Python AtomPairsFeaturizer.transform Examples

Example #1

File: test_featurizer.py Project: cxhernandez/msmbuilder

def test_that_all_featurizers_run():
    # TODO: include all featurizers, perhaps with generator tests

    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)

    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all = featurizer.transform(trajectories)

    featurizer = SuperposeFeaturizer(np.arange(15), trj0)
    X_all = featurizer.transform(trajectories)

    featurizer = DihedralFeaturizer(["phi", "psi"])
    X_all = featurizer.transform(trajectories)

    featurizer = VonMisesFeaturizer(["phi", "psi"])
    X_all = featurizer.transform(trajectories)

    # Below doesn't work on ALA dipeptide
    # featurizer = msmbuilder.featurizer.ContactFeaturizer()
    # X_all = featurizer.transform(trajectories)

    featurizer = RMSDFeaturizer(trj0)
    X_all = featurizer.transform(trajectories)

Example #2

def test_that_all_featurizers_run():
    # TODO: include all featurizers, perhaps with generator tests

    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)

    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all = featurizer.transform(trajectories)

    featurizer = SuperposeFeaturizer(np.arange(15), trj0)
    X_all = featurizer.transform(trajectories)

    featurizer = DihedralFeaturizer(["phi", "psi"])
    X_all = featurizer.transform(trajectories)

    featurizer = VonMisesFeaturizer(["phi", "psi"])
    X_all = featurizer.transform(trajectories)

    # Below doesn't work on ALA dipeptide
    # featurizer = msmbuilder.featurizer.ContactFeaturizer()
    # X_all = featurizer.transform(trajectories)

    featurizer = RMSDFeaturizer(trj0)
    X_all = featurizer.transform(trajectories)

Example #3

File: test_featurizer_subset.py Project: Eigenstate/msmbuilder

def test_SubsetAtomPairs_2():
    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0,
                                 subset=np.arange(len(pair_indices)))
    X_all = featurizer.transform(trajectories)

    any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])

Example #4

def test_SubsetAtomPairs_1():
    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0)
    featurizer.subset = np.arange(len(pair_indices))
    X_all = featurizer.transform(trajectories)

    any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])

Example #5

File: test_featurizer_subset.py Project: evanfeinberg/msmbuilder

def test_SubsetAtomPairs_2():
    dataset = fetch_alanine_dipeptide()
    trajectories = dataset["trajectories"]
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0,
                                 subset=np.arange(len(pair_indices)))
    X_all = featurizer.transform(trajectories)

    any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])

Example #6

def test_SubsetAtomPairs_1():
    dataset = fetch_alanine_dipeptide()
    trajectories = dataset["trajectories"]
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0)
    featurizer.subset = np.arange(len(pair_indices))
    X_all = featurizer.transform(trajectories)

    any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])

Example #7

File: test_featurizer_subset.py Project: Eigenstate/msmbuilder

def test_SubsetAtomPairs_3():
    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0, subset=np.array([0, 1]))
    X_all = featurizer.transform(trajectories)

    try:
        any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])
    except AssertionError:
        pass
    else:
        raise AssertionError("Did not raise an assertion!")

Example #8

def test_SubsetAtomPairs_3():
    trajectories = AlanineDipeptide().get_cached().trajectories
    trj0 = trajectories[0][0]
    atom_indices, pair_indices = get_atompair_indices(trj0)
    featurizer = AtomPairsFeaturizer(pair_indices)
    X_all0 = featurizer.transform(trajectories)

    featurizer = SubsetAtomPairs(pair_indices, trj0, subset=np.array([0, 1]))
    X_all = featurizer.transform(trajectories)

    try:
        any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])
    except AssertionError:
        pass
    else:
        raise AssertionError("Did not raise an assertion!")

Example #9

File: test_feature_descriptor.py Project: rgejman/msmbuilder

def test_AtomPairsFeaturizer_describe_features():
    current_atom_ind = list(itertools.combinations(atom_ind, 2))
    feat = AtomPairsFeaturizer(current_atom_ind)
    rnd_traj = np.random.randint(len(trajectories))
    features = feat.transform([trajectories[rnd_traj]])
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))

    for f in range(25):
        f_index = np.random.choice(len(df))
        atom_inds = df.iloc[f_index].atominds
        feature_value = md.compute_distances(trajectories[rnd_traj],
                                             [atom_inds])

        assert (features[0][:, f_index] == feature_value.flatten()).all()

Example #10

File: test_feature_descriptor.py Project: msmbuilder/msmbuilder

def test_AtomPairsFeaturizer_describe_features():
    current_atom_ind = list(itertools.combinations(atom_ind, 2))
    feat = AtomPairsFeaturizer(current_atom_ind)
    rnd_traj = np.random.randint(len(trajectories))
    features = feat.transform([trajectories[rnd_traj]])
    df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
    
    for f in range(25):
        f_index = np.random.choice(len(df))
        atom_inds = df.iloc[f_index].atominds
        feature_value = md.compute_distances(trajectories[rnd_traj],
                                             [atom_inds])

        assert (features[0][:, f_index] == feature_value.flatten()).all()