell == (0, 0, 0):
assert atoms == [1]
else:
assert atoms == []
def test_get_cells(self):
"""
Test that coordinates are split into cell appropriately.
"""
# The coordinates span the cube of side-length 2 set on (-1, 1)
coords = np.array(
[[1., 1., 1.],
[-1., -1., -1.]])
# Set cell size (neighbor_cutoff) at 1 angstrom.
neighbor_cutoff = 1
# We should get 2 bins in each dimension
x_bins, y_bins, z_bins = get_cells(coords, neighbor_cutoff)
# Check bins are lists
assert isinstance(x_bins, list)
assert isinstance(y_bins, list)
assert isinstance(z_bins, list)
assert len(x_bins) == 2
assert x_bins ==[(-1.0, 0.0), (0.0, 1.0)]
assert len(y_bins) == 2
assert y_bins ==[(-1.0, 0.0), (0.0, 1.0)]
assert len(z_bins) == 2
assert z_bins ==[(-1.0, 0.0), (0.0, 1.0)]
