In the main part of the algorithm (Line 4 to Line 12) a loop over all the optimized cluster geometries for all the computational methods which should be compared to the reference method is performed (Line 6). Now, this cluster geometry should compared to the reference geometry. This is done in such a way that, if the two structures are identical, a lot of zeroes are computed, such that there are as many numbers as possible to analyse in the later part of the algorithm. The idea is that if two clusters are identical then the rotation matrix from any pair of equivalent monomers should be equal and equal to the rotation matrix for the entire cluster. So if this is assumed and the rotation matrix for all monomer pairs (Line 9)