# Sat Apr 12 10:19:38 PDT 2008 Kevin Karplus # This script is not a complete undertaker script, but handles initializations # needed for many cost functions. # The idea is that this can be included in an undertaker script before # including a cost function, so that cost function scripts can be # short and so that multiple cost functions can be used in an # undertaker script without problems from trying to create components # with the same names. # # This script also standardizes the names for various cost function # components that are read at run time, and makes sure that all the # necessary alphabets are read in. # It needs to be included *AFTER* the target has been set. # Also, it needs to be preprocessed to replace the T0403 # placeholders with the target name. InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.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 /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp2-pdb.types ReadClashTable exp2-pdb-dunbrack-40pc-3157-2symm.clash SetClashDefinition exp2-pdb-dunbrack-40pc-3157-2symm # residue-based burial alphabets InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost cb14 CB smoothed-monomeric-50pc-CB14.hist CB 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 CreateBurialCost CB8-sep9 CB dunbrack-40pc-3157-CB8-sep9.hist spot min_sep 9 # atom-based burial alphabets CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist # CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-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 # backbone-conformation alphabets CreateAlphaCost alpha dunbrack-2191-alpha.hist CreateAlphaCost alpha_prev dunbrack-2191-alpha-1.hist -1 InFilePrefix // Secondary Structure predictions // predalpha CreateCombinedNNet pred_alpha_back background alpha11 geommean T0403.t2k.alpha.rdb 0.4 T0403.t04.alpha.rdb 0.2 T0403.t06.alpha.rdb 0.4 CreatePredAlphaCost pred_alpha_back alpha11 pred_alpha_back 2 alpha alpha_prev sum // bystroff CreateCombinedNNet bys_back background BystroffAV geommean T0403.t2k.bys.rdb 0.4 T0403.t04.bys.rdb 0.2 T0403.t06.bys.rdb 0.4 CreatePredAngleVectorCost pred_bys_back BystroffAV bys_back // deBrevern CreateCombinedNNet pb_back background deBrevernAV geommean T0403.t2k.pb.rdb 0.4 T0403.t04.pb.rdb 0.2 T0403.t06.pb.rdb 0.4 CreatePredAngleVectorCost pred_pb_back deBrevernAV pb_back // nsep CreateCombinedNNet n_sep_back background n_sep mean T0403.t2k.n_sep.rdb 0.4 T0403.t04.n_sep.rdb 0.2 T0403.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 T0403.t2k.o_sep.rdb 0.4 T0403.t04.o_sep.rdb 0.2 T0403.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 T0403.t2k.n_notor.rdb 0.4 T0403.t04.n_notor.rdb 0.2 T0403.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 T0403.t2k.o_notor.rdb 0.4 T0403.t04.o_notor.rdb 0.2 T0403.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 T0403.t2k.n_notor2.rdb 0.4 T0403.t04.n_notor2.rdb 0.2 T0403.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 T0403.t2k.o_notor2.rdb 0.4 T0403.t04.o_notor2.rdb 0.2 T0403.t06.o_notor2.rdb 0.4 CreatePredHbondCost pred_o_notor2_back o_notor2 o_notor2_back // str4 CreateCombinedNNet str4_back background str4 mean T0403.t2k.str4.rdb 0.4 T0403.t04.str4.rdb 0.2 T0403.t06.str4.rdb 0.4 CreatePredHbondCost pred_str4_back str4 str4_back // Burial predictions // nb11 CreateCombinedNNet pred_nb11_back background near-backbone-11 mean T0403.t2k.near-backbone-11.rdb 0.4 T0403.t04.near-backbone-11.rdb 0.2 T0403.t06.near-backbone-11.rdb 0.4 CreatePredBurialCost pred_nb11_back near-backbone-11 pred_nb11_back near_backbone simple // cb14 CreateCombinedNNet pred_cb14_back background CB_burial_14_7 mean T0403.t2k.CB_burial_14_7.rdb 0.4 T0403.t04.CB_burial_14_7.rdb 0.2 T0403.t06.CB_burial_14_7.rdb 0.4 CreatePredBurialCost pred_cb14_back CB_burial_14_7 pred_cb14_back cb14 simple // sep9 CreateCombinedNNet pred_CB8_sep9_back background CB8-sep9 single T0403.t06.CB8-sep9.rdb CreatePredBurialCost pred_CB8_sep9_back CB8-sep9 pred_CB8_sep9_back CB8-sep9 simple // Constraints from alignments ConstraintSet align_constraints Include align.constraints ConstraintSet align_bonus Include align_bonus.constraints ConstraintSet rejected_constraints Include rejected.constraints ConstraintSet rejected_bonus Include rejected_bonus.constraints ConstraintSet noncontact Include noncontact.constraints ConstraintSet noncontact_bonus Include noncontact_bonus.constraints // Constraints from secondary structure predictions ConstraintSet ehl2_constraints include T0403.dssp-ehl2.constraints // Helix-strand constraints from initial alignments ConstraintSet align_sheets include T0403.undertaker-align.sheets // Constraints from residue-residue contact prediction ConstraintSet two_stage include T0403.648_17.730_47.rr.nn1000.constraints ConstraintSet nn1000 include nn1000.constraints