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

[Steffen N. <sne...@ip...>]

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
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