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)
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)
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)])
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)])
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)])
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)])
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!")
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!")
def test_that_all_featurizers_run():
trajectories = AlanineDipeptide().get_cached().trajectories
trj0 = trajectories[0][0]
atom_indices, pair_indices = get_atompair_indices(trj0)
atom_featurizer0 = SubsetAtomPairs(pair_indices, trj0, exponent=-1.0)
cosphi = SubsetCosPhiFeaturizer(trj0)
sinphi = SubsetSinPhiFeaturizer(trj0)
cospsi = SubsetCosPsiFeaturizer(trj0)
sinpsi = SubsetSinPsiFeaturizer(trj0)
featurizer = SubsetFeatureUnion([("pairs", atom_featurizer0),
("cosphi", cosphi), ("sinphi", sinphi),
("cospsi", cospsi), ("sinpsi", sinpsi)])
featurizer.subsets = [
np.arange(1) for i in range(featurizer.n_featurizers)
]
X_all = featurizer.transform(trajectories)
eq(X_all[0].shape[1], 1 * featurizer.n_featurizers)
def test_that_all_featurizers_run():
trajectories = AlanineDipeptide().get_cached().trajectories
trj0 = trajectories[0][0]
atom_indices, pair_indices = get_atompair_indices(trj0)
atom_featurizer0 = SubsetAtomPairs(pair_indices, trj0, exponent=-1.0)
cosphi = SubsetCosPhiFeaturizer(trj0)
sinphi = SubsetSinPhiFeaturizer(trj0)
cospsi = SubsetCosPsiFeaturizer(trj0)
sinpsi = SubsetSinPsiFeaturizer(trj0)
featurizer = SubsetFeatureUnion([
("pairs", atom_featurizer0),
("cosphi", cosphi),
("sinphi", sinphi),
("cospsi", cospsi),
("sinpsi", sinpsi)
])
featurizer.subsets = [np.arange(1) for i in range(featurizer.n_featurizers)]
X_all = featurizer.transform(trajectories)
eq(X_all[0].shape[1], 1 * featurizer.n_featurizers)
