Hi Nick,

Please use the 1.5.3 release. Technically 1.5 is unstable but it has a lot problems (like this) fixed.

Thanks,
J

On 5 Sep 2013, at 10:56, "Nick Vandewiele" <Nick.Vandewiele@UGent.be> wrote:

Hi,
 
I read in an inchi, converted it into an IAtomContainer with one AtomParity. I clone it and suddenly, the reference of the central atom in the IAtomContainer is lost, i.e. the atom number for that central atom in that cloned molecule is -1. Cloning keeps the stereoelements, but somehow forgets the references.
 
Is that normal behavior or just a bug?
 
Below, example code that I used.
 
String inchi = "InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H3/t4-/m1/s1";// (R)-2-butanol
            InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
            // Get InChIToStructure
            InChIToStructure intostruct = factory.getInChIToStructure(inchi,
                        DefaultChemObjectBuilder.getInstance());
 
            IAtomContainer ac = intostruct.getAtomContainer();
            for(IStereoElement el : ac.stereoElements())
                  if(el instanceof AtomParity){
                        AtomParity ap = (AtomParity)el;
                        IAtom a = ap.getAtom();
                        System.out.println(ac.getAtomNumber(a));//3
                  }
           
           
           
            IAtomContainer molCl = null;
            try {
                  molCl = (IAtomContainer) ac.clone();
            } catch (CloneNotSupportedException e) {
            }
           
           
            for(IStereoElement el : molCl.stereoElements())
                  if(el instanceof AtomParity){
                        AtomParity ap = (AtomParity)el;
                        IAtom a = ap.getAtom();
                        System.out.println(molCl.getAtomNumber(a));//-1
                  }
           
regards
Nick
 
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