code: protected List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
              throws CDKException {
  
          mappings = new ArrayList<Map<IAtom, IAtom>>();
          connectedBondOrder = new TreeMap<Integer, Double>();
          this.source = source;
          this.target = target;
  
          if (source.getAtomCount() == 1 || (source.getAtomCount() > 0 && source.getBondCount() == 0)) {
              setSourceSingleAtomMap(removeHydrogen);
          }
          if (target.getAtomCount() == 1 || (target.getAtomCount() > 0 && target.getBondCount() == 0)) {
              setTargetSingleAtomMap(removeHydrogen);
          }
  
          postFilter();
          return mappings;
      }
docs: Returns single mapping solutions.
  @param source
  @param target
  @param removeHydrogen
  @return Mappings
  @throws CDKException