dear all,
please look out this code. It creates a IMolecule object from SMILES of
benzene, uses the aromaticity detector and than generates again the
SMILES from the molecule.
The code print out the string: "C1CCCCC1", so a molecule without
aromaticity.
Is it correct? What's the matter?
thank you
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);
//generation of new fingerprint
SmilesGenerator sg = new SmilesGenerator();
System.out.print(sg.createSMILES(m));
}
catch (Exception e){
e.printStackTrace();
}
--
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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