Recipe: Helix Rebuild V2 1.0

created by spvincent

Profile

• Name: Helix Rebuild V2 1.0
• ID: 40280
• Shared with: Public
• Parent: None
• Children: None
• Created on: April 03, 2012 at 00:49 AM UTC
• Updated on: April 03, 2012 at 00:49 AM UTC
• Description:

  See first comment.

Code

    
monit =  false                                            -- prints debug and performance info.

kBest = 1						  -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot
						
kQs10 = 10                                                -- the rebuilt structure that comes closest in score to the original without actually exceeding it
                                                                    -- will be stored here

original_secondary_structure = {}

helix_starts = {}
helix_ends  = {}
n_helices = 0

loop_spacer = 2
min_residue = 1
max_residue = 999

function roundto3 ( i )

-- printing convenience

   return i - i % 0.001

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

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 IsSegmentALoop ( first , last )

   non_loop_found = false
   for i = first , last do
       if ( structure.GetSecondaryStructure ( i ) ~= "L" ) then
          non_loop_found= true
        end
     end

   return  not non_loop_found
end

function ConvertToLoop ( first , last )

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

    selection.SelectAll ()
    recentbest.Save ()
    behavior.SetClashImportance ( 0.2  + 0.2 * pseudorandom ( score ) )
    structure.WiggleSelected ( 1 )
    behavior.SetClashImportance ( 1 )
    structure.WiggleSelected ( 8 )
    recentbest.Restore ()
 end


function  ShakeWiggleShakeNudge ()

     -- returns the score after doing a SWSW:  short-circuiting if things don't look promising

    structure.ShakeSidechainsSelected ( 2 )
    score_after_first_shake = GetScore ()

    structure.WiggleSelected ( 15 )
    score_after_wiggle = GetScore ()

    if ( score_after_wiggle - score_after_first_shake  < 10 and best_score - score_after_wiggle > 30 ) then
        --    The wiggle got stuck and didn't achieve anything
        nudge ( score_after_wiggle )
        score_after_wiggle = GetScore ()
    end
    
    structure.ShakeSidechainsSelected ( 1 )
    
    score_after_second_shake = GetScore ()

    if ( score_after_second_shake - score_after_wiggle > 0.5 ) then
        nudge ( score_after_second_shake )
 
        score = GetScore  ()

        return  score
     else
        return  score_after_second_shake
    end

end

function rebuild_helix ( start_helix , end_helix  )

    if (  start_helix < min_residue or  end_helix > max_residue ) then
        return false
    end
   
    improvement_made = false

    save.Quickload ( kBest )
 
    rb = rb + 1
    print ( "rb : " .. rb .. " (" .. start_helix .. "-" .. end_helix .. ")" )

    best_score = GetScore ()

    start_idx = start_helix - loop_spacer

    if ( start_idx < 1 ) then
       start_idx = 1
    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

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

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

     -- for some reason, do_local_rebuild ( 1)  often leaves  the protein unchanged

    k  = 0 
    repeat 
        k = k + 1
         structure.RebuildSelected ( k )
        score_after_rebuild = GetScore ()
    until  math.abs ( score_after_rebuild - best_score ) >= 1e-5 or k  > 2  

    if ( math.abs ( score_after_rebuild - best_score ) < 1e-5 ) then
               
        -- If  the scores are still equal we probably have a locked segment

        return false
    
    end

    selection.SelectAll ()

    curr_score = ShakeWiggleShakeNudge ()

    if ( curr_score > best_score ) then

        improvement_made = true

        best_score = curr_score

        save.Quicksave ( kBest )
        print ( "Improvement to " ..  roundto3 ( best_score ) )
                     
    end

    curr_score = GetScore ()

    if (  curr_score > qs10_best_score  and improvement_made == false ) then
      
       qs10_best_score = curr_score
 
      -- Bracket the area with frozen segments for easy recognition
     
      selection.DeselectAll ()
                 
      if ( start_idx > 1 ) then
          selection.Select ( start_idx - 1 )
      end
                
      if ( end_idx <  n_residues ) then
         selection.Select ( end_idx + 1 )
      end

      freeze.FreezeSelected ( true , false )

      save.Quicksave ( kQs10 )

      print ( "Storing " .. roundto3 ( qs10_best_score ) .. " in " .. kQs10 )

    end

    save.LoadSecondaryStructure ()

    return true

end

function get_parameters ()

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

  dlog.loop_spacer= dialog.AddSlider ( "Loop spacer" , loop_spacer , 0 , 6 , 0 )  
  dlog.min_residue = dialog.AddSlider ( "Min residue" , 1 , 1 , n_residues , 0 )  
  dlog.max_residue = dialog.AddSlider ( "Max residue" , n_residues , 1 , n_residues , 0 )  

  dlog.ok = dialog.AddButton ( "OK" , 1 )
  dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

  if ( dialog.Show ( dlog ) > 0 ) then
    
    loop_spacer = dlog.loop_spacer.value
    min_residue = dlog.min_residue.value
    max_residue = dlog.max_residue.value
    return true
  else
    return false
 end

end

print (  "Helix  rebuild" )

-- Tidy up if necessary

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 : " .. roundto3  ( best_score )  )

if ( start_score == 0 ) then
    print ( "Suggest quitting as starting score < = 0" )
end

if ( get_parameters () == false ) then
  return                -- graceful exit
end

rb = 0
save.Quicksave ( kBest )


get_helices ()

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

qs10_best_score = 0

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

--  Well it'll never get here as things stand but the tidying up below would be nice to do

save.Quickload ( kBest )

band.EnableAll  ()



    
monit =  false                                            -- prints debug and performance info.

kBest = 1						  -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot
						
kQs10 = 10                                                -- the rebuilt structure that comes closest in score to the original without actually exceeding it
                                                                    -- will be stored here

original_secondary_structure = {}

helix_starts = {}
helix_ends  = {}
n_helices = 0

loop_spacer = 2
min_residue = 1
max_residue = 999

function roundto3 ( i )

-- printing convenience

   return i - i % 0.001

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

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 IsSegmentALoop ( first , last )

   non_loop_found = false
   for i = first , last do
       if ( structure.GetSecondaryStructure ( i ) ~= "L" ) then
          non_loop_found= true
        end
     end

   return  not non_loop_found
end

function ConvertToLoop ( first , last )

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

    selection.SelectAll ()
    recentbest.Save ()
    behavior.SetClashImportance ( 0.2  + 0.2 * pseudorandom ( score ) )
    structure.WiggleSelected ( 1 )
    behavior.SetClashImportance ( 1 )
    structure.WiggleSelected ( 8 )
    recentbest.Restore ()
 end


function  ShakeWiggleShakeNudge ()

     -- returns the score after doing a SWSW:  short-circuiting if things don't look promising

    structure.ShakeSidechainsSelected ( 2 )
    score_after_first_shake = GetScore ()

    structure.WiggleSelected ( 15 )
    score_after_wiggle = GetScore ()

    if ( score_after_wiggle - score_after_first_shake  < 10 and best_score - score_after_wiggle > 30 ) then
        --    The wiggle got stuck and didn't achieve anything
        nudge ( score_after_wiggle )
        score_after_wiggle = GetScore ()
    end
    
    structure.ShakeSidechainsSelected ( 1 )
    
    score_after_second_shake = GetScore ()

    if ( score_after_second_shake - score_after_wiggle > 0.5 ) then
        nudge ( score_after_second_shake )
 
        score = GetScore  ()

        return  score
     else
        return  score_after_second_shake
    end

end

function rebuild_helix ( start_helix , end_helix  )

    if (  start_helix < min_residue or  end_helix > max_residue ) then
        return false
    end
   
    improvement_made = false

    save.Quickload ( kBest )
 
    rb = rb + 1
    print ( "rb : " .. rb .. " (" .. start_helix .. "-" .. end_helix .. ")" )

    best_score = GetScore ()

    start_idx = start_helix - loop_spacer

    if ( start_idx < 1 ) then
       start_idx = 1
    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

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

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

     -- for some reason, do_local_rebuild ( 1)  often leaves  the protein unchanged

    k  = 0 
    repeat 
        k = k + 1
         structure.RebuildSelected ( k )
        score_after_rebuild = GetScore ()
    until  math.abs ( score_after_rebuild - best_score ) >= 1e-5 or k  > 2  

    if ( math.abs ( score_after_rebuild - best_score ) < 1e-5 ) then
               
        -- If  the scores are still equal we probably have a locked segment

        return false
    
    end

    selection.SelectAll ()

    curr_score = ShakeWiggleShakeNudge ()

    if ( curr_score > best_score ) then

        improvement_made = true

        best_score = curr_score

        save.Quicksave ( kBest )
        print ( "Improvement to " ..  roundto3 ( best_score ) )
                     
    end

    curr_score = GetScore ()

    if (  curr_score > qs10_best_score  and improvement_made == false ) then
      
       qs10_best_score = curr_score
 
      -- Bracket the area with frozen segments for easy recognition
     
      selection.DeselectAll ()
                 
      if ( start_idx > 1 ) then
          selection.Select ( start_idx - 1 )
      end
                
      if ( end_idx <  n_residues ) then
         selection.Select ( end_idx + 1 )
      end

      freeze.FreezeSelected ( true , false )

      save.Quicksave ( kQs10 )

      print ( "Storing " .. roundto3 ( qs10_best_score ) .. " in " .. kQs10 )

    end

    save.LoadSecondaryStructure ()

    return true

end

function get_parameters ()

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

  dlog.loop_spacer= dialog.AddSlider ( "Loop spacer" , loop_spacer , 0 , 6 , 0 )  
  dlog.min_residue = dialog.AddSlider ( "Min residue" , 1 , 1 , n_residues , 0 )  
  dlog.max_residue = dialog.AddSlider ( "Max residue" , n_residues , 1 , n_residues , 0 )  

  dlog.ok = dialog.AddButton ( "OK" , 1 )
  dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

  if ( dialog.Show ( dlog ) > 0 ) then
    
    loop_spacer = dlog.loop_spacer.value
    min_residue = dlog.min_residue.value
    max_residue = dlog.max_residue.value
    return true
  else
    return false
 end

end

print (  "Helix  rebuild" )

-- Tidy up if necessary

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 : " .. roundto3  ( best_score )  )

if ( start_score == 0 ) then
    print ( "Suggest quitting as starting score < = 0" )
end

if ( get_parameters () == false ) then
  return                -- graceful exit
end

rb = 0
save.Quicksave ( kBest )


get_helices ()

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

qs10_best_score = 0

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

--  Well it'll never get here as things stand but the tidying up below would be nice to do

save.Quickload ( kBest )

band.EnableAll  ()

Comments

[spvincent]

Helix rebuilding is probably best done by eyeballing but this script can be used instead: probably best used as a middle game script.

This script brackets each helix with a loop on either end, rebuilds it once, and then does a Shake, Wiggle, Shake, Wiggle, nudging the protein slightly if a wiggle gets stuck. If this results in a new high score all well and good. If not it may still be a useful candidate for further investigation as the script doesn't do any fusing. The best result that comes closest to the highest score is stored in Quicksave slot 10 (changeable to any other number). After terminating the script and if the score hasn't improved, it's recommended that you load the result in Quicksave 10, unfreeze it (the rebuilt area will be bracketed with frozen segments to identify the helix that was rebuilt, and try a fuze 9or something else.

Loop spacer: a value of 2 seems to give decent results: larger values will mean greater structural changes.

Min residue, Max residue. By default it does the whole protein but these values can be modified to only rebuild helices within a certain range.