// To be run from pce/casp5/t0176

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

InfilePrefix 1jrmA/
   include read-alignments.under

InfilePrefix

Time

// ReadConformPDB decoys/T0176.try2-opt-scwrl.pdb
// 	nameConform T0176.try3-try2

// ReadConformPDB decoys/T0176.try3-opt.pdb
//	nameConform T0176.try4-try3


// ReadConformPDB decoys/T0176.try2-opt-scwrl.pdb
//  	nameConform T0176.try5-try2
// ReadConformPDB decoys/T0176.try3-opt.pdb
// 	nameConform T0176.try5-try3
// ReadConformPDB decoys/T0176.try4-opt.pdb
// 	nameConform T0176.try5-try4
// ReadConformPDB decoys/T0176.try4.8.160.pdb
// 	nameConform T0176.try5-try4-8

ReadConformPDB decoys/T0176.try2-opt-scwrl.pdb
 	nameConform T0176.try6-try2
ReadConformPDB decoys/T0176.try3-opt.pdb
	nameConform T0176.try6-try3
ReadConformPDB decoys/T0176.try4-opt.pdb
	nameConform T0176.try6-try4
ReadConformPDB decoys/T0176.try4.8.160.pdb
	nameConform T0176.try6-try4-8
ReadConformPDB decoys/T0176.try5.0.200.pdb
	nameConform T0176.try6-try5-0


ReportCost undertaker-try6.rdb

// ConformFromSeq	replace // get a random conformation, removing all-zero one
// NameConform T0176.rand
// Time


//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0176.try6-al2
// PrintConformPDB T0176.try6-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0176.try6-al4
// PrintConformPDB T0176.try6-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0176.try6-al6
// PrintConformPDB T0176.try6-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0176.try6-al8
//  PrintConformPDB T0176.try6-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0176.try6-al10
//  PrintConformPDB T0176.try6-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0176.try6-al12
//  PrintConformPDB T0176.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 T0176.t2k.frag
Include T0176.t2k.undertaker-align.script 
ReadFragmentAlignment T0176.t2k-2track-undertaker.a2m


// 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 0.5 \
	OneRotamer 0.2 \
	InsertFragment 10 \
	CrossAndInsert 1 \
	Crossover 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 2 \
	CloseGap 0.5 \
	ReduceClash 1 \
	JiggleSubtree 0.01 \
	OptSubtree 0.02 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0176.try6
OptConform pool_size 40 num_gen 200 gen_size 180 super_iter 10 pdb
NameConform T0176.try6-opt
PrintConformPDB T0176.try6-opt.pdb edges
SCWRLConform
NameConform T0176.try6-opt-scwrl
PrintConformPDB T0176.try6-opt-scwrl.pdb

CostConform
Time

quit