SMILES for carbon and other common organic elements already assume implicit
hydrogens, implicitly.
this is not RDKit thing, it's the definition of SMILES.
I'm not sure there is such thing as "implicit" hydrogens for Silicone even
though it's so similar to Carbon.
HTH,
Igor
On Fri, Sep 27, 2013 at 7:14 AM, Toby Wright <toby.wri...@inhibox.com>wrote:
> Hi,
>
> I've observed an odd behaviour in RDKit with listing explicit hydrogens in
> smiles where the original molecules were generated from SD files. As the
> code below shows if I ask "What is the smiles for a single C atom?" I get
> "C" but if I ask for silicon I get "[SiH4]". Any reason why this might be?
> I've also observed that in RDKit 2013 Q2 I get "[Fe]" as the smiles from a
> single iron atom, but in RDKit 2011 Q4 I get "[FeH6]" but I can't see
> anything in the release notes to explain this change. I also have examples
> involving atoms in larger molecules but I thought these provided the
> simplest examples.
>
> Example files and interactive python snippet:
>
> >>> sup = Chem.SDMolSupplier("SingleSi.sdf")
> >>> sup2 = Chem.SDMolSupplier("SingleC.sdf")
> >>> print Chem.MolToSmiles(sup[0], canonical=True, isomericSmiles=True)
> [SiH4]
> >>> print Chem.MolToSmiles(sup2[0], canonical=True, isomericSmiles=True)
> C
>
> SingleC.sdf:
> SingleC
> RDKit 2D
>
> 1 0 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> M END
> $$$$
>
> SingleSi.sdf:
> SingleSi
> RDKit 2D
>
> 1 0 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
> M END
> $$$$
>
> Thanks,
>
> Toby
>
> --
> InhibOx Ltd
>
>
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