def setUp(self):
self.u = MDAnalysis.Universe(PDB, XTC)
self.dist = diffusionmap.DistanceMatrix(self.u, select='backbone')
self.dmap = diffusionmap.DiffusionMap(self.dist)
self.dmap.run()
self.eigvals = self.dmap.eigenvalues
self.eigvects = self.dmap._eigenvectors
def test_transform(u, dmap):
eigvects = dmap._eigenvectors
n_eigenvectors = 4
dmap = diffusionmap.DiffusionMap(u)
dmap.run()
diffusion_space = dmap.transform(n_eigenvectors, 1)
assert diffusion_space.shape == (eigvects.shape[0], n_eigenvectors)
def test_transform(self):
self.n_eigenvectors = 4
self.dmap = diffusionmap.DiffusionMap(self.u)
self.dmap.run()
diffusion_space = self.dmap.transform(self.n_eigenvectors, 1)
assert_equal(diffusion_space.shape,
(self.eigvects.shape[0], self.n_eigenvectors))
def test_dist_weights(u):
backbone = u.select_atoms('backbone')
weights_atoms = np.ones(len(backbone.atoms))
dist = diffusionmap.DistanceMatrix(u,
select='backbone',
weights=weights_atoms)
dist.run(step=3)
dmap = diffusionmap.DiffusionMap(dist)
dmap.run()
assert_array_almost_equal(dmap.eigenvalues, [1, 1, 1, 1], 4)
assert_array_almost_equal(dmap._eigenvectors,
([[0, 0, 1, 0], [0, 0, 0, 1],
[-.707, -.707, 0, 0], [.707, -.707, 0, 0]]), 2)
def test_different_steps(self):
self.dmap = diffusionmap.DiffusionMap(self.u, select='backbone', step=3)
self.dmap.run()
assert_equal(self.dmap._eigenvectors.shape, (4,4))
def test_different_steps(u):
dmap = diffusionmap.DiffusionMap(u, select='backbone')
dmap.run(step=3)
assert dmap._eigenvectors.shape == (4, 4)
def dmap(dist):
d_map = diffusionmap.DiffusionMap(dist)
d_map.run()
return d_map