On Tue, Apr 1, 2008 at 3:31 PM, Gianfranco <[EMAIL PROTECTED]> wrote:
> 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!
That is intended, because that's what the SMILES defines: no explicit
bond orders.
Egon
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