Re: [Joelib-help] canonifier?

[Andreas M. <an...@ma...>]

Hi Joerg,
 
this code is derived from your advice:
 
public static void main(String args[]) {
                String smiles = args[0];
                JOEMol mol=new JOEMol();
                Morgan morgan = new Morgan(new BasicTieResolver());
 
                JOESmilesParser.smiToMol(mol, smiles, smiles);
                JOEMol tMol = (JOEMol) mol.clone(false);
                morgan.calculate(tMol);
                JOEMol rMol = morgan.renumber(tMol);
 
        }
 
and it returns the following error:
 
Exception in thread "main" java.lang.NullPointerException
        at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
        at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
        at SmilesCanonifier.main(SmilesCanonifier.java:64)
 
What's wrong here?
 
Greetings
Andreas

On Mon, Oct 18, 2004 at 05:44:03PM +0200, Joerg K. Wegner wrote:
> Hi Andreas,
> 
> sorry for the late reply i was in holiday for three weeks.
> 
> >does Joelib provide a functionality to obtain a canonified version of a 
> >SMILES string?
> Definitely, as far as the Morgan algorithm can be used for canonization.
> 
> Just set
> joelib.io.types.Smiles.canonical=false
> in joelib.properties to 'true'
> 
> or copy code fragment from:
> joelib.io.types.Smiles
>