Re: [Cdk-user] Susbtructure detection problem

[Rajarshi G. <rg...@in...>]

On Oct 1, 2007, at 10:19 AM, allouche miriame wrote:

>  Hi,
> I am using the class UniversalIsomorphismTester to detect  
> subtructures.
> I have a problem with the method isSubgraph() which does not return  
> what I expect for some fragments .
> Here is an example :
> fragment 1 represented by the SMILES : "CCCC"
> fragment 2 represented by the SMILES : "c1ccc2c(c1)ccc3ccccc2"
>
> SmilesParser sp = new SmilesParser 
> (DefaultChemObjectBuilder.getInstance());
> IAtomContainer atomContainer;
> atomContainer = sp.parseSmiles("c1ccc2c(c1)ccc3ccccc2");

I think you'll need to detect aromaticity by doing

HueckelAromaticityDetector.detectAromaticity(atomContainer);

After doing this, the call to the UIT should work

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Rajarshi Guha  <rg...@in...>
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A bug in the hand is better than one as yet undetected.