Recipe: Helix Rebuild 5.1 No Mutate

created by Bruno Kestemont

Profile

• Name: Helix Rebuild 5.1 No Mutate
• ID: 102337
• Shared with: Public
• Parent: Helix Rebuild 5.1
• Children: None
• Created on: April 24, 2017 at 18:34 PM UTC
• Updated on: April 24, 2017 at 18:34 PM UTC
• Description:

  see first comment, Never Mutate

Code

-- Globals Version 5.1 No Mutate by BK for some contest puzzles

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 = false -- 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

[Bruno Kestemont]

This "never mutate" version is safe for some Contests with user-defined sequences.

See here:
https://fold.it/portal/node/2003391