// To be run from pce/casp5/t0170

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0170.t2k.undertaker-align.script 
ReadFragmentAlignment T0170.t2k-2track-undertaker.a2m

InfilePrefix 1b2vA/
  include read-alignments.under
InfilePrefix 1dk0A/
  include read-alignments.under
InfilePrefix 2igd/
  include read-alignments.under
InfilePrefix 1g59A/
  include read-alignments.under
InfilePrefix 1gln/
  include read-alignments.under
InfilePrefix 1gb4/
  include read-alignments.under
InfilePrefix 1em7A/
  include read-alignments.under
InfilePrefix

Time

PopConform

// ReadConformPDB decoys/T0170.try3-opt-scwrl.pdb
//   NameConform T0170.try4-try3

// ReadConformPDB decoys/T0170.try1-opt.pdb
//    NameConform T0170.try6-try1
// ReadConformPDB decoys/T0170.try2-opt.pdb
//    NameConform T0170.try6-try2
// ReadConformPDB decoys/T0170.try3-opt.pdb
//    NameConform T0170.try6-try3
// ReadConformPDB decoys/T0170.try4-opt.pdb
//    NameConform T0170.try6-try4
// ReadConformPDB decoys/T0170.try5-opt.pdb
//    NameConform T0170.try6-try5

// ReadConformPDB decoys/T0170-moved6.pdb
//    NameConform T0170.try7-moved

// ReadConformPDB decoys/T0170.try6-try4.14.100.pdb
//    NameConform T0170.try8-try6

// ReadConformPDB decoys/T0170.try8.2.100.pdb
//    NameConform T0170.try9-try8-2

// ReadconformPDB decoys/T0170.cut-and-paste.pdb
//    NameConform T0170.try12-cut

// ReadConformPDB decoys/T0170.try9.7.150.pdb
//     NameConform T0170.try13-try9-7
// ReadConformPDB decoys/T0170.try11-opt.pdb
//     NameConform T0170.try13-try11
// ReadConformPDB decoys/T0170.try12-opt.pdb
//     NameConform T0170.try13-try12

// 
// ReadConformPDB decoys/T0170.try11-opt.pdb
//     NameConform T0170.try14-try11
// ReadConformPDB decoys/T0170.try12-opt.pdb
//     NameConform T0170.try14-try12
// ReadConformPDB decoys/T0170.try13-try11.0.200.pdb
//     NameConform T0170.try14-try13-0
// ReadConformPDB decoys/T0170.try13-try11.9.200.pdb
//     NameConform T0170.try14-try13-9
// ReadConformPDB decoys/T0170.try13-opt.pdb
//     NameConform T0170.try14-try13



ReadConformPDB decoys/T0170.try10-opt.pdb
    NameConform T0170.try15-try10
ReadConformPDB decoys/T0170.try11-opt.pdb
    NameConform T0170.try15-try11
ReadConformPDB decoys/T0170.try12-opt.pdb
    NameConform T0170.try15-try12
ReadConformPDB decoys/T0170.try13-try11.0.200.pdb
    NameConform T0170.try15-try13-0
ReadConformPDB decoys/T0170.try13-try11.9.200.pdb
    NameConform T0170.try15-try13-9
ReadConformPDB decoys/T0170.try13-try11.10.200.pdb
    NameConform T0170.try15-try13-10
ReadConformPDB decoys/T0170.try13-opt.pdb
    NameConform T0170.try15-try13
ReadConformPDB decoys/T0170.try14-opt.pdb
    NameConform T0170.try15-try14
ReadConformPDB decoys/T0170.try14.1.200.pdb
    NameConform T0170.try15-try14-1


ReportCost undertaker-try15.rdb

// ConformFromSeq replace
//  NameConform T0170.rand

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0170.try15-al2
//PrintConformPDB T0170.try15-al2.pdb edges

//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0170.try15-al4
//PrintConformPDB T0170.try15-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0170.try15-al6
//PrintConformPDB T0170.try15-al6.pdb edges

//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0170.try15-al8
// PrintConformPDB T0170.try15-al8.pdb edges

//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0170.try15-al10
// PrintConformPDB T0170.try15-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0170.try15-al12
// PrintConformPDB T0170.try15-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 T0170.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 5 \
	CrossOver 0 \
	CrossAndInsert 5 \
	TwoFragment 0.1 \
	InsertSpecificFragment 1 \
	ReduceBreak 1 \
	CloseGap 0.3 \
	ReduceConstraint 1 \
	ReduceClash 1 \
	JiggleSubtree 0.04 \
	OptSubtree 0.04 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0170.try15
OptConform pool_size 100 num_gen 200 gen_size 150 super_iter 5 \
	use_all scwrl_each pdb
NameConform T0170.try15-opt
PrintConformPDB T0170.try15-opt.pdb edges
SCWRLConform
NameConform T0170.try15-opt-scwrl
PrintConformPDB T0170.try15-opt-scwrl.pdb

CostConform
Time

quit