def test_mol2smarts(caffeine_smarts): m = Molecule(caffeine_smarts, 'smarts') m.to_smarts() assert isinstance(m.rdkit_molecule, Chem.Mol) assert m.smarts == caffeine_smarts m.to_smarts(isomericSmiles=False) assert m.smarts == caffeine_smarts
def test_load_xyzfile(xyz_path): path = os.path.join(xyz_path, '1_opt.xyz') m = Molecule(path, 'xyz') assert m.creator == ('XYZ', path) assert isinstance(m.pybel_molecule, pybel.Molecule) assert m.xyz.geometry.shape == (28, 3) m.to_smiles() assert m.smiles == 'c1ccc(CC2CCCC2)cc1' m.to_smarts() assert m.smarts == '[#6]1-[#6]-[#6]-[#6](-[#6]-1)-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1' m.to_inchi() assert m.inchi == 'InChI=1S/C12H16/c1-2-6-11(7-3-1)10-12-8-4-5-9-12/h1-3,6-7,12H,4-5,8-10H2'
def test_mol2smarts_defaultargs(caffeine_smarts): m = Molecule(caffeine_smarts, 'smarts') m.to_smarts() m.to_smarts(**m._default_rdkit_smarts_args) # all the args & isomericSmiles=False args = m._default_rdkit_smarts_args args['isomericSmiles'] = False m.to_smarts(**args) assert m.smarts_args['isomericSmiles'] is False