Re: [Rdkit-discuss] Isomeric smiles and explicit hydrogens

[Noel O'B. <bao...@gm...>]

Wait a second, that molecule has five substituents on the isomeric C.
But I think we share the blame again this time, Greg, because I took
that structure from the RDKit Python tutorial Section 2.3. :-)

Noel

On 14/04/2008, Noel O'Boyle <bao...@gm...> wrote:
> If I found a bug earlier, it was completely by accident. The following
>  though I think is also a bug. I find that I can invert the
>  stereocenter by adding and removing Hs.
>
>  >>> mol = rdk.readstring("smi", "C[C@@H](O)(Cl)c1ccccc1")
>  >>> mol.write("iso")
>  'C[C@@H](O)(Cl)c1ccccc1'
>  >>> mol.addh()
>  >>> mol.write("iso")
>  '[H]O[C@](Cl)(C([H])([H])[H])([H])c1c([H])c([H])c([H])c([H])c1[H]'
>  >>> mol.removeh()
>  >>> mol.write("iso")
>  'C[C@H](O)(Cl)c1ccccc1'
>
>  Can you tell whether the problem is when I add the Hs, or when I
>  remove them? I might be able to workaround if the adding is working
>  okay.
>
>
>  Noel
>