Recipe: Helix Rebuild 5.1

created by spvincent

Profile

• Name: Helix Rebuild 5.1
• ID: 109297
• Shared with: Public
• Parent: None
• Children: None
• Created on: December 22, 2025 at 00:18 AM UTC
• Updated on: February 19, 2026 at 00:36 AM UTC

Code

-- Globals

original_secondary_structure = {}
fixed_residues = {}

helix_starts = {}
helix_ends    = {}
use_helix = {}
n_helices = 0

n_residues = 0

loop_spacer = 4

n_rebuilds = 6

score_type = 1
original_slow_filters_setting = 0
best_score = 0

mutate_not_shake = false
test_for_credit = false

-- Quicksave slots

kOriginalStructureOrNewBest = 1	    -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot
kBestPostRebuild_a = 2
kBestPostRebuild_b = 3
kBestPostRebuild_a_post_wiggle = 4
kTemp = 5
kBestWithSpacers = 6

kWiggleDuration = 12

inner_cylinder = {}
outer_cylinder = {}

inner_cylinder_radius = 12
outer_cylinder_radius = 16

pw_threshold_value = 100

function r3 ( i )

-- printing convenience

      return i - i % 0.001

end

function GetScore ()

        if ( score_type == 1 ) then

                score = current.GetEnergyScore () 

        elseif ( score_type == 2 ) then

                behavior.SetSlowFiltersDisabled ( false )
                score = current.GetScore () 
                behavior.SetSlowFiltersDisabled ( true )

        end

        return score

end

function DoesPuzzleHaveSlowFilters ()

        init_setting = behavior.GetSlowFiltersDisabled ()
 
        if ( init_setting == false ) then
              score_without_sf = current.GetScore () 
              behavior.SetSlowFiltersDisabled ( true )
              score_with_sf = current.GetScore () 
          else
              score_with_sf = current.GetScore () 
              behavior.SetSlowFiltersDisabled ( false )
              score_without_sf = current.GetScore () 
        end

        behavior.SetSlowFiltersDisabled ( init_setting )
 
        if ( math.abs ( score_without_sf - score_with_sf ) >1e-3 ) then
                return true
            else
                return false
        end

end


function IsPuzzleMutable ()

        for i = 1 , n_residues do
              if ( structure.IsMutable ( i ) ) then
                      return true
              end
        end

        return false

end


function GetHelices ()

        within_helix = false
    
        for i = 1, n_residues do

                if ( structure.GetSecondaryStructure ( i ) == "H" ) then
        
                      if ( within_helix == false ) then

                                -- start of a new helix

                                within_helix = true

                                n_helices = n_helices + 1
                                helix_starts [ n_helices ] = i

                      end
                elseif ( within_helix == true ) then

                        -- end of a helix
                      
                        within_helix = false
                        helix_ends [ n_helices ] = i -1
                end
        end        -- for i
    
        if ( within_helix == true ) then
            helix_ends [ n_helices ] = n_residues
        end

end


function IsWithinASelectedHelix ( residue )

        for i = 1 , n_helices do
                if ( use_helix [ i ] == true ) then
                      if ( ( residue >= helix_starts [ i ] ) and ( residue <= helix_ends [ i ] ) ) then
                                return true
                      end
                end
        end

        return false

end

function ConvertToLoop ( first , last )

        for    k = first , last do
                if ( original_secondary_structure [ k ] ~= "L" ) then
                        if ( IsWithinASelectedHelix ( k ) == false ) then
                                selection.DeselectAll ()
                                selection.SelectRange ( k , k )
                                structure.SetSecondaryStructureSelected ( "L" )
                        end
                end
        end
end

function pseudorandom ( score )

        -- Returns a pseudorandom number >= 0 and < 1.
        -- Based on the fractional    part of the    score

        if ( score >= 0 ) then
            return    score % 1
          else
            return (-score ) % 1
        end

end

function GetListOfFixedResidues ()

        for i = 1 , n_residues do
                fixed_residues [ i ] = false
        end

        for i = 1 , n_residues do
                
                  seg_backbone_frozen, seg_sidechain_frozen = freeze.IsFrozen ( i )

                  if ( seg_backbone_frozen == true ) then
                        fixed_residues [ i ] = true
                  end

                  s = structure.IsLocked ( i )
        
                  if ( s == true ) then 
                      fixed_residues [ i ] = true
                  end

        end

end

function IsHelixFrozen ( start_idx , end_idx )

        for i = start_idx , end_idx do
                if ( fixed_residues [ i ] == true ) then
                        return true
                end
        end

        return false

end

function ConstructListOfResiduesWithinInnerCylinder ( start_idx , end_idx )

        for i = 1 , n_residues do
                inner_cylinder [ i ] = false
        end

        for    i = 1 , n_residues do
                  for j = start_idx , end_idx do
                          if ( structure.GetDistance ( i , j ) < inner_cylinder_radius ) then
                                inner_cylinder [ i ] = true
                          end
                end
        end

end

function SelectInnerCylinder ()

        selection.DeselectAll ()
 
        for i = 1 , n_residues do
                if ( inner_cylinder [ i ] == true ) then
                        selection.Select ( i )
                end
        end

end

function ConstructListOfResiduesWithinOuterCylinder ( start_idx , end_idx )

        for i = 1 , n_residues do
                outer_cylinder [ i ] = false
        end

          for    i = 1 , n_residues do
                  for j = start_idx , end_idx do
                          if ( structure.GetDistance ( i , j ) < outer_cylinder_radius ) then
                                outer_cylinder [ i ] = true
                          end
                end
        end

end

function SelectOuterCylinder ()

        selection.DeselectAll ()
 
        for i = 1 , n_residues do
                if ( outer_cylinder [ i ] == true ) then
                        selection.Select ( i )
                end
        end

end

function WiggleNudge ( init_score )

        save.Quicksave ( kTemp )

        structure.WiggleSelected ( kWiggleDuration )
        score = GetScore ()
 
        if ( score < init_score ) then
                save.Quickload ( kTemp )      -- Filters can cause reduction in score
                score = init_score
        end

        save.Quicksave ( kTemp )
        score_in_temp = score

        behavior.SetClashImportance ( 0.1 )
        structure.WiggleSelected ( 1 )

        behavior.SetClashImportance ( 1 )
        structure.WiggleSelected ( kWiggleDuration )
        
        score = GetScore ()
        if ( score < score_in_temp ) then
                  save.Quickload ( kTemp )      -- Filters can cause reduction in score
                  score = score_in_temp
        end
 
      return score

end


function SelectBestPostRebuild ()

        save.Quickload ( kBestPostRebuild_a )
        structure.WiggleSelected ( kWiggleDuration )    
        score_a = GetScore ()

        save.Quicksave ( kBestPostRebuild_a_post_wiggle )
 
        save.Quickload ( kBestPostRebuild_b )
        structure.WiggleSelected ( kWiggleDuration )    
        score_b = GetScore ()

        if ( score_a > score_b ) then
                save.Quickload ( kBestPostRebuild_a_post_wiggle )
                return score_a
            else
                return score_b
        end

end

function ShakeLowCIWiggle ( init_score )

        save.Quicksave ( kTemp )
        
        behavior.SetClashImportance ( 0.10 )
        structure.ShakeSidechainsSelected ( 1 )

        behavior.SetClashImportance ( 1 )
        structure.WiggleSelected ( kWiggleDuration )

        score = GetScore ()
        
        if ( score <    init_score ) then
              save.Quickload ( kTemp )
              score = init_score 
        end
      
        return score

end

function ShakeWiggleNudge ( init_score )

        save.Quicksave ( kTemp )

        if ( mutate_not_shake == true ) then
                structure.MutateSidechainsSelected ( 1 )
            else
                structure.ShakeSidechainsSelected ( 1 )
        end
 
        score_after_shake = GetScore ()

        if ( score_after_shake < init_score ) then
                save.Quickload( kTemp )
                score_after_shake = init_score
        end

        return WiggleNudge ( score_after_shake )

end



function DetermineSpacers ( start_helix , end_helix )

        local	i
        local	ok

        start_idx = start_helix - loop_spacer

        if ( start_idx < 1 ) then
              start_idx = 1
        end

        i = start_helix - 1
        ok = true
        while ( i >= start_idx and ok == true ) do
                if ( structure.IsLocked ( i ) == true ) then
                      ok = false
                      start_idx = i + 1
                  else
                        i = i -1
                end
        end

        end_idx = end_helix + loop_spacer

        if ( end_idx > n_residues ) then
                end_idx = n_residues
        end

        i = end_helix + 1
        ok = true
        while ( i <= end_idx and ok == true ) do
                  if ( structure.IsLocked ( i ) == true ) then
                      ok = false
                      end_idx = i - 1
                  else
                        i = i +1
                end
        end

        return start_idx , end_idx

end

function ConstructSpacers ( start_idx , start_helix , end_helix , end_idx )

        if ( start_helix > 1 ) then
                ConvertToLoop ( start_idx , start_helix - 1 )
        end

        if ( end_helix < n_residues ) then
                ConvertToLoop ( end_helix + 1 , end_idx )
        end

end

function RebuildHelix ( helix_index , start_helix , end_helix    )

        best_score_after_rebuild_and_shake_a = -99999
        best_score_after_rebuild_and_shake_b = -99999
      
        improvement_made = false
        
        rb = rb + 1

        start_idx , end_idx = DetermineSpacers ( start_helix , end_helix )

        save.Quickload (    kOriginalStructureOrNewBest )

        ConstructSpacers ( start_idx , start_helix , end_helix , end_idx )

        save.Quicksave (    kBestWithSpacers )
    
        ConstructListOfResiduesWithinInnerCylinder ( start_idx , end_idx )
        ConstructListOfResiduesWithinOuterCylinder ( start_idx , end_idx )

        print ( "rb : " .. rb .. " (" .. start_helix .. "-" .. end_helix .. ")" )
 
        for i = 1 , n_rebuilds do

                if ( i > 1 ) then
                        save.Quickload (    kBestWithSpacers )
                end

                selection.DeselectAll ()
                selection.SelectRange ( start_idx , end_idx )

                structure.RebuildSelected ( 1 )
                score_after_rebuild = GetScore ()
 
                SelectInnerCylinder ()

                structure.ShakeSidechainsSelected ( 1 )
                structure.WiggleSelected ( 1 )

                score_after_shake_wiggle = GetScore ()

                if ( score_after_shake_wiggle > math.min ( best_score_after_rebuild_and_shake_a , best_score_after_rebuild_and_shake_b ) ) then
	          
                        if ( best_score_after_rebuild_and_shake_b < best_score_after_rebuild_and_shake_a ) then
                                best_score_after_rebuild_and_shake_b = score_after_shake_wiggle
                                save.Quicksave ( kBestPostRebuild_b )
                          else
                                best_score_after_rebuild_and_shake_a = score_after_shake_wiggle
	                save.Quicksave ( kBestPostRebuild_a )
                        end

                end

        end

        SelectOuterCylinder ()
 
        c_score = SelectBestPostRebuild ()

        score_below_best = best_score - c_score

        if ( score_below_best < pw_threshold_value ) then

                d_score = ShakeWiggleNudge ( c_score )

                if ( ( d_score > best_score ) and 
                              ( test_for_credit == false or creditbest.AreConditionsMet () == true ) ) then

                        e_score = ShakeLowCIWiggle ( d_score )

                          print ( "          " .. r3 ( -score_below_best ) .. "    " .. r3 ( d_score - c_score )    .. "    " .. r3 ( e_score - d_score ) )
                          improvement_made = true

                        best_score = e_score

                        save.LoadSecondaryStructure () 

                        save.Quicksave ( kOriginalStructureOrNewBest )
                        print ( "Improvement to " ..    r3 ( best_score ) )
                    else
                        print ( "          " .. r3 ( -score_below_best ) .. "    " .. r3 ( d_score - c_score ) )
 
                end

            else
              print ( "          " .. r3 ( -score_below_best ) )
        end

        save.LoadSecondaryStructure ()

end

function GetParameters ()

        local dlog = dialog.CreateDialog ( "Helix rebuild 5.1" )

        dlog.loop_spacer = dialog.AddSlider ( "Loop spacer" , loop_spacer , 0 , 6 , 0 )    
    
        for i = 1 , n_helices do
                dlog [ "helix" .. i ] = dialog.AddCheckbox ( helix_starts [ i ] .. "-" .. helix_ends [ i ]    , true )    
        end

        dlog.n_rebuilds = dialog.AddSlider ( "Rebuilds" , n_rebuilds , 1 , 20 , 0 )    
    
        dlog.pw_threshold = dialog.AddSlider ( "Post wiggle threshold" , pw_threshold_value , 0 , 200 , 0 )    
        
        design_puzzle = IsPuzzleMutable ()

        if ( design_puzzle == true ) then
                dlog.mutate= dialog.AddCheckbox ( "Mutate not shake" , true )    
        end

        dlog.credit_check = dialog.AddCheckbox ( "Check conditions met " , test_for_credit )    

        dlog.pw_threshold = dialog.AddSlider ( "Post wiggle threshold" , pw_threshold_value , 0 , 200 , 0 )    
        
        if ( DoesPuzzleHaveSlowFilters () == true ) then
                score_type = 2
        end

        dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )    
        dlog.tp = dialog.AddLabel ( "1 = Normal : 2 = Normal for Slow Filters"    )

        dlog.ok = dialog.AddButton ( "OK" , 1 )
        dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
    
        if ( dialog.Show ( dlog ) > 0 ) then
        
                loop_spacer = dlog.loop_spacer.value

                for i = 1 , n_helices do
                        use_helix [ i ] = dlog [ "helix" .. i ].value
                end
        
                if ( design_puzzle == true ) then
                        mutate_not_shake = dlog.mutate.value
                end

                test_for_credit = dlog.credit_check.value

                n_rebuilds = dlog.n_rebuilds.value
                pw_threshold_value = dlog. pw_threshold.value
                  score_type = dlog.score_type.value
        
                return true
            else
                return false
        end

end

function main ()

        print (    "Helix rebuild 5.1" )

        band.DisableAll ()

        n_residues = structure.GetCount ()

        for i = 1, n_residues do
                  original_secondary_structure [ i ] = structure.GetSecondaryStructure ( i )
        end

        save.SaveSecondaryStructure () 

        behavior.SetClashImportance ( 1 )

        GetHelices ()

        GetListOfFixedResidues ()

      -- Delete locked/frozen helices

        for i = n_helices , 1 , -1 do 
                if ( IsHelixFrozen ( helix_starts [ i ] , helix_ends [ i ] ) == true ) then
                          table.remove ( helix_starts , i )
                          table.remove ( helix_ends , i )
                end
        end

        n_helices = #helix_starts

        print ( n_helices .. " helices" )

        qs10_best_score = 0

        original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()

        if ( GetParameters () == false ) then
              print ( "error" )
              error ()
        end

        best_score = GetScore ()
        print (    "Start score : " .. r3    ( best_score )    )

        if ( score_type == 1 ) then
                print (    "Score type : Normal" )
            elseif ( score_type == 2 ) then
                print (    "Score type : Normal/Slow Filters" )
        end

        -- Delete unused helices

        for i = n_helices , 1 , -1 do 
                if ( use_helix [ i ] == false ) then
                          table.remove ( helix_starts , i )
                          table.remove ( helix_ends , i )
                end
        end

        n_helices = #helix_starts

        if ( n_helices == 0 ) then
              print ( "No helix selected" )
              error ()
        end

        for i = 1 , n_helices    do 
                  print ( "Helix " .. i .. " : (" .. helix_starts [ i ] .. "-" .. helix_ends [ i ] .. ")" )
        end

        print ( "Loop spacer " .. loop_spacer )
        print ( n_rebuilds .. " rebuilds" )

        rb = 0
        save.Quicksave ( kOriginalStructureOrNewBest )

        while ( true ) do
                for i = 1 , n_helices do 
                        RebuildHelix ( i , helix_starts [ i ] , helix_ends [ i ] )
                end
        end

end

function cleanup ()
      
        print ( "Cleaning up" )
        behavior.SetClashImportance ( 1.0 )
        save.Quickload ( kOriginalStructureOrNewBest )

        behavior.SetSlowFiltersDisabled ( original_slow_filters_setting )

        band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

Got omitted somehow when the website got updated.