def assertBondStereoRoundTrips(self, fname):
path = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', fname)
mol = Chem.MolFromMolFile(path)
refSmiles = mol.GetProp("_Name")
self.assertTrue(len(refSmiles) > 0)
self.assertEqual(Chem.MolToSmiles(mol, isomericSmiles=True), refSmiles)
# now test Chem.DetectBondStereoChemistry more directly by constructing the molecule from scratch
oldconf = mol.GetConformer(0)
newconf = Chem.Conformer(mol.GetNumAtoms())
newmol = Chem.RWMol()
for atm in mol.GetAtoms():
ratm = Chem.Atom(atm.GetAtomicNum())
ratm.SetFormalCharge(atm.GetFormalCharge())
newmol.AddAtom(ratm)
atomidx = atm.GetIdx()
pos = oldconf.GetAtomPosition(atomidx)
newconf.SetAtomPosition(atomidx, pos)
for bnd in mol.GetBonds():
newmol.AddBond(bnd.GetBeginAtomIdx(), bnd.GetEndAtomIdx(), Chem.BondType(bnd.GetBondType()))
newmol.AddConformer(newconf)
Chem.SanitizeMol(newmol)
Chem.DetectBondStereoChemistry(newmol, newmol.GetConformer())
# these aren't necessary for this specific test case, but are for
# a more general conversion routine, so would like to see them
# tested eventually
# Chem.AssignAtomChiralTagsFromStructure(newmol)
# Chem.AssignStereochemistry(newmol)
self.assertEqual(Chem.MolToSmiles(newmol, isomericSmiles=True), refSmiles)
