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

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

I think I've been misunderstanding the square brackets. I need to
RTFM, I think, after which I'll post here again if still confused.

Noel

On 14/04/2008, Noel O'Boyle <bao...@gm...> wrote:
> I've been trying to get my head around what's happening when I read
>  and write isomeric smiles. As a user, I hope that the same molecule
>  will also have the same isomeric SMILES. However, look at the
>  following examples using cinfony which read a SMILES string and write
>  an isomeric SMILES string...
>
>  I'm trying to specify the chirality of the carbon in
>  chlorobromomethane, but RDKit is not picking up on the chirality:
>
>  >>> rdk.readstring("smi", "[C](Cl)Br").write("iso")
>  'ClCBr'
>  (No chirality, as expected)
>
>  >>> rdk.readstring("smi", "[C@@H](Cl)Br").write("iso")
>  'Cl[CH]Br'
>  >>> rdk.readstring("smi", "[C@](Cl)Br").write("iso")
>  'ClCBr'
>  >>> rdk.readstring("smi", "Cl[C@]Br").write("iso")
>  'ClCBr'
>  >>> rdk.readstring("smi", "Cl[C@@H]Br").write("iso")
>  'Cl[CH]Br'
>  (Expected chirality, but didn't get it)
>
>  Let's try 1-chloro,1-bromoethane:
>
>  >>> rdk.readstring("smi", "Cl[C@@](Br)C").write("iso")
>  'CC(Cl)Br'
>  (Expected chirality, but didn't get it)
>  >>> rdk.readstring("smi", "Cl[C@@H](Br)C").write("iso")
>  'C[C@@H](Cl)Br'
>  (Expected chirality, and got it)
>
>  Is the problem with me or with RDKit?
>
>  On a related note, I have found that RDKit, when reading SDF files,
>  turns all of the hydrogens into implicit hydrogens. However, when
>  reading SMILES strings, it retains any explicit hydrogens specified in
>  C@@H expressions. This doesn't seem to be consistent and requires the
>  user to remove hydrogens if he/she wants to create a canonical smiles
>  string.
>
>  Apologies in advance if my understanding of SMILES is shaky.
>
>  Regards,
>
>     Noel
>