code: @Override
      public IAtomContainer containerFromPermutation(int[] permutation) {
          try {
              IAtomContainer permutedContainer = (IAtomContainer) atomContainer.clone();
              IAtom[] atoms = new IAtom[atomContainer.getAtomCount()];
              for (int i = 0; i < atomContainer.getAtomCount(); i++) {
                  atoms[permutation[i]] = permutedContainer.getAtom(i);
              }
              permutedContainer.setAtoms(atoms);
              return permutedContainer;
          } catch (CloneNotSupportedException c) {
              return null;
          }
      }
docs: Generate the atom container with this permutation of the atoms.
  
  @param permutation the permutation to use
  @return the