output_dir = . ### name of the output directory (note: no quotes, can be absolute path or path from cwd) output_to_screen = True ### write output to screen in addition to writing to "log.txt" use_TER = True ### use "TER" to split protein and ligand, otherwise uses "HETATM" and chain ID do_reverse = False ### swap the protein and the ligand (i.e. map the surface of the ligand) use_naccess = True ### use Naccess program to calculate ASAs use_NP_wt = True ### use ASAs for non-polar weighting of alpha-spaces for pocket scoring use_exact_ACSA = False ### use exact pocket ASAs for non-polar weighting (more expensive calculation) get_face = True ### calculate the interface atom list screen_by_face = False ### select pockets that include atoms from the interface atom list screen_face_perc = 0.5 ### minimum percentage of atoms that must be in the interface atom list screen_by_lig_cntct = False ### select only pockets in "contact" with the ligand expand_around_cntct = False ### expand selection to include all pockets overlapping the "contact" pockets screen_by_score = False min_score = 100 ### select only pockets above a minimum score screen_by_perc_rank = False min_perc_rank = 0.9 ### select only pockets above of minimum percentage ranking screen_out_subsurf = False max_desolv_perc = 0.95 ### screen out pocket if too much of the alpha-cluster ASA is desolvated by the pocket ### (i.e. pocket is beneath the surface) (more expensive calculation) screen_by_res = False res_file = screen_resID.pdb ### select all pockets containing any atom from any residue within the residue pdb file pocket_communities = True ###calculate and output the pocket communities