On Dec 7, 2007, at 10:40 AM, Gianfranco wrote:
> Thanks for you reply.
>
> I sooved my problem but I got another:
>
> IMolecularDescriptor descriptor = new
> AromaticBondsCountDescriptor();
> Object[] params = {true};
> descriptor.setParameters(params);
> SmilesParser sp = new SmilesParser
> (DefaultChemObjectBuilder.getInstance());
> IAtomContainer mol = sp.parseSmiles("c1ccccc1"); // ethanol
> HydrogenAdder hd = new HydrogenAdder();
> hd.addExplicitHydrogensToSatisfyValency(mol);
> System.out.println(mol.getAtomCount());
> assertEquals(6, ((IntegerResult) descriptor.calculate
> (mol).getValue()).intValue());
> it prints 18 total atoms instead of 12 (6C + 6H).
It's a good idea to use the current code from SVN since hydrogen
addition and aromaticity detection has been very much improved.
The following code (based on the nightly build) works correctly:
IMolecularDescriptor descriptor = new AromaticBondsCountDescriptor
();
Object[] params = {true};
descriptor.setParameters(params);
SmilesParser sp = new SmilesParser
(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("c1ccccc1"); // ethanol
CDKHueckelAromaticityDetector.detectAromaticity(mol);
CDKHydrogenAdder hd = CDKHydrogenAdder.getInstance
(DefaultChemObjectBuilder.getInstance());
hd.addImplicitHydrogens(mol);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
System.out.println(mol.getAtomCount());
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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