code: private int getAtomPosition(IAtom atom, IAtomContainer container) {
          for (int i = 0; i < container.getAtomCount(); i++) {
              if (atom.equals(container.getAtom(i))) {
                  return i;
              }
          }
          return -1;
      }
docs: Helper method, used to help construct a configuration.
  @param atom
  @param container
  @return the array position of atom in container