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