# 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 InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet anglevector.alphabet ReadAlphabet burial.alphabet ReadAlphabet burial-sep.alphabet ReadAlphabet two-spot-burial.alphabet ReadAlphabet hbonds.alphabet ReadAlphabet str4.alphabet ReadBackgroundProbs dunbrack-in-scop.backgrounds InFilePrefix // bystroff CreateCombinedNNet bys_back background BystroffAV geommean TARGET.t2k.bys.rdb 0.2 TARGET.t04.bys.rdb 0.4 TARGET.t06.bys.rdb 0.4 CreatePredAngleVectorCost pred_bys_back BystroffAV bys_back // deBrevern CreateCombinedNNet pb_back background deBrevernAV geommean TARGET.t2k.pb.rdb 0.2 TARGET.t04.pb.rdb 0.4 TARGET.t06.pb.rdb 0.4 CreatePredAngleVectorCost pred_pb_back deBrevernAV pb_back // predalpha CreateCombinedNNet pred_alpha_back background alpha11 geommean TARGET.t2k.alpha.rdb 0.2 TARGET.t04.alpha.rdb 0.4 TARGET.t06.alpha.rdb 0.4 CreatePredAlphaCost pred_alpha_back alpha11 pred_alpha_back 2 alpha alpha_prev sum // nb11 CreateCombinedNNet pred_nb11_back background near-backbone-11 mean TARGET.t2k.near-backbone-11.rdb 0.2 TARGET.t04.near-backbone-11.rdb 0.4 TARGET.t06.near-backbone-11.rdb 0.4 CreatePredBurialCost pred_nb11_back near-backbone-11 pred_nb11_back near_backbone simple // cb14 InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost cb14 CB smoothed-monomeric-50pc-CB14.hist CB InFilePrefix CreateCombinedNNet pred_cb14_back background CB_burial_14_7 mean TARGET.t2k.CB_burial_14_7.rdb 0.2 TARGET.t04.CB_burial_14_7.rdb 0.4 TARGET.t06.CB_burial_14_7.rdb 0.4 CreatePredBurialCost pred_cb14_back CB_burial_14_7 pred_cb14_back cb14 simple // sep9 InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost CB8-sep9 CB dunbrack-40pc-3157-CB8-sep9.hist spot min_sep 9 InFilePrefix CreateCombinedNNet pred_CB8_sep9_back background CB8-sep9 single TARGET.t06.CB8-sep9.rdb CreatePredBurialCost pred_CB8_sep9_back CB8-sep9 pred_CB8_sep9_back CB8-sep9 simple // nsep CreateCombinedNNet n_sep_back background n_sep mean TARGET.t2k.n_sep.rdb 0.2 TARGET.t04.n_sep.rdb 0.4 TARGET.t06.n_sep.rdb 0.4 CreatePredHbondCost pred_n_sep_back n_sep n_sep_back // osep CreateCombinedNNet o_sep_back background o_sep mean TARGET.t2k.o_sep.rdb 0.2 TARGET.t04.o_sep.rdb 0.4 TARGET.t06.o_sep.rdb 0.4 CreatePredHbondCost pred_o_sep_back o_sep o_sep_back // n notor CreateCombinedNNet n_notor_back background n_notor mean TARGET.t2k.n_notor.rdb 0.2 TARGET.t04.n_notor.rdb 0.4 TARGET.t06.n_notor.rdb 0.4 CreatePredHbondCost pred_n_notor_back n_notor n_notor_back // o notor CreateCombinedNNet o_notor_back background o_notor mean TARGET.t2k.o_notor.rdb 0.2 TARGET.t04.o_notor.rdb 0.4 TARGET.t06.o_notor.rdb 0.4 CreatePredHbondCost pred_o_notor_back o_notor o_notor_back // n notor2 CreateCombinedNNet n_notor2_back background n_notor2 mean TARGET.t2k.n_notor2.rdb 0.2 TARGET.t04.n_notor2.rdb 0.4 TARGET.t06.n_notor2.rdb 0.4 CreatePredHbondCost pred_n_notor2_back n_notor2 n_notor2_back // o notor2 CreateCombinedNNet o_notor2_back background o_notor2 mean TARGET.t2k.o_notor2.rdb 0.2 TARGET.t04.o_notor2.rdb 0.4 TARGET.t06.o_notor2.rdb 0.4 CreatePredHbondCost pred_o_notor2_back o_notor2 o_notor2_back // str4 CreateCombinedNNet str4_back background str4 mean TARGET.t2k.str4.rdb 0.2 TARGET.t04.str4.rdb 0.4 TARGET.t06.str4.rdb 0.4 CreatePredHbondCost pred_str4_back str4 str4_back Include constraint-best.costfcn 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 cb14 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 1 \ bad_peptide 1 \ soft_clashes 1 backbone_clashes 1 \ clashes 1 sidechain_clashes 1 \ breaks 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 \ pred_bys_back 1 \ pred_pb_back 1 \ pred_alpha_back 1 \ pred_nb11_back 1 \ pred_cb14_back 1 \ pred_CB8_sep9_bacK 1 \ pred_n_sep_back 1 \ pred_o_sep_back 1 \ pred_n_notor_back 1 \ pred_o_notor_back 1 \ pred_n_notor2_back 1 \ pred_o_notor2_back 1 \ pred_str4_back 1 \ constraints 1