def test_that_all_featurizers_run():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
trj0 = trajectories[0][0]
atom_indices, pair_indices = mixtape.subset_featurizer.get_atompair_indices(trj0)
featurizer = mixtape.featurizer.AtomPairsFeaturizer(pair_indices)
X_all = featurizer.transform(trajectories)
featurizer = mixtape.featurizer.SuperposeFeaturizer(np.arange(15), trj0)
X_all = featurizer.transform(trajectories)
featurizer = mixtape.featurizer.DihedralFeaturizer(["phi" ,"psi"])
X_all = featurizer.transform(trajectories)
#featurizer = mixtape.featurizer.ContactFeaturizer() # Doesn't work on ALA dipeptide
#X_all = featurizer.transform(trajectories)
featurizer = mixtape.featurizer.RMSDFeaturizer(trj0)
X_all = featurizer.transform(trajectories)
atom_featurizer0 = mixtape.subset_featurizer.SubsetAtomPairs(pair_indices, trj0, exponent=-1.0)
cosphi = mixtape.subset_featurizer.SubsetCosPhiFeaturizer(trj0)
sinphi = mixtape.subset_featurizer.SubsetSinPhiFeaturizer(trj0)
cospsi = mixtape.subset_featurizer.SubsetCosPsiFeaturizer(trj0)
sinpsi = mixtape.subset_featurizer.SubsetSinPsiFeaturizer(trj0)
featurizer = mixtape.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 = mixtape.subset_featurizer.get_atompair_indices(trj0)
featurizer = mixtape.featurizer.AtomPairsFeaturizer(pair_indices)
X_all0 = featurizer.transform(trajectories)
featurizer = mixtape.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)])
