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

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

# ReadTargetPDB XXX0000.blank.pdb
ReadTargetSeq XXX0000.a2m START_COL
NameTarget XXX0000
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID REAL_PDB

# DO READ
ReadConformPDBids
# ReadConformPDB XXX0000_domain.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 real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \
	real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \
	knot 10 clens 200  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0.2

include costfcn-init-eval.under
# start with no cost function
SetCost
# override the cost function here:
include COSTFCN.costfcn

Time
ReadFragmentAlignment NOFILTER force_alignment all-align.a2m
Time

OutFilePrefix decoys/
ReportCost eval_alignments.COSTFCN.rdb
CostAlignments
Time

quit