// To be run from pce/casp5/t0192

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0192.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms
// include try-alignments.under

ReadFragmentAlignment T0192-1qsmA.vast-hand.a2m
ReadFragmentAlignment T0192-1i1dA.vast-hand.a2m


// ReadConformPDB decoys/T0192.try5-opt.pdb
//  NameConform T0192.try6-try5

// ReadConformPDB decoys/T0192.try7-opt.pdb
//  NameConform T0192.try9-try7

// ReadConformPDB decoys/T0192.try7-opt.pdb
//   NameConform T0192.try10-try7
// ReadConformPDB decoys/T0192.try9-opt.pdb
//  NameConform T0192.try10-try9

// ReadConformPDB decoys/T0192.try12-opt.pdb
//   NameConform T0192.try13-try12
// ReadConformPDB decoys/T0192.try10-opt.pdb
//   NameConform T0192.try13-try10

Time

ReadConformPDB decoys/T0192.try16-opt.pdb
   NameConform T0192.try17-try16


ReportCost undertaker-try17.rdb

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0192.try17-al2
// PrintConformPDB T0192.try17-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0192.try17-al4
// PrintConformPDB T0192.try17-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0192.try17-al6
// PrintConformPDB T0192.try17-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0192.try17-al8
// PrintConformPDB T0192.try17-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0192.try17-al10
// PrintConformPDB T0192.try17-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0192.try17-al12
// PrintConformPDB T0192.try17-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 T0192.t2k.frag
 include try-alignments.under

// 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 \
        OneRotamer 0.06 \
	ClashingRotamer 0.5 \
	InsertFragment 5 \
	CrossAndInsert 10 \
	CrossOver 0 \
	TwoFragment 10 \
	InsertSpecificFragment 5 \
	ReduceBreak 2 \
	CloseGap 0.2 \
	ReduceClash 1 \
	ReduceConstraint 2 \
	JiggleSubtree 0.02 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0192.try17
OptConform pool_size 40 num_gen 200 gen_size 180 super_iter 1 \
	pdb use_all
	// scwrl_each 
NameConform T0192.try17-opt
PrintConformPDB T0192.try17-opt.pdb edges
SCWRLConform
NameConform T0192.try17-opt-scwrl
PrintConformPDB T0192.try17-opt-scwrl.pdb

CostConform
Time

quit