Align the query pharmacophores to the reference pharmacophore. This node computes the aligned query pharmacophore, the transformation matrix and Root-mean-square deviation (RMSD).
- Find pairs probe and reference points that are same type and are not too far apart.
- Find biggest clique of pairs, using BronKerbosch clique detection algorithm .
- Calculate optimal translation and rotation using Kabsch algorithm for all the found cliques.
- Calculate RMSD and aligned pharmacophore based on points in each clique.