// To be run from pce/casp5/t0175

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0175.t2k.undertaker-align.script 
ReadFragmentAlignment T0175.t2k-2track-undertaker.a2m

InfilePrefix 1kpgA/
   include read-alignments.under
InfilePrefix 1dl5A/
   include read-alignments.under
InfilePrefix 1i1nA/
   include read-alignments.under
InfilePrefix 1jg1A/
   include read-alignments.under
InfilePrefix 1xvaA/
   include read-alignments.under
InfilePrefix 1g6q2/
   include read-alignments.under
InfilePrefix 1i9gA/
   include read-alignments.under
InfilePrefix 1l1eA/
   include read-alignments.under
InfilePrefix 1kphB/
   include read-alignments.under
InfilePrefix 1bhjA/
   include read-alignments.under
InfilePrefix 1kpiA/
   include read-alignments.under

InfilePrefix

Time
// ReadConformPDB decoys/T0175.try1-opt-scwrl.pdb
//    NameConform T0175.try2-try1

// ReadConformPDB decoys/T0175.try2-opt.pdb
//     NameConform T0175.try3-try2

// ReadConformPDB decoys/T0175.try3-opt.pdb
//    NameConform T0175.try5-try3

ReadConformPDB decoys/T0175.try3-opt.pdb
    NameConform T0175.try6-try3
ReadConformPDB decoys/T0175.try4-opt.pdb
    NameConform T0175.try6-try4
ReadConformPDB decoys/T0175.try5-opt.pdb
    NameConform T0175.try6-try5

ReportCost undertaker-try6.rdb

// ConformFromSeq
// NameConform T0175.rand
// Time


//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0175.try6-al2
// PrintConformPDB T0175.try6-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0175.try6-al4
// PrintConformPDB T0175.try6-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0175.try6-al6
// PrintConformPDB T0175.try6-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0175.try6-al8
//  PrintConformPDB T0175.try6-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0175.try6-al10
//  PrintConformPDB T0175.try6-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0175.try6-al12
//  PrintConformPDB T0175.try6-al12.pdb edges

CostConform
Time



// The following alignments are not as good as the ones tried above,
// so are not used in getting the starting point.

InFilePrefix 
ReadFragmentAlignment T0175.t2k.frag

// The next 3 lines save the templates in a single file, to avoid having
// to reread the PDB files.  Note that ReadTemplateAtoms should be called
// before any ReadFragmentAlignments to take full advantage of this
// cached results.
OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time


InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 1 \
	OneRotamer 0.1 \
	InsertFragment 12 \
	CrossAndInsert 4 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.2 \
	ReduceClash 1 \
	RedcuceConstraint 1 \
	JiggleSubtree 0.02 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0175.try6
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 4 \
	use_all  pdb
	// scwrl_each
NameConform T0175.try6-opt
PrintConformPDB T0175.try6-opt.pdb edges
SCWRLConform
NameConform T0175.try6-opt-scwrl
PrintConformPDB T0175.try6-opt-scwrl.pdb

CostConform
Time

quit