def test_that_all_featurizers_run():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
trj0 = trajectories[0][0]
atom_indices, pair_indices = subset_featurizer.get_atompair_indices(trj0)
featurizer = msmbuilder.featurizer.AtomPairsFeaturizer(pair_indices)
X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.SuperposeFeaturizer(np.arange(15), trj0)
X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.DihedralFeaturizer(["phi" ,"psi"])
X_all = featurizer.transform(trajectories)
#featurizer = msmbuilder.featurizer.ContactFeaturizer() # Doesn't work on ALA dipeptide
#X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.RMSDFeaturizer(trj0)
X_all = featurizer.transform(trajectories)
atom_featurizer0 = subset_featurizer.SubsetAtomPairs(pair_indices, trj0, exponent=-1.0)
cosphi = subset_featurizer.SubsetCosPhiFeaturizer(trj0)
sinphi = subset_featurizer.SubsetSinPhiFeaturizer(trj0)
cospsi = subset_featurizer.SubsetCosPsiFeaturizer(trj0)
sinpsi = subset_featurizer.SubsetSinPsiFeaturizer(trj0)
featurizer = subset_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_SubsetAtomPairs2():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
trj0 = trajectories[0][0]
atom_indices, pair_indices = subset_featurizer.get_atompair_indices(trj0)
featurizer = msmbuilder.featurizer.AtomPairsFeaturizer(pair_indices)
X_all0 = featurizer.transform(trajectories)
featurizer = subset_featurizer.SubsetAtomPairs(pair_indices, trj0, subset=np.array([0, 1]))
X_all = featurizer.transform(trajectories)
any([eq(x, x0) for (x, x0) in zip(X_all, X_all0)])
def test_SubsetAtomPairs0():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
trj0 = trajectories[0][0]
atom_indices, pair_indices = subset_featurizer.get_atompair_indices(trj0)
featurizer = msmbuilder.featurizer.AtomPairsFeaturizer(pair_indices)
X_all0 = featurizer.transform(trajectories)
featurizer = subset_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_that_all_featurizers_run():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
trj0 = trajectories[0][0]
atom_indices, pair_indices = subset_featurizer.get_atompair_indices(trj0)
featurizer = msmbuilder.featurizer.AtomPairsFeaturizer(pair_indices)
X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.SuperposeFeaturizer(np.arange(15), trj0)
X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.DihedralFeaturizer(["phi", "psi"])
X_all = featurizer.transform(trajectories)
#featurizer = msmbuilder.featurizer.ContactFeaturizer() # Doesn't work on ALA dipeptide
#X_all = featurizer.transform(trajectories)
featurizer = msmbuilder.featurizer.RMSDFeaturizer(trj0)
X_all = featurizer.transform(trajectories)
atom_featurizer0 = subset_featurizer.SubsetAtomPairs(pair_indices,
trj0,
exponent=-1.0)
cosphi = subset_featurizer.SubsetCosPhiFeaturizer(trj0)
sinphi = subset_featurizer.SubsetSinPhiFeaturizer(trj0)
cospsi = subset_featurizer.SubsetCosPsiFeaturizer(trj0)
sinpsi = subset_featurizer.SubsetSinPsiFeaturizer(trj0)
featurizer = subset_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)
