def test_upper_tri_coulomb_matrix(self):
"""
Test upper triangular CoulombMatrix.
"""
f = cm.CoulombMatrix(self.mol.GetNumAtoms(), upper_tri=True)
rval = f([self.mol])
size = np.triu_indices(self.mol.GetNumAtoms())[0].size
assert rval.shape == (1, self.mol.GetNumConformers(), size)
def test_coulomb_matrix(self):
"""
Test CoulombMatrix.
"""
f = cm.CoulombMatrix(self.mol.GetNumAtoms())
rval = f([self.mol])
assert rval.shape == (1, self.mol.GetNumConformers(),
self.mol.GetNumAtoms(), self.mol.GetNumAtoms())
def test_coulomb_matrix_padding(self):
"""
Test CoulombMatrix with padding.
"""
f = cm.CoulombMatrix(max_atoms=self.mol.GetNumAtoms() * 2)
rval = f([self.mol])
size = np.triu_indices(self.mol.GetNumAtoms() * 2)[0].size
assert rval.shape == (1, self.mol.GetNumConformers(), size)
def test_coulomb_matrix_padding(self):
"""
Test CoulombMatrix with padding.
"""
max_atoms = self.mol.GetNumAtoms() * 2
f = cm.CoulombMatrix(max_atoms=max_atoms)
rval = f([self.mol])
assert rval.shape == (1, self.mol.GetNumConformers(), max_atoms,
max_atoms)
def test_coulomb_matrix_hydrogens(self):
"""
Test no hydrogen removal.
"""
f = cm.CoulombMatrix(max_atoms=self.mol.GetNumAtoms(),
remove_hydrogens=False)
rval = f([self.mol])
size = np.triu_indices(self.mol.GetNumAtoms())[0].size
assert rval.shape == (1, self.mol.GetNumConformers(), size)
def test_coulomb_matrix_no_hydrogens(self):
"""
Test hydrogen removal.
"""
mol = Chem.RemoveHs(self.mol)
assert mol.GetNumAtoms() < self.mol.GetNumAtoms()
f = cm.CoulombMatrix(max_atoms=mol.GetNumAtoms(),
remove_hydrogens=True)
rval = f([self.mol]) # use the version with hydrogens
size = np.triu_indices(mol.GetNumAtoms())[0].size
assert rval.shape == (1, mol.GetNumConformers(), size)