def test_two_refs_omitting_indices():
# This test verifies that the result produced when
# atom_indices are omitted is the same as the result
# produced when atom_indices is all atom indices.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer_indices = RMSDFeaturizer(trajectories[0][0:2],
np.arange(trajectories[0].n_atoms))
data_indices = featurizer_indices.transform(trajectories[0:1])
featurizer = RMSDFeaturizer(trajectories[0][0:2])
data = featurizer.transform(trajectories[0:1])
np.testing.assert_array_almost_equal(data[0], data_indices[0], decimal=4)
def test_two_refs_omitting_indices():
# This test verifies that the result produced when
# atom_indices are omitted is the same as the result
# produced when atom_indices is all atom indices.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer_indices = RMSDFeaturizer(trajectories[0][0:2],
np.arange(trajectories[0].n_atoms))
data_indices = featurizer_indices.transform(trajectories[0:1])
featurizer = RMSDFeaturizer(trajectories[0][0:2])
data = featurizer.transform(trajectories[0:1])
np.testing.assert_array_almost_equal(data[0], data_indices[0], decimal=4)
def test_omitting_indices():
# This test verifies that the result produced when
# atom_indices are omitted is the same as the result
# produced when atom_indices is all atom indices.
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
featurizer_indices = RMSDFeaturizer(trajectories[0][0],
np.arange(trajectories[0].n_atoms))
data_indices = featurizer_indices.transform(trajectories[0:1])
featurizer = RMSDFeaturizer(trajectories[0][0])
data = featurizer.transform(trajectories[0:1])
np.testing.assert_array_almost_equal(data[0][:, 0],
data_indices[0][:, 0], decimal=4)
def test_different_indices():
# This test verifies that the rmsd's calculated from
# different sets of atom indices are not the same,
# but that the arrays are still the same shape.
trajectories = AlanineDipeptide().get_cached().trajectories
n_atoms = trajectories[0].n_atoms
halfway_point = n_atoms // 2
featurizer_first_half = RMSDFeaturizer(trajectories[0][0],
np.arange(halfway_point))
data_first_half = featurizer_first_half.transform(trajectories[0:1])
featurizer_second_half = RMSDFeaturizer(trajectories[0][0],
np.arange(halfway_point, n_atoms))
data_second_half = featurizer_second_half.transform(trajectories[0:1])
assert data_first_half[0].shape == data_second_half[0].shape
# janky way to show that the arrays shouldn't be equal here
assert sum(data_first_half[0][:, 0]) != sum(data_second_half[0][:, 0])
def test_different_indices():
# This test verifies that the rmsd's calculated from
# different sets of atom indices are not the same,
# but that the arrays are still the same shape.
trajectories = AlanineDipeptide().get_cached().trajectories
n_atoms = trajectories[0].n_atoms
halfway_point = n_atoms // 2
featurizer_first_half = RMSDFeaturizer(trajectories[0][0],
np.arange(halfway_point))
data_first_half = featurizer_first_half.transform(trajectories[0:1])
featurizer_second_half = RMSDFeaturizer(trajectories[0][0],
np.arange(halfway_point, n_atoms))
data_second_half = featurizer_second_half.transform(trajectories[0:1])
assert data_first_half[0].shape == data_second_half[0].shape
# janky way to show that the arrays shouldn't be equal here
assert sum(data_first_half[0][:, 0]) != sum(data_second_half[0][:, 0])
def test_alanine_dipeptide_basic():
# This test takes the rmsd of the 0th set of alanine dipeptide
# trajectories relative to the 0th frame of the dataset.
# The test asserts that all rmsd's calculated will be equal
# to the ones that would be calculated straight from mdtraj.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer = RMSDFeaturizer(trajectories[0][0])
data = featurizer.transform(trajectories[0:1])
true_rmsd = md.rmsd(trajectories[0], trajectories[0][0])
np.testing.assert_array_almost_equal(data[0][:, 0], true_rmsd, decimal=4)
def test_alanine_dipeptide_basic():
# This test takes the rmsd of the 0th set of alanine dipeptide
# trajectories relative to the 0th frame of the dataset.
# The test asserts that all rmsd's calculated will be equal
# to the ones that would be calculated straight from mdtraj.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer = RMSDFeaturizer(trajectories[0][0])
data = featurizer.transform(trajectories[0:1])
true_rmsd = md.rmsd(trajectories[0], trajectories[0][0])
np.testing.assert_array_almost_equal(data[0][:, 0], true_rmsd, decimal=4)
def test_two_refs_basic():
# This test uses the 0th and 1st frames of the 0th set of
# adp trajectories as the two reference trajectories and
# ensures that the rmsd of the 0th frame of the dataset with
# the 0th reference are identical and the 1st frame of the
# dataset with the 1st reference are identical.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer = RMSDFeaturizer(trajectories[0][0:2])
data = featurizer.transform(trajectories[0:1])
true_rmsd = np.zeros((trajectories[0].n_frames, 2))
for frame in range(2):
true_rmsd[:, frame] = md.rmsd(trajectories[0], trajectories[0][frame])
np.testing.assert_almost_equal(data[0][0, 0], data[0][1, 1], decimal=3)
np.testing.assert_almost_equal(data[0][1, 0], data[0][0, 1], decimal=3)
np.testing.assert_array_almost_equal(data[0], true_rmsd, decimal=4)
def test_two_refs_basic():
# This test uses the 0th and 1st frames of the 0th set of
# adp trajectories as the two reference trajectories and
# ensures that the rmsd of the 0th frame of the dataset with
# the 0th reference are identical and the 1st frame of the
# dataset with the 1st reference are identical.
trajectories = AlanineDipeptide().get_cached().trajectories
featurizer = RMSDFeaturizer(trajectories[0][0:2])
data = featurizer.transform(trajectories[0:1])
true_rmsd = np.zeros((trajectories[0].n_frames, 2))
for frame in range(2):
true_rmsd[:, frame] = md.rmsd(trajectories[0], trajectories[0][frame])
np.testing.assert_almost_equal(data[0][0, 0], data[0][1, 1], decimal=3)
np.testing.assert_almost_equal(data[0][1, 0], data[0][0, 1], decimal=3)
np.testing.assert_array_almost_equal(data[0], true_rmsd, decimal=4)
