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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