code: private double getDistanceValue(String id1, String id2) {
          String dkey = "";
          if (pSet.containsKey(("bond" + id1 + ";" + id2))) {
              dkey = "bond" + id1 + ";" + id2;
          } else if (pSet.containsKey(("bond" + id2 + ";" + id1))) {
              dkey = "bond" + id2 + ";" + id1;
          } else {
              //			logger.debug("DistanceKEYError:pSet has no key:" + id2 + " ; " + id1 + " take default bond length:" + DEFAULT_BOND_LENGTH_H);
              return DEFAULT_BOND_LENGTH_H;
          }
          return ((Double) (((List) pSet.get(dkey)).get(0))).doubleValue();
      }
docs: Gets the distance between two atoms out of the parameter set.
  
  @param  id1            id of the parameter set for atom1 (atom1.getAtomTypeName())
  @param  id2            id of the parameter set for atom2
  @return                The distanceValue value
  @exception  Exception  Description of the Exception