Recipe: Helix Twister 1.0

created by spvincent

Profile

• Name: Helix Twister 1.0
• ID: 47646
• Shared with: Public
• Parent: None
• Children:
  • Helix Twister 1.01
• Created on: December 31, 2013 at 16:39 PM UTC
• Updated on: December 31, 2013 at 16:39 PM UTC
• Description:

  See first comment

Code

-- Globals

original_secondary_structure = {}

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

n_residues = 0

loop_spacer = 3
co_twist = false

clk_twist = true
band_length = 5
band_strength = 1

mutate_not_shake = false
test_for_credit = false

keep_trying = false

-- Quicksave slots

kOriginalStructureOrNewBest = 1	  -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot


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 GetClosestHelix ( i )

    -- From the list of selected helices, choose the one closest to helix i
    -- Very crude, looks at the distance between helix centres

    mid_i = ( helix_starts [ i ] + helix_ends [ i ] ) / 2
    closest_j = -1
    closest_distance = 99999

    for j = 1 , n_helices do

        if ( j ~=i ) then

            mid_j = ( helix_starts [ j ] + helix_ends [ j ] ) / 2

            d = structure.GetDistance ( mid_i , mid_j )
       
            if ( d < closest_distance ) then

                closest_distance = d
                closest_j = j

            end

        end

    end

    return closest_j

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 nudge ()

    selection.SelectAll ()
    recentbest.Save ()
    behavior.SetClashImportance ( 0.4 )
    structure.WiggleSelected ( 1 )
    behavior.SetClashImportance ( 1 )
    structure.WiggleSelected ( 8 )
    recentbest.Restore ()
 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 ConstructBands ( start_helix , end_helix )

    for i = math.max ( start_helix , 2 ) , math.min ( end_helix , n_residues - 1 ) do
      
        if ( clk_twist ) then
            band.Add ( i , i + 1 , i - 1 , band_length , math.pi/2 , math.rad ( 315 ) )
          else
            band.Add ( i , i - 1 , i + 1 , band_length , math.pi/2 , math.rad ( 315 ) )
        end

    end

    if ( math.abs ( band_strength - 1.0 ) > 1e-3 ) then

        n_bands = band.GetCount ()

        for i = 1 , n_bands do
            band.SetStrength (  i , band_strength )
        end

    end

end

function TwistHelix ( helix_index , start_helix , end_helix , closest_helix_idx  )

    if ( clk_twist == true ) then
       print ( "H " ..  helix_index .. " (c)" )
      else
       print ( "H " ..  helix_index .. " (a)" )
    end

    improvement_made = false

    save.Quickload ( kOriginalStructureOrNewBest )
 
    best_score = GetScore ()
    selection.DeselectAll ()

    start_idx , end_idx = ConstructSpacers ( start_helix , end_helix )

    ConstructBands ( start_helix , end_helix )

    selection.SelectRange ( start_idx , end_idx )

    if ( closest_helix_idx ~= 0 ) then
        start_idx , end_idx = ConstructSpacers ( helix_starts [ closest_helix_idx ] , helix_ends [ closest_helix_idx ]  )
        ConstructBands ( helix_starts [ closest_helix_idx ] , helix_ends [ closest_helix_idx ] )
        selection.SelectRange ( start_idx , end_idx )
    end

    structure.WiggleSelected ( 1 )
    score_after_wiggle= GetScore ()

    if ( math.abs ( score_after_wiggle - best_score ) < 1e-5 ) then
               
        -- If  the scores are still equal we probably have a locked segment
        print ( "Possible issue with helix " .. helix_index .. " (" .. start_helix .. "-" .. end_helix .. ")" )
    
        -- Trying to unfreeze: if successful rebuild will work next time this function is called

        for i = start_idx , end_idx do
            freeze.Unfreeze ( i , true , true )
        end

        return false
    
    end

    band.DeleteAll ()

    selection.SelectAll ()

    if ( mutate_not_shake == true ) then
        structure.MutateSidechainsSelected ( 1 )
      else
        structure.ShakeSidechainsSelected ( 1 )
    end
    
    structure.WiggleSelected ( 2 , false , true )    -- sidechains
    structure.WiggleSelected ( 12 )
 
    selection.SelectAll ()

    curr_score = GetScore ()

    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 ()

    return true

end

function get_parameters ()

  local dlog = dialog.CreateDialog ( "Helix twister 1.0" )

  dlog.loop_spacer = dialog.AddSlider ( "Loop spacer" , loop_spacer , 0 , 6 , 0 )  
  
  dlog.band_length = dialog.AddSlider ( "Band length" , band_length , 0.01 , 20 , 2 )  
  
  dlog.band_strength = dialog.AddSlider ( "Band strength" , band_strength , 0.01 , 10 , 2 )  
  
  for i = 1 , n_helices do
        dlog [ "helix" .. i ] = dialog.AddCheckbox ( helix_starts [ i ] .. "-" .. helix_ends [ i ]  , true )  
   end

  dlog.co_twist = dialog.AddCheckbox ( "Co-twist" , co_twist )  

  design_puzzle = IsPuzzleMutable ()

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

  dlog.clk = dialog.AddCheckbox ( "Clockwise " , clk_twist )  

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

  dlog.keep_trying = dialog.AddCheckbox ( "Keep trying " , keep_trying  )  

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

  if ( dialog.Show ( dlog ) > 0 ) then
    
    loop_spacer = dlog.loop_spacer.value
    band_length = dlog.band_length.value
    band_strength = dlog.band_strength.value

    for i = 1 , n_helices do
        use_helix [ i ] = dlog [ "helix" .. i ].value
    end
    
    clk_twist = dlog.clk.value

    co_twist = dlog.co_twist.value

    if ( design_puzzle == true ) then
       mutate_not_shake = dlog.mutate.value
    end

    test_for_credit = dlog.credit_check.value
    keep_trying = dlog.keep_trying.value

    return true
  else
     return false
   end

end

function main ()

    print (  "Helix twister 1" )

    band.DeleteAll ()

    n_residues = structure.GetCount ()

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

    save.SaveSecondaryStructure () 
    save.Quicksave ( kOriginalStructureOrNewBest )

    behavior.SetClashImportance ( 1 )

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

    get_helices ()

    print ( n_helices .. " helices" )

    qs10_best_score = 0

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

    print ( "Band length : " .. r3 ( band_length ) )
    print ( "Band strength : " .. r3 ( band_strength ) )

    -- 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 
        if ( co_twist == true ) then
            closest_helix [ i ] = GetClosestHelix ( i )

            if ( closest_helix [ i ] == -1 ) then
                print ( "Co-rebuild needs more then one selected helix" )
                error ()
            end

          else
            closest_helix [ i ] = 0
        end
    end

    for i = 1 , n_helices  do 
        if ( co_twist == true ) then
             print ( "Helix " .. i .. " : (" .. helix_starts [ i ] .. "-" .. helix_ends [ i ] .. ")" .. "  + (" .. helix_starts [ closest_helix [ i ]  ] .. " - " .. helix_ends [ closest_helix [ i ]  ] .. " )" ) 
           else
             print ( "Helix " .. i .. " : (" .. helix_starts [ i ] .. "-" .. helix_ends [ i ] .. ")" )
        end
    end

 
    for i = 1 , n_helices  do 
       TwistHelix ( i , helix_starts [ i ] , helix_ends [ i ] , closest_helix [ i ] )
    end

    clk_twist = not clk_twist
    for i = 1 , n_helices  do 
       TwistHelix ( i , helix_starts [ i ] , helix_ends [ i ] , closest_helix [ i ] )
    end

    if ( keep_trying == true ) then

        original_band_length = band_length
        original_band_strength = band_strength

        while ( true ) do

            band_length = original_band_length + 0.5*( math.random () - 0.5 )
            band_strength = original_band_strength + 0.2*( math.random () - 0.5 )
           
            clk_twist = true
            for i = 1 , n_helices do 
                TwistHelix ( i , helix_starts [ i ] , helix_ends [ i ] , closest_helix [ i ] )
            end

            clk_twist = false
            for i = 1 , n_helices do 
                TwistHelix ( i , helix_starts [ i ] , helix_ends [ i ] , closest_helix [ i ] )
            end
        end

    end

    band.DeleteAll ()
    save.Quickload ( kOriginalStructureOrNewBest )

end

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

    band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

This is an attempt to mimic some of the functionality of the tweak tool using bands. It doesn't take long to run and often produces a few points in the endgame but doesn't seem to be a big point getter.

Algorithm outline

For each helix
Bracket it with loops of the specified size
For each residue of the helix, create a band from the alpha carbon into empty space parallel to the backbone (more or less: not sure if I've understood the spherical coordinate system correctly)
Wiggle a region making up the helix plus spacers on other side.
Wiggle
Delete bands
Shake or mutate
Wiggle sidechains
Wiggle
Record any improvements as appropriate
end

Repeat in other direction (clockwise/anticlockwise)

Parameters

Loop spacer

Just as when using the Tweak tool you have to bracket a sheet or helix with loop segments; so you can do something similar here.

Band length

Adjust to taste but the default value seems to be reasonable.

Band strength

Ditto.

Helix list

All selected by default</b>

Co-twist

If set to true, twists a helix together with the nearest selected helix. Seemed like a good idea at the time but not sure how useful it really is: I haven't seen gain from it.

Mutate not shake

For design puzzles only. If set will replace Shake after banded wiggle by Mutate as indicated in the algorithm outline above.

Clockwise

Whether a clockwise twist is done first or an anti-clockwise one. Kind of unnecessary.

Check conditions met

When set, will only accept a score improvement if all conditions are met. For puzzles where some restrictions are imposed.

Keep trying

Repeats everything indefinitely with minor random changes to band length and band strength.