def test_add_atom_map(toolkit):
smiles = 'CCCC'
mol = utils.load_molecule(smiles, toolkit=toolkit, strict=False)
mapped_mol = utils.add_atom_map(mol, in_place=False)
assert utils.has_atom_map(mapped_mol)
assert not utils.has_atom_map(mol)
assert not utils.is_missing_atom_map(mapped_mol)
assert utils.is_missing_atom_map(mol)
def test_remove_restore_atom_map(toolkit):
mapped_smiles = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mapped_mol = utils.load_molecule(mapped_smiles, toolkit=toolkit)
utils.remove_atom_map(mapped_mol)
assert utils.has_atom_map(mapped_mol) == False
assert utils.is_missing_atom_map(mapped_mol) == True
utils.restore_atom_map(mapped_mol)
assert utils.has_atom_map(mapped_mol) == True
assert utils.is_missing_atom_map(mapped_mol) == False
smiles = 'OCCO'
mol = utils.load_molecule(smiles, toolkit=toolkit)
with pytest.warns(UserWarning):
utils.restore_atom_map(mol)
def test_is_missing_map(toolkit, input, output):
#ToDo - Known problem that RDKit does not add explicit H to molecules even with explicit H SMILES so if map of H is missing it will not pick it up
mol = utils.load_molecule(input, toolkit=toolkit)
assert utils.is_missing_atom_map(mol) == output