// To be run from pce/casp5/t0168

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/



InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment T0168-1mfoA.vast-hand.a2m
ReadFragmentAlignment T0168-1bul.vast-hand.a2m
ReadFragmentAlignment T0168-1dy6A.vast-hand.a2m

Time

// ReadConformPDB decoys/T0168.try1-opt-scwrl.pdb
// nameConform T0168.try2-try1

// ReadConformPDB decoys/T0168.try2.17.80.pdb
// nameConform T0168.try5-try2-17
// ReadConformPDB decoys/T0168.try3-opt-scwrl.pdb
// nameConform T0168.try5-try3

// ReadConformPDB decoys/T0168.try2-opt-scwrl.pdb
//  nameConform T0168.try6-try2
// ReadConformPDB decoys/T0168.try3-opt-scwrl.pdb
//  nameConform T0168.try6-try3
// ReadConformPDB decoys/T0168.try4-opt-scwrl.pdb
//  nameConform T0168.try6-try4
// ReadConformPDB decoys/T0168.try5-opt-scwrl.pdb
//  nameConform T0168.try6-try5
// ReadConformPDB decoys/T0168.try2.17.80.pdb
//  nameConform T0168.try6-try2-17

// ReadConformPDB decoys/T0168-moved7.pdb
//    NameConform T0168.try7-moved

// ReadConformPDB decoys/T0168-moved8.pdb
//    NameConform T0168.try8-moved

// ReadConformPDB decoys/T0168.try8-opt.pdb
//     NameConform T0168.try9-try8
// ReadConformPDB decoys/T0168-moved9.pdb
//    NameConform T0168.try9-moved

// ReadConformPDB decoys/T0168.try9-opt.pdb
//     NameConform T0168.try10-try9

// ReadConformPDB decoys/T0168.try6-try2-17.8.60.pdb
//  nameConform T0168.try11-try6-8
// ReadConformPDB decoys/T0168.try5.6.60.pdb
//  nameConform T0168.try11-try5-6
// ReadConformPDB decoys/T0168.try4.0.40.pdb
//  nameConform T0168.try11-try4-0
// ReadConformPDB decoys/T0168.try5.2.60.pdb
//  nameConform T0168.try11-try5-2

// ReadConformPDB decoys/T0168.try1.18.20.pdb
//   nameConform T0168.try12-try1-18
// ReadConformPDB decoys/T0168.try2.3.80.pdb
//   nameConform T0168.try12-try2-3
// ReadConformPDB decoys/T0168.try3.6.80.pdb
//   nameConform T0168.try12-try3-6
// ReadConformPDB decoys/T0168.try4.14.40.pdb
//   nameConform T0168.try12-try4-14
// ReadConformPDB decoys/T0168.try5.2.60.pdb
//   nameConform T0168.try12-try5-2
// ReadConformPDB decoys/T0168.try11-opt-scwrl.pdb
//   nameConform T0168.try12-try11

// ReadConformPDB decoys/T0168.try12-opt.pdb
//   nameConform T0168.try13-try12

// ReadConformPDB decoys/T0168.try6-opt-scwrl.pdb
//    nameConform T0168.try14-try6
// ReadConformPDB decoys/T0168.try12-opt-scwrl.pdb
//    nameConform T0168.try14-try11
// ReadConformPDB decoys/T0168.try12-opt.pdb
//    nameConform T0168.try14-try12
// ReadConformPDB decoys/T0168.try13-opt.pdb
//    nameConform T0168.try14-try13

ReadConformPDB decoys/T0168.try14.0.120.pdb
    nameConform T0168.try15-try14-0


ReportCost undertaker-try15.rdb

// ConformFromSeq // get a random conformation
// NameConform T0168.rand

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0168.try15-al2
// PrintConformPDB T0168.try15-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0168.try15-al4
// PrintConformPDB T0168.try15-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0168.try15-al6
// PrintConformPDB T0168.try15-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0168.try15-al8
//  PrintConformPDB T0168.try15-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0168.try15-al10
//  PrintConformPDB T0168.try15-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0168.try15-al12
//  PrintConformPDB T0168.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 T0168.t2k.frag

Include T0168.t2k.undertaker-align.script 
ReadFragmentAlignment T0168.t2k-2track-undertaker.a2m

InfilePrefix 1i2sA/
  include read-alignments.under
InfilePrefix 4blmA/
  include read-alignments.under
InfilePrefix 1bsg/
  include read-alignments.under
InfilePrefix 1alq/
  include read-alignments.under
InfilePrefix 1bza/
  include read-alignments.under
InfilePrefix 1ghpA/
  include read-alignments.under
InfilePrefix 1pioA/
  include read-alignments.under
InfilePrefix 1hzoA/
  include read-alignments.under
InfilePrefix 1l7uA/
  include read-alignments.under
InfilePrefix 1fqgA/
  include read-alignments.under
InfilePrefix 4pgaA/
  include read-alignments.under
InfilePrefix


// 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 \
	ClashingRotamer 1 \
	OneRotamer 0.25 \
	InsertFragment 4 \
	CrossAndInsert 4 \
	TwoFragment 1 \
	InsertSpecificFragment 8 \
	ReduceBreak 1 \
	CloseGap 0.15 \
	ReduceClash 1 \
	ReduceConstraint 0 \
	JiggleSubtree 0.07 \
	OptSubtree 0.06 \
	InsertSSBond 0 \
	ImproveSSBond 0.1
	
NameConform T0168.try15
OptConform pool_size 70 num_gen 300 gen_size 180 super_iter 1 \
	use_all pdb 
	// scwrl_each no_initial_fill
NameConform T0168.try15-opt
PrintConformPDB T0168.try15-opt.pdb edges
SCWRLConform
NameConform T0168.try15-opt-scwrl
PrintConformPDB T0168.try15-opt-scwrl.pdb

CostConform
Time

quit