def test_connect_mat():
connect_mat_true = [[1, 2],
[1, 3],
[1, 5],
[1, 6],
[2, 4],
[2, 7],
[2, 8],
[3, 9],
[3, 10],
[3, 11],
[4, 12],
[4, 13],
[4, 14]]
d = Molecule('data/xyz/butane.xyz')
assert np.allclose(connect_mat_true,d.connect)
sigma = 2.5
K = get_local_kernels(X, X, [sigma], cut_distance=10.0)[0]
K[np.diag_indices_from(K)] += 1e-8
alpha = cho_solve(K, y)
np.save('/ihome/ghutchison/dlf57/ml-benchmark/alpha-sig25-5k.npz', alpha)
data = []
for out in sorted(glob.iglob(
'/ihome/ghutchison/dlf57/ml-benchmark/molecules/stretch/*/sdf/*.sdf'),
key=numericalSort):
name = out.split('stretch/')[1].split('/sdf')[0]
pt = out.split('sdf/')[1].split('.')[0]
if name != 'HF':
mol = Molecule(out)
coords = mol.xyz
at_num = mol.at_num
rep = generate_representation(coords, at_num, max_size=45)
rep = np.array([rep])
K_pred = get_local_kernels(rep, X, [sigma], cut_distance=10.0)[0]
energy = list(np.dot(K_pred, alpha))[0]
d = {}
d.update({'name': name})
d.update({'point': pt})
d.update({'fchl_energy': energy})
data.append(d)
else:
def test_sdf_import():
d = Molecule('data/sdf/butane.sdf')
assert d.n_atom == 14
def test_symbol():
with pt.raises(KeyError):
Molecule('data/incorrect/butane_incorrectsymbol.xyz')
def test_import_failure():
with pt.raises(NotImplementedError):
Molecule('data/incorrect/empty.abc')
def test_cif_import():
d = Molecule('data/cif/cyclo_pentane.cif')
assert d.n_atom == 15
def test_cml_import():
d = Molecule('data/cml/butane.cml')
assert d.n_atom == 14
def test_cclib_import():
d = Molecule('data/cclib/butane.cclib')
assert d.n_atom == 14
def test_xyz_import():
d = Molecule('data/xyz/butane.xyz')
assert d.n_atom == 14