# 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 T0325.t2k.bys.rdb 0.2 T0325.t04.bys.rdb 0.4 T0325.t06.bys.rdb 0.4 CreatePredAngleVectorCost pred_bys_back BystroffAV bys_back // deBrevern CreateCombinedNNet pb_back background deBrevernAV geommean T0325.t2k.pb.rdb 0.2 T0325.t04.pb.rdb 0.4 T0325.t06.pb.rdb 0.4 CreatePredAngleVectorCost pred_pb_back deBrevernAV pb_back // predalpha CreateCombinedNNet pred_alpha_back background alpha11 geommean T0325.t2k.alpha.rdb 0.2 T0325.t04.alpha.rdb 0.4 T0325.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 T0325.t2k.near-backbone-11.rdb 0.2 T0325.t04.near-backbone-11.rdb 0.4 T0325.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 T0325.t2k.CB_burial_14_7.rdb 0.2 T0325.t04.CB_burial_14_7.rdb 0.4 T0325.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 T0325.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 T0325.t2k.n_sep.rdb 0.2 T0325.t04.n_sep.rdb 0.4 T0325.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 T0325.t2k.o_sep.rdb 0.2 T0325.t04.o_sep.rdb 0.4 T0325.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 T0325.t2k.n_notor.rdb 0.2 T0325.t04.n_notor.rdb 0.4 T0325.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 T0325.t2k.o_notor.rdb 0.2 T0325.t04.o_notor.rdb 0.4 T0325.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 T0325.t2k.n_notor2.rdb 0.2 T0325.t04.n_notor2.rdb 0.4 T0325.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 T0325.t2k.o_notor2.rdb 0.2 T0325.t04.o_notor2.rdb 0.4 T0325.t06.o_notor2.rdb 0.4 CreatePredHbondCost pred_o_notor2_back o_notor2 o_notor2_back // str4 CreateCombinedNNet str4_back background str4 mean T0325.t2k.str4.rdb 0.2 T0325.t04.str4.rdb 0.4 T0325.t06.str4.rdb 0.4 CreatePredHbondCost pred_str4_back str4 str4_back ConstraintSet align_constraint include align.constraints ConstraintSet align_bonus include align_bonus.constraints ConstraintSet rejected_constraint include rejected.constraints ConstraintSet rejected_bonus include rejected_bonus.constraints ConstraintSet noncontacts include non_contacts.constraints ConstraintSet noncontacts_bonus include non_contacts_bonus.constraints # Fri Jul 11 22:51:24 PDT 2008 John Archie # The CASP7 target to make these no longer works. # These constraint sets don't seem to do better than their non-log # counterparts, so I'm just commenting them out and removing them from # the cost function definition below. # #ConstraintSet log_align_constraint #include log_align.constraints #ConstraintSet log_align_bonus #include log_align_bonus.constraints #ConstraintSet log_rejected_constraint #include log_rejected.constraints #ConstraintSet log_rejected_bonus #include log_rejected_bonus.constraints #ConstraintSet log_noncontact #include log_noncontact.constraints #ConstraintSet log_noncontact_bonus #include log_noncontact_bonus.constraints # ConstraintSet align_constraints_meta01 include align.constraints_meta01 ConstraintSet align_bonus_constraints_meta01 include align_bonus.constraints_meta01 ConstraintSet non_contacts_constraints_meta01 include non_contacts.constraints_meta01 ConstraintSet non_contacts_bonus_constraints_meta01 include non_contacts_bonus.constraints_meta01 ConstraintSet rejected_constraints_meta01 include rejected.constraints_meta01 ConstraintSet rejected_bonus_constraints_meta01 include rejected_bonus.constraints_meta01 ConstraintSet align_constraints_meta02 include align.constraints_meta02 ConstraintSet align_bonus_constraints_meta02 include align_bonus.constraints_meta02 ConstraintSet non_contacts_constraints_meta02 include non_contacts.constraints_meta02 ConstraintSet non_contacts_bonus_constraints_meta02 include non_contacts_bonus.constraints_meta02 ConstraintSet rejected_constraints_meta02 include rejected.constraints_meta02 ConstraintSet rejected_bonus_constraints_meta02 include rejected_bonus.constraints_meta02 ConstraintSet nn75_constraint include T0325.647_47_75_01.rr.constraints ConstraintSet nn75_constraint_9 include T0325.647_47_75_01_9.0.rr.constraints ConstraintSet nn1000_constraint include T0325.647_47_200_0.rr.constraints ConstraintSet nn700_constraint include T0325.647_47_700_0_6.5_8.5.rr.constraints ConstraintSet ehl2_constraint include T0325.dssp-ehl2.constraints ConstraintSet sheet_constraint include T0325.undertaker-align.sheets #ConstraintSet two_stage #include T0325.648_17.730_47.rr.constraints # two_stage 0 \ SetCost CAContact 0 \ alpha 0 \ alpha_prev 0 \ backbone_clashes 0 \ bad_peptide 0 \ break 0 \ bystroff 0 \ cb14 0 \ clashes 0 \ contact 0 \ contact_order 0 \ dry12 0 \ dry5 0 \ dry6.5 0 \ dry8 0 \ hbond_dist 0 \ hbond_geom 0 \ hbond_geom_backbone 0 \ hbond_geom_beta 0 \ hbond_geom_beta_pair 0 \ is_align 0 \ knot 0 \ maybe_metal 0 \ maybe_ssbond 0 \ n_ca_c 0 \ near_backbone 0 \ nn1000_constraint 0 \ nn700_constraint 0 \ nn75_constraint 0 \ nn75_constraint_9 0 \ noncontacts 0 \ noncontacts_bonus 0 \ old_n_ca_c 0 \ phobic_fit 0 \ phobic_norm 0 \ phobic_radius 0 \ pred_CB8_sep9_back 0 \ pred_bys_back 0 \ pred_n_notor2_back 0 \ pred_n_notor_back 0 \ pred_n_sep_back 0 \ pred_o_notor2_back 0 \ pred_o_notor_back 0 \ pred_pb_back 0 \ pred_str4_back 0 \ radius 0 \ radius_fit 0 \ radius_norm 0 \ soft_clashes 0 \ way_back 0 \ wet6.5 0 \ align_constraints_meta01 0 \ align_bonus_constraints_meta01 0 \ non_contacts_constraints_meta01 0 \ non_contacts_bonus_constraints_meta01 0 \ rejected_constraints_meta01 0 \ rejected_bonus_constraints_meta01 0 \ align_constraints_meta02 0 \ align_bonus_constraints_meta02 0 \ non_contacts_constraints_meta02 0 \ non_contacts_bonus_constraints_meta02 0 \ rejected_constraints_meta02 0 \ rejected_bonus_constraints_meta02 0 \ missing_atoms 0.000853992 \ sidechain 2.17017e-05 \ deep_knot 1.48294 \ sheet_constraint 0.25592 \ rejected_bonus 6.07784 \ pred_o_sep_back 2.40196 \ sidechain_clashes 1.51318 \ align_constraint 1.0601 \ hbond_count 5.92238 \ rejected_constraint 3.36005 \ CBContact 1.02884 \ ehl2_constraint 0.222048 \ pred_nb11_back 9.23897 \ pred_cb14_back 8.68011 \ pred_alpha_back 8.92183 \ align_bonus 49.8329