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))
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_universe():
u1 = mda.Universe(waterPSF, waterDCD)
u2 = mda.Universe(waterPSF, waterDCD)
pca_test = PCA(u1).run()
pca_test.transform(u2)