def test_cosine_content(): rand = mda.Universe(RANDOM_WALK_TOPO, RANDOM_WALK) pca_random = PCA(rand).run() dot = pca_random.transform(rand.atoms) content = cosine_content(dot, 0) assert_almost_equal(content, .99, 1)
def test_transform_rerun(u): atoms = u.select_atoms('bynum 1-10') u.transfer_to_memory() pca = PCA(u, select='bynum 1-10', stop=5) dot = pca.transform(atoms) assert_equal(dot.shape, (98, atoms.n_atoms * 3))
def test_transform_universe(): u1 = mda.Universe(waterPSF, waterDCD) u2 = mda.Universe(waterPSF, waterDCD) pca_test = PCA(u1).run() pca_test.transform(u2)
def test_pca_not_run(u): atoms = u.select_atoms('bynum 1-10') u.transfer_to_memory() pca = PCA(u, select='bynum 1-10') with pytest.raises(ValueError): dot = pca.transform(atoms, stop=5)
def test_transform_rerun(u): atoms = u.select_atoms('bynum 1-10') u.transfer_to_memory() pca = PCA(u, select='bynum 1-10').run(stop=5) dot = pca.transform(atoms) assert_equal(dot.shape, (98, atoms.n_atoms * 3))