but the problem seems to be at the level of the parser:
IMolecule m = builder.newMolecule( sp.parseSmiles("c1ccccc1"));
AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(m);
CDKHueckelAromaticityDetector.detectAromaticity(m);
hdx.addImplicitHydrogens(m);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(m);
for(int t=0; t < m.getBondCount(); t ++){
System.out.println( m.getBond(t).getOrder() );
}
this code returns 1.0 for all the 12 bonds in this molecule!
G.
> On Tue, Apr 1, 2008 at 3:14 PM, Gianfranco <[EMAIL PROTECTED]> wrote:
>
>> I'm sorry but this code, with the code that you suggested, returns the
>> same output (C1CCCCC1):
>>
>
> I filed a bug report.
>
> Egon
>
>
--
Gianfranco Frau
CRS4 - Bioinformatics
Phone +39 070 9250 438
Loc. Pixina Manna Edificio 1 Pula 09010 (CA), Italy
http://www.bioinformatica.crs4.org
msn contact: [EMAIL PROTECTED]
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