gistfile1.java

public void clone(IAtomContainer source, IAtomContainer target) {
  for (int i = 0; i < source.getAtomCount(); i++) {
    IAtom atom = (IAtom) source.getAtom(i).clone();
    target.addAtom(atom);
  }
               
  for (IBond bond : source.bonds()) {
    IBond newBond = (IBond)bond.clone();
    IAtom[] newAtoms = new IAtom[bond.getAtomCount()];
    for (int j = 0; j < bond.getAtomCount(); ++j) {
      IAtom atom = bond.getAtom(j);
      newAtoms[j] = getAtomByEquals(target, source, atom);
  //  newAtoms[j] = getAtomByID(target, atom.getID());
    }                    
    newBond.setAtoms(newAtoms);
    target.addBond(newBond);
  }
}

public IAtom getAtomByID(IAtomContainer container, String id) {
  for (IAtom atom : container.atoms()) {
    if (atom.getID().equals(id)) {
      return atom;
    }
  }
  return null;
}

public IAtom getAtomByEquals(IAtomContainer target, IAtomContainer source, IAtom atom) {
   return target.getAtom(source.getAtomNumber(atom));
}