The encoding of the ligand-protein complex consists of creating a multiset of atoms for the ligand and one for the protein, respectively. The set L representing the ligand is constructed by iterating over the atoms of the ligand, and adding those that are within a radius of r from any atom in the protein to the set. The set M representing the protein is constructed in the same way, however, with the roles of the ligand and protein reversed. The optimal value of r = 5.5