# evaluate all the built-in non-cheating cost functions # plus some standard residue-propensity functions # The weights are all set to 1, so the sum is really rather meaningless. InFilePrefix /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp2-pdb.types ReadClashTable exp2-pdb-dunbrack-40pc-3157-2symm.clash SetClashDefinition exp2-pdb-dunbrack-40pc-3157-2symm CreateBurialCost CB_14 CB smoothed-monomeric-50pc-CB14.hist CB # The following are already defined in evaulate.under # CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log # CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist # CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist # CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist # CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist # CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist # CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist # CreateBurialCost near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot # CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot # CreateAlphaCost alpha dunbrack-2191-alpha.hist # CreateAlphaCost alpha_prev dunbrack-2191-alpha-1.hist -1 SetCost \ CAContact 1 CBContact 1 contact 1 \ contact_order 1 \ wet6.5 1 dry5 1 dry6.5 1 dry8 1 dry12 1 \ near_backbone 1 way_back 1 CB_14 1 \ alpha 1 alpha_prev 1 bystroff 1 \ phobic_fit 1 phobic_norm 1 phobic_radius 1 \ radius_fit 1 radius_norm 1 radius 1 \ sidechain 1 \ old_n_ca_c 1 n_ca_c 5 \ bad_peptide 1 \ soft_clashes 1 backbone_clashes 1 \ clashes 1 sidechain_clashes 1 \ break 1 \ hbond_count 1 hbond_dist 1 \ hbond_geom 1 \ hbond_geom_backbone 1 \ hbond_geom_beta 1 \ hbond_geom_beta_pair 1 \ maybe_metal 1 maybe_ssbond 1 \ knot 1 deep_knot 1 \ missing_atoms 1 \ is_align 1 # real cost is combination of several score functions, set so that # different contributors to score have comparable weight. SetRealCost real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \ real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \ knot 10 clens 200 \ rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 \ GDT 1 smooth_GDT 1 \ missing_atoms 0.2