def test_RC(mols):
cm = CoulombMatrix('RC', n_jobs=10)
h2o = cm.represent(mols )
assert h2o.shape == (1, cm.nPerm * cm.max_n_atoms_ * (cm.max_n_atoms_ + 1) / 2)
a = np.array([[
0.5, 8.35237809, 73.51669472, 0.66066557, 8.3593106, 0.5, 73.51669472, 8.35237809, 0.5,
8.3593106, 0.66066557, 0.5, 0.5, 8.3593106, 73.51669472, 0.66066557, 8.35237809, 0.5
]])
def test_SC(mols):
cm = CoulombMatrix('SC', n_jobs=1)
h2o = cm.represent(mols)
assert h2o.shape == (1, cm.max_n_atoms_ * (cm.max_n_atoms_ + 1) / 2)
a = np.array([[73.51669472, 8.3593106, 0.5, 8.35237809, 0.66066557, 0.5]])
assert a[0][0] == pytest.approx( h2o.values[0][0])
assert a[0][1] == pytest.approx( h2o.values[0][1])
assert a[0][-1] == pytest.approx( h2o.values[0][-1])
def test_E(mols):
cm = CoulombMatrix('E', n_jobs=2)
h2o = cm.represent(mols )
assert h2o.shape == (1, cm.max_n_atoms_)
a = np.array([[75.39770052, -0.16066482, -0.72034098]])
assert a[0][0] == pytest.approx( h2o.values[0][0])
assert a[0][1] == pytest.approx( h2o.values[0][1])
assert a[0][-1] == pytest.approx( h2o.values[0][-1])
def test_UM(mols):
cm = CoulombMatrix('UM')
h2o = cm.represent(mols)
assert h2o.shape == (1, cm.max_n_atoms_ ** 2)
a = np.array([[
73.51669472, 8.3593106, 8.35237809, 8.3593106, 0.5, 0.66066557, 8.35237809, 0.66066557, 0.5
]])
assert a[0][0] == pytest.approx(h2o.values[0][0], 0.001)
assert a[0][1] == pytest.approx(h2o.values[0][1], 0.001)
assert a[0][-1] == pytest.approx(h2o.values[0][-1], 0.001)
def test_exception(mols):
# Value error: molecule object
cm = CoulombMatrix('UM')
with pytest.raises(ValueError):
cm.represent('fake')
with pytest.raises(ValueError):
cm.represent(['fake'])
# Value error ndim>1
with pytest.raises(ValueError):
cm.represent(np.array([[mols],[mols]]))
def test_SC_mollist(mols2):
cm = CoulombMatrix('SC', n_jobs=-1, verbose=False)
features = cm.represent(mols2)
assert features.shape == (4, cm.max_n_atoms_ * (cm.max_n_atoms_ + 1) / 2)