Fragments consisting of more than 4 atoms, in which at least two atoms are rigid, that is, are connected by a non-rotatable bond, are considered as seed fragments. These are subsequently rigidly docked into the protein binding site. All other non-seed fragments are considered as linking fragments during the compound reconstruction process. This result is shown in Figure . This function calculates a fitness score for each compound's or fragment's atom in a protein by considering all protein atoms within 6 Å radius of that atom. It is an atomic level radial distribution function with mean reference state that averages over all pairwise atom types from a reduced atom type composition (protein's and compound's atom types), using experimentally determined intermolecular complexes in the Cambridge Structural Database (CSD) and in the Protein Data Bank (PDB) as the information sources.