Re: Re: [Cdk-user] Aromatic -> Kekule

[<ala...@nt...>]

Chris

Yes, I'm parsing a SMILES string eg c1ccccc1 which, as I understand it, imports the aromatic bonds as bonds of order 1.5.  Is it possible to convert this to bonds of order 1.0 and 2.0 ie C1=C-C=C-C=C1 for display purposes?

Here is a code snippetfrom a simple Java Swing application:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

        Molecule m = new Molecule();
        
	try {
        SmilesParser sp = new SmilesParser();
        m = sp.parseSmiles("c1ccccc1");
        }catch (InvalidSmilesException ise) {
        }

        
        SetOfMolecules set = new SetOfMolecules();
        set.addMolecule(m);

        MoleculeViewer2D mV = new MoleculeViewer2D();
        
        mV.display(m, true);
        
        getContentPane().add(mV, java.awt.BorderLayout.CENTER);

~~~~~~~~~~~~~~~~~~~~~~~~~~

Regards

Alastair


> 
> From: Christoph Steinbeck <c.s...@un...>
> Date: 2004/04/16 Fri PM 02:03:15 GMT
> To: ala...@nt...
> CC: cdk...@li...
> Subject: Re: [Cdk-user] Aromatic -> Kekule
> 
> ala...@nt... wrote:
> 
> > Hello All
> > 
> > Is it possible to display (2D) an aromatic ring in kekule form (alternating single and double bonds) rather than as a ring with a circle in it?
> > 
> > I can turn the ring drawing off with...
> > 
> > r2dm.setShowAromaticity(false);
> > 
> > ...but the rings are just shown as singly bonded atoms.
> > 
> > Thanks
> > 
> > Alastair
> 
> Alastair,
> 
> Please provide some more information on the way you are going in order 
> to create the situation you are describing.
> Are you parsing a SMILES, if yes, which one, etc...
> 
> Cheers,
> 
> Chris
> 
> -- 
> Dr. rer. nat. habil. Christoph Steinbeck (c.s...@un...)
> Groupleader Junior Research Group for Applied Bioinformatics
> Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
> Zülpicher Str. 47, 50674 Cologne
> Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786
> 
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
> 

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