The matrix forms can be build for the relations among 2, 3 and 4 atoms. For n = 2 [duplex option, (2-tuple)], the index calculations are performed over vertex pairs i and j. For n = 3 (3-tuple), the index calculations are performed over vertices i, j and k. Finally, for n = 4 (4-tuple) the index calculations are performed over vertices i, j, k and l. See Section 2 for mathematical definition.