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_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_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)