code: public static CDKRGraph buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
              throws CDKException {
          CDKRGraph rGraph = new CDKRGraph();
          nodeConstructor(rGraph, sourceGraph, targetGraph, shouldMatchBonds);
          arcConstructor(rGraph, sourceGraph, targetGraph);
          return rGraph;
      }
docs: Builds the CDKRGraph ( resolution graph ), from two atomContainer
  (description of the two molecules to compare)
  This is the interface point between the CDK model and
  the generic MCSS algorithm based on the RGRaph.
  
  @param  sourceGraph  Description of the first molecule
  @param  targetGraph  Description of the second molecule
  @param shouldMatchBonds
  @return     the rGraph
  @throws CDKException