Recipe: Helix Rebuild 4.0

created by spvincent

Profile

• Name: Helix Rebuild 4.0
• ID: 48811
• Shared with: Public
• Parent: None
• Children:
  • Helix Rebuild 4.01
  • Helix Rebuild 4.0 Filter
• Created on: April 07, 2014 at 20:42 PM UTC
• Updated on: April 07, 2014 at 20:42 PM UTC
• Description:

  See first comment

Code

-- Globals

original_secondary_structure = {}
fixed_residues = {}

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

n_residues = 0

loop_spacer = 3

n_rebuilds = 6

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

kWiggleDuration = 12

inner_cylinder = {}
outer_cylinder = {}

inner_cylinder_radius = 12
outer_cylinder_radius = 16


function r3 ( i )

-- printing convenience

   return i - i % 0.001

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

end

function IsPuzzleMutable ()

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

    return false

end


function get_helices ()

    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.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 WiggleNIN ()

--  NIN = Nudge If Necessary

     aa_score = GetScore ()
     structure.WiggleSelected ( kWiggleDuration )
     score = GetScore ()
 
     if ( ( score - aa_score ) < 1 ) then

         recentbest.Save ()

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

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

   end

end


function SelectBestPostRebuildNew ()

    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 )
    end

    init_score = GetScore ()

    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

         WiggleNIN ()

         score_after_end_wiggle = GetScore ()

         if ( math.abs ( score_after_end_wiggle - score_after_shake ) < 1 ) then

             -- Unstick

            recentbest.Save ()
            behavior.SetClashImportance ( 0.4 )
            structure.WiggleSelected ( 1 )
            behavior.SetClashImportance ( 1 )
            structure.WiggleSelected ( kWiggleDuration )
            recentbest.Restore ()
        end

    end

end



function ConstructSpacers ( 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

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

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

    return start_idx , end_idx

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 = ConstructSpacers ( start_helix , end_helix )

    ConstructListOfResiduesWithinInnerCylinder ( start_idx , end_idx )
    ConstructListOfResiduesWithinOuterCylinder ( start_idx , end_idx )

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

        save.Quickload (  kOriginalStructureOrNewBest )

        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 ()
    SelectBestPostRebuildNew ()

    curr_score = GetScore ()
    print ( "     " .. r3 ( best_score - curr_score ) )

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

        improvement_made = true

        best_score = curr_score

        save.LoadSecondaryStructure () 

        save.Quicksave ( kOriginalStructureOrNewBest )
        print ( "Improvement to " ..  r3 ( best_score ) )
                    
    end

    save.LoadSecondaryStructure ()

end

function get_parameters ()

  local dlog = dialog.CreateDialog ( "Helix rebuild 4" )

  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 )  
  
  design_puzzle = IsPuzzleMutable ()

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

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

  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
    
    return true
  else
     return false
   end

end

function main ()

    print (  "Helix rebuild 4" )

    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 )

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

    get_helices ()

    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

    print ( n_helices .. " helices" )

    qs10_best_score = 0

    if ( get_parameters () == false ) then
       print ( "error" )
       error ()
    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 )

    band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

This script is probably most usefully used in the early/middle game (although the chess analogy can be pushed too far). Best used at Low Wiggle Power I think: the script never terminates.

Algorithm outline

For each helix
    For however many rebuilds specified
        Bracket it with a loop on either end
        Rebuild once
        Shake and wiggle briefly
        Record score
    end
    Take two best poses from above
    Wiggle each
    Take the best scoring of those two, shake and wiggle.
    Nudge if appropriate
    Record any gain
end


Selection is restricted to the local vicinity of the helix for the sake of efficiency.
See values of inner_cylinder_radius and outer_cylinder_radius, which are probably unnecessarily conservative.

Loop spacer

Specifies the length of the loops at either end of the helix. The greater the value, the more freedom there is for the helix to adopt new configurations but the less likely you are to get small refinements.

Helix List

Initially all are selected. Helices with locked or frozen backbones will not appear in this list: frozen sidechains are allowable though.

Rebuilds

How many times to rebuild each helix

Mutate not shake

For puzzles with mutable residues only

Check conditions met:

If set, check that conditions are met before accepting any improvement. For puzzles with RMSD conditions, etc.

[Primalsoul]

I really like turning off the blue fuze option just to see if the rebuild is going to give good points. Then I can either go with that rebuild or rebuild with the fuze from the last best.