InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet anglevector.alphabet ReadAlphabet burial.alphabet ReadAlphabet burial-sep.alphabet ReadAlphabet two-spot-burial.alphabet ReadBackgroundProbs dunbrack-in-scop.backgrounds InFilePrefix // bystroff alphabet CreateCombinedNNet bys_t2k single T0378.t2k.bys.rdb CreateCombinedNNet bys_t04 single T0378.t04.bys.rdb CreateCombinedNNet bys_t06 single T0378.t06.bys.rdb CreateCombinedNNet bys_wmean mean T0378.t2k.bys.rdb 0.2 T0378.t04.bys.rdb 0.4 T0378.t06.bys.rdb 0.4 CreateCombinedNNet bys_back background BystroffAV mean T0378.t2k.bys.rdb 0.2 T0378.t04.bys.rdb 0.4 T0378.t06.bys.rdb 0.4 CreateCombinedNNet bys_info info background BystroffAV mean T0378.t2k.bys.rdb 0.2 T0378.t04.bys.rdb 0.4 T0378.t06.bys.rdb 0.4 CreatePredAngleVectorCost pred_bys_t2k BystroffAV bys_t2k CreatePredAngleVectorCost pred_bys_t04 BystroffAV bys_t04 CreatePredAngleVectorCost pred_bys_t06 BystroffAV bys_t06 CreatePredAngleVectorCost pred_bys_wmean BystroffAV bys_wmean CreatePredAngleVectorCost pred_bys_back BystroffAV bys_back CreatePredAngleVectorCost pred_bys_info BystroffAV bys_info // deBrevern's protein blocks CreateCombinedNNet pb_t2k single T0378.t2k.pb.rdb CreateCombinedNNet pb_t04 single T0378.t04.pb.rdb CreateCombinedNNet pb_t06 single T0378.t06.pb.rdb CreateCombinedNNet pb_wmean mean T0378.t2k.pb.rdb 0.2 T0378.t04.pb.rdb 0.4 T0378.t06.pb.rdb 0.4 CreateCombinedNNet pb_back background deBrevernAV mean T0378.t2k.pb.rdb 0.2 T0378.t04.pb.rdb 0.4 T0378.t06.pb.rdb 0.4 CreateCombinedNNet pb_info info background deBrevernAV mean T0378.t2k.pb.rdb 0.2 T0378.t04.pb.rdb 0.4 T0378.t06.pb.rdb 0.4 CreatePredAngleVectorCost pred_pb_t2k deBrevernAV pb_t2k CreatePredAngleVectorCost pred_pb_t04 deBrevernAV pb_t04 CreatePredAngleVectorCost pred_pb_t06 deBrevernAV pb_t06 CreatePredAngleVectorCost pred_pb_wmean deBrevernAV pb_wmean CreatePredAngleVectorCost pred_pb_back deBrevernAV pb_back CreatePredAngleVectorCost pred_pb_info deBrevernAV pb_info CreatePredAlphaCost pred_alpha2k alpha11 T0378.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0378.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0378.t06.alpha.rdb 2 alpha alpha_prev sum CreateCombinedNNet pred_alpha_wmean mean T0378.t2k.alpha.rdb 0.2 T0378.t04.alpha.rdb 0.4 T0378.t06.alpha.rdb 0.4 CreateCombinedNNet pred_alpha_back background alpha11 mean T0378.t2k.alpha.rdb 0.2 T0378.t04.alpha.rdb 0.4 T0378.t06.alpha.rdb 0.4 CreateCombinedNNet pred_alpha_info info background alpha11 mean T0378.t2k.alpha.rdb 0.2 T0378.t04.alpha.rdb 0.4 T0378.t06.alpha.rdb 0.4 CreatePredAlphaCost pred_alpha_wmean alpha11 pred_alpha_wmean 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha_back alpha11 pred_alpha_back 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha_info alpha11 pred_alpha_info 2 alpha alpha_prev sum CreatePredBurialCost pred_nb11_2k near-backbone-11 T0378.t2k.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_2k_simple near-backbone-11 T0378.t2k.near-backbone-11.rdb near_backbone simple CreatePredBurialCost pred_nb11_04 near-backbone-11 T0378.t04.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_04_simple near-backbone-11 T0378.t04.near-backbone-11.rdb near_backbone simple CreatePredBurialCost pred_nb11_06 near-backbone-11 T0378.t06.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_06_simple near-backbone-11 T0378.t06.near-backbone-11.rdb near_backbone simple CreateCombinedNNet pred_nb11_wmean mean T0378.t2k.near-backbone-11.rdb 0.2 T0378.t04.near-backbone-11.rdb 0.4 T0378.t06.near-backbone-11.rdb 0.4 CreateCombinedNNet pred_nb11_back background near-backbone-11 mean T0378.t2k.near-backbone-11.rdb 0.2 T0378.t04.near-backbone-11.rdb 0.4 T0378.t06.near-backbone-11.rdb 0.4 CreateCombinedNNet pred_nb11_info info background near-backbone-11 mean T0378.t2k.near-backbone-11.rdb 0.2 T0378.t04.near-backbone-11.rdb 0.4 T0378.t06.near-backbone-11.rdb 0.4 CreatePredBurialCost pred_nb11_wmean near-backbone-11 pred_nb11_wmean near_backbone simple CreatePredBurialCost pred_nb11_back near-backbone-11 pred_nb11_back near_backbone simple CreatePredBurialCost pred_nb11_info near-backbone-11 pred_nb11_info near_backbone simple InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost cb14 CB smoothed-monomeric-50pc-CB14.hist CB InFilePrefix CreatePredBurialCost pred_cb14_2k CB_burial_14_7 T0378.t2k.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_2k_simple CB_burial_14_7 T0378.t2k.CB_burial_14_7.rdb cb14 simple CreatePredBurialCost pred_cb14_04 CB_burial_14_7 T0378.t04.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_04_simple CB_burial_14_7 T0378.t04.CB_burial_14_7.rdb cb14 simple CreatePredBurialCost pred_cb14_06 CB_burial_14_7 T0378.t06.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_06_simple CB_burial_14_7 T0378.t06.CB_burial_14_7.rdb cb14 simple CreateCombinedNNet pred_cb14_wmean mean T0378.t2k.CB_burial_14_7.rdb 0.2 T0378.t04.CB_burial_14_7.rdb 0.4 T0378.t06.CB_burial_14_7.rdb 0.4 CreateCombinedNNet pred_cb14_back background CB_burial_14_7 mean T0378.t2k.CB_burial_14_7.rdb 0.2 T0378.t04.CB_burial_14_7.rdb 0.4 T0378.t06.CB_burial_14_7.rdb 0.4 CreateCombinedNNet pred_cb14_info info background CB_burial_14_7 mean T0378.t2k.CB_burial_14_7.rdb 0.2 T0378.t04.CB_burial_14_7.rdb 0.4 T0378.t06.CB_burial_14_7.rdb 0.4 CreatePredBurialCost pred_cb14_wmean CB_burial_14_7 pred_cb14_wmean cb14 simple CreatePredBurialCost pred_cb14_back CB_burial_14_7 pred_cb14_back cb14 simple CreatePredBurialCost pred_cb14_info CB_burial_14_7 pred_cb14_info cb14 simple InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost CB8-sep9 CB dunbrack-40pc-3157-CB8-sep9.hist spot min_sep 9 InFilePrefix CreatePredBurialCost pred_CB8-sep9_06 CB8-sep9 T0378.t06.CB8-sep9.rdb CB8-sep9 CreatePredBurialCost pred_CB8-sep9_06_simple CB8-sep9 T0378.t06.CB8-sep9.rdb CB8-sep9 simple CreateCombinedNNet pred_CB8-sep9_back background CB8-sep9 single T0378.t06.CB8-sep9.rdb CreateCombinedNNet pred_CB8-sep9_info info background CB8-sep9 single T0378.t06.CB8-sep9.rdb CreatePredBurialCost pred_CB8-sep9_back CB8-sep9 pred_CB8-sep9_back CB8-sep9 simple CreatePredBurialCost pred_CB8-sep9_info CB8-sep9 pred_CB8-sep9_info CB8-sep9 simple SetCost \ pred_nb11_2k_simple 5 \ pred_nb11_2k 5 \ pred_nb11_04_simple 5 \ pred_nb11_04 5 \ pred_nb11_06_simple 5 \ pred_nb11_06 5 \ pred_nb11_wmean 5 \ pred_nb11_back 5 \ pred_nb11_info 5 \ pred_cb14_2k_simple 5 \ pred_cb14_2k 5 \ pred_cb14_04_simple 5 \ pred_cb14_04 5 \ pred_cb14_06_simple 5 \ pred_cb14_06 5 \ pred_cb14_wmean 5 \ pred_cb14_back 5 \ pred_cb14_info 5 \ pred_alpha2k 3 \ pred_alpha04 4 \ pred_alpha06 5 \ pred_alpha_wmean 5 \ pred_alpha_back 5 \ pred_alpha_info 5 \ pred_CB8-sep9_06 5 \ pred_CB8-sep9_06_simple 5 \ pred_CB8-sep9_back 5 \ pred_CB8-sep9_info 5 \ pred_bys_t2k 5 \ pred_bys_t04 5 \ pred_bys_t06 5 \ pred_bys_wmean 5 \ pred_bys_back 5 \ pred_bys_info 5 \ pred_pb_t2k 5 \ pred_pb_t04 5 \ pred_pb_t06 5 \ pred_pb_wmean 5 \ pred_pb_back 5 \ pred_pb_info 5