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" <[email protected]> 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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