code: public double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds) {
          double overlapScore = 0;
          overlapScore = getAtomOverlapScore(ac, overlappingAtoms);
          //overlapScore += getBondOverlapScore(ac, overlappingBonds);
          return overlapScore;
      }
docs: Calculates a score based on the overlap of atoms and intersection of bonds.
  The overlap is calculated by summing up the distances between all pairs of
  atoms, if they are less than half the standard bondlength apart.
  
  @param  ac                The Atomcontainer to work on
  @param  overlappingAtoms  Description of the Parameter
  @param  overlappingBonds  Description of the Parameter
  @return                   The overlapScore value