Dear Egon
I'm sorry but this code, with the code that you suggested, returns the
same output (C1CCCCC1):
>
>> try{
>>
>> //create molecule parsing the smile
>> SmilesParser sp = new
>> SmilesParser(DefaultChemObjectBuilder.getInstance());
>> IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
>> IMolecule m = builder.newMolecule( sp.parseSmiles("c1ccccc1"));
>>
>> //aromaticity
>> AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(m);
>> CDKHueckelAromaticityDetector.detectAromaticity(m);
>>
>
> DeduceBondSystemTool dbst = new DeduceBondSystemTool();
> molecule = dbst.fixAromaticBondOrders(molecule);
>
>
>> //generation of new fingerprint
>> SmilesGenerator sg = new SmilesGenerator();
>>
>> System.out.print(sg.createSMILES(m));
>>
>> }
>>
>> catch (Exception e){
>> e.printStackTrace();
>> }
>>
Thanks for you patience.
Gianfranco
--
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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