So the desired output is 1,2,3,4,5 instead of 3,3,3,4,5?
If so, isn't SetImplicitValence what you are looking for?
>>> mol = pybel.readstring("smi", "[AlH3]").OBMol
>>> mol.DeleteHydrogens()
True
>>> print pybel.Molecule(mol).write("smi")
[AlH3]
>>> print mol.GetAtom(1).GetImplicitValence() # 3
Hi Noel,
On Tue, Mar 19, 2013 at 3:16 PM, Noel O'Boyle wrote:
> I believe that the key value is the _impval property on an OBAtom,
> which is assigned by the atomtyper. Can you ask your program to print
> out the values after the EndModify() using atom->GetImplicitValence()?
>
It looks like y
