// a quick script to test the new per-residue cost reporting from undertaker
// for the burial and anglevector alphabets

SetSeed

// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-1332.rot

InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet anglevector.alphabet
ReadAlphabet two-spot-burial.alphabet
Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.
InFilePrefix 

# ReadTargetPDB T0303.blank.pdb
ReadTargetSeq T0303.a2m START_COL
NameTarget T0303
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID 2hszA

# DO READ
ReadConformPDBids
# ReadConformPDB T0303.real.pdb

SaveConformAsReal

OutFilePrefix decoys/
# PrintConformGDT real-vs-real.gdt
# quit


# perfect match should be cost -1.
# different components are scaled to have roughly equal weight
# (roughly a difference of 1 between great models and totally wrong ones)
SetRealCost GDT 1

# start with no cost function
SetCost
# override the cost function here:

InFilePrefix /projects/compbio/experiments/undertaker/spots/
CreateBurialCost nb11 near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot
InFilePrefix

CreatePredBurialCost pred_nb11_2k near-backbone-11 T0303.t2k.near-backbone-11.rdb nb11 simple

CreateCombinedNNet bys_t2k  single T0303.t2k.bys.rdb
CreatePredAngleVectorCost pred_bys_t2k  BystroffAV bys_t2k

SetCost pred_bys_t2k 1 pred_nb11_2k 1

Time

OutFilePrefix decoys/
ReportCost evaluate.alphabet_test.rdb
CostConform alphabet_test_per_residue.rdb
PrintConformPhiPsi alphabet_test_phi_psi.rdb
PrintConformBurial nb11 alphabet_test_burial_cost.rdb
Time

quit