IAtom subsCloneAtom = rgrpClone.getAtom(getAtomPosition(subsAt, substitute.getGroup())); cloneBond.setAtom(subsCloneAtom, whichAtomInBond); IAtom discarded = rootClone.getAtom(getAtomPosition(rAtom, root)); for (IBond r0Bond : rootClone.bonds()) { if (r0Bond.contains(discarded)) {