code: @Override
      public IAtomContainer containerFromPermutation(int[] permutation) {
          try {
              IAtomContainer permutedContainer = (IAtomContainer) super.atomContainer.clone();
              int n = permutedContainer.getBondCount();
              IBond[] permutedBonds = new IBond[n];
              for (int i = 0; i < n; i++) {
                  permutedBonds[i] = permutedContainer.getBond(permutation[i]);
              }
              permutedContainer.setBonds(permutedBonds);
              return permutedContainer;
          } catch (CloneNotSupportedException cne) {
              return null;
          }
      }
docs: /*
  (non-Javadoc)
  @see
  org.openscience.cdk.graph.AtomContainerPermutor#containerFromPermutation
  (int[])