The following code does not yield a molecule with the same atom order as the xyz:
xyz5 = str_to_xyz(""" C 1.50048866 -0.50848248 -0.64006761
F 0.27568368 0.01156702 -0.41224910
Cl 3.09727149 -1.18647281 -0.93707550
O 1.93561914 0.74741610 -1.16759033
O 2.33727805 1.90670710 -1.65453438
H 3.25580294 1.83954553 -1.92546105""")
spc5 = ARCSpecies(label='chiralOOH', smiles='OO[C](F)Cl', xyz=xyz5)
for atom, symbol in zip(spc5.mol.atoms, xyz5['symbols']):
self.assertEqual(atom.symbol, symbol)
The problem is in converter.molecules_from_xyz(), and specifically in converter.order_atoms() where the if mol_is_iso_copy.is_isomorphic(ref_mol_is_iso_copy, save_order=True, strict=False): check gives False: One mol has the radical, the other doesn't.
alongd
commented
4 years ago
The following code does not yield a molecule with the same atom order as the xyz:
The problem is in
converter.molecules_from_xyz(), and specifically inconverter.order_atoms()where theif mol_is_iso_copy.is_isomorphic(ref_mol_is_iso_copy, save_order=True, strict=False):check givesFalse: One mol has the radical, the other doesn't.