// To be run from pce/casp5/t0154

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0154.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0154.t2k.undertaker-align.script 
ReadFragmentAlignment T0154.t2k-2track-undertaker.a2m

InFilePrefix 1ihoA/
Include read-alignments.under
InFilePrefix 1cozA/
Include read-alignments.under
InFilePrefix 1qjcA/
Include read-alignments.under
InFilePrefix 1ej2A/
Include read-alignments.under
InFilePrefix 1b6tA/
Include read-alignments.under
InFilePrefix 1jhdA/
Include read-alignments.under
InFilePrefix 1g8fA/
Include read-alignments.under
InFilePrefix 


Time

// ReadConformPDB decoys/T0154.try2-opt.pdb
// ReadConformPDB decoys/T0154.try2-opt-scwrl.pdb
// ReadConformPDB decoys/T0154.try3-opt.pdb
// ReadConformPDB decoys/T0154.try3-opt-scwrl.pdb
// ReadConformPDB decoys/T0154.try4-opt.pdb
// ReadConformPDB decoys/T0154.try4-opt-scwrl.pdb

// ReadConformPDB decoys/T0154.try4-opt.pdb
// NameConform T0154.try5-try4
// ReadConformPDB decoys/T0154.try3-opt.pdb
// NameConform T0154.try5-try3
// ReadConformPDB decoys/T0154.try3.5.20.pdb
// NameConform T0154.try5-try3-5
// ReadConformPDB decoys/T0154.try3-opt.pdb.3.20.pdb
// NameConform T0154.try5-try4-3
// ReadConformPDB decoys/T0154.try3-opt.pdb.16.20.pdb
// NameConform T0154.try5-try4-16

ReadConformPDB decoys/T0154.try5-opt-scwrl.pdb
NameConform T0154.try6-try5

ReportCost undertaker-try6.rdb

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0154.try6-al2
//PrintConformPDB T0154.try6-al2.pdb edges

//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0154.try6-al4
//PrintConformPDB T0154.try6-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0154.try6-al6
//PrintConformPDB T0154.try6-al6.pdb edges

//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0154.try6-al8
// PrintConformPDB T0154.try6-al8.pdb edges

//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0154.try6-al10
// PrintConformPDB T0154.try6-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0154.try6-al12
// PrintConformPDB T0154.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.

ReadFragmentAlignment T0154.t2k.frag
InFilePrefix 


OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.3 \
	ClashingRotamer 1 \
	InsertFragment 5 \
	CrossAndInsert 3 \
	CrossOver 0.001 \
	TwoFragment 5 \
	InsertSpecificFragment 2.5 \
	ReduceBreak 0 \
	CloseGap 1 \
	JiggleSubtree 0.05 \
	OptSubtree 0.05 \
	ReduceClash 0 \
	InsertSSBond 0 \
	ImproveSSBond 0

NameConform T0154.try6
OptConform pool_size 60 num_gen 80 gen_size 160 super_iter 20 \
	pdb use_all scwrl_each
NameConform T0154.try6-opt
PrintConformPDB T0154.try6-opt.pdb edges

SCWRLConform
NameConform T0154.try6-opt-scwrl
PrintConformPDB T0154.try6-opt-scwrl.pdb

CostConform
Time

quit