Re: [Cdk-devel] Generating a SMARTS from a subset of atoms in an IAtomContainer

[John M. <joh...@gm...>]

Hi Steffen,

I'm not aware of any way to do this. In the case aromaticity, the generator/parser should preserve this (but it probably doesn't). If it's only the aromaticity you need it might be possible to patch this but if you need other patterns then it is difficult.

Sorry,
J

On 12 Mar 2013, at 23:32, Steffen Neumann <sne...@ip...> wrote:

> Hi,
> 
> our http://msbi.ipb-halle.de/MetFrag/ uses the CDK 
> to fragment a molecule (by disconnecting the bonds
> in different places). We can then check whether the 
> mass of the two fragments match what was measured 
> in tandem mass spectrum. If we now want two write 
> the fragment structure to disc, we could do that 
> as e.g. a SMILES. 
> 
> The problem is that the resulting SMILES might not anymore 
> be considered a substructure of the full molecule:
> If we have an aromatic ring, then a fragment of that 
> will be written as non-aromatic SMILES.
> 
> Question: is there a way to directly create a SMARTS
> from a subset of atoms in an AtomContainer ?
> The SMARTS could then capture that I am looking 
> for e.g. three connected aromatic carbons.
> 
> Yours,
> Steffen
> 
> 
> 
> 
> 
> 
> -- 
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                  +49 (0) 345 5582 - 0
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> 
> 
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