Recipe: Loop explorer 1.0

created by spvincent

Profile

• Name: Loop explorer 1.0
• ID: 44410
• Shared with: Public
• Parent: None
• Children:
  • Loop explorer 1.0 With Mutate
• Created on: October 24, 2012 at 21:23 PM UTC
• Updated on: October 24, 2012 at 21:23 PM UTC
• Description:

  See first comment

Code

-- Repeatedly rebuild/shake/wiggle a particular segment

-- Constants

kWorstAllowableAngle = 75                -- ignore rebuilds with backbone angles less than this (degrees)
kMaxSphereDistance = 13                  -- Residues further than this away won't be shaken

-- Globals

best_score = 0
min_residue = 0
max_residue = 0
n_residues = 0
rb = 0
SphereSegList = {}				-- store list of residues within kMaxSphereDistance of any residue in the segment.
							-- speeds things up when shaking

best_post_rebuild_weighted_score_delta_1 = 999999
best_post_rebuild_weighted_score_delta_2 = 999999

--  Difference heuristic variables

weight_by_difference = false

closest_to_mid = -1
init_differences = {}
curr_differences = {}


-- Quicksave slots

kOriginalStructureOrNewBest = 1
kTemp = 2
kPostRebuild_1 = 11
kPostRebuild_2 = 12

function r3 ( x )

-- Round to 3 decimal places

  t  = 10 ^ 3

  return math.floor ( x*t + 0.5 ) /  t 

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

end

function FindResidueClosestToMidRebuild ( start_idx , end_idx )

    mid_x = ( start_idx + end_idx ) / 2

    closest_to_mid =  -1
    cv = 999999

    for  i = 1 , n_residues do
         if ( i < start_idx or i > end_idx ) then
            d = structure.GetDistance ( i , mid_x )
            if ( d < cv ) then
               closest_to_mid = i
               cv = d
            end
        end
    end
 
 end

function FindDifferenceValues ( table , start_idx , end_idx )

  for i = start_idx , end_idx do
     table [ i ] = structure.GetDistance ( i , mid_x )
  end

end

function ComputeDifferenceHeuristic ( start_idx , end_idx )

  d = 0
  for i = start_idx , end_idx do
     d = d + ( init_differences [ i ] - curr_differences [ i ] ) * ( init_differences [ i ] - curr_differences [ i ] ) 
  end

  return ( math.sqrt ( d ) )
end

function ComputeWeightedDifference ( score , dh )

  if ( dh < 1e-5 ) then
    return 1e10
   else
    return ( best_score - score ) / dh
  end

end

function ConstructListOfResiduesWithinRange ( start_idx , end_idx )

-- Mildly inefficient but it's only done once at startup

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

   for j = start_idx , end_idx do
      for  i = 1 , n_residues do
         if ( ( i >= start_idx and i <= end_idx ) or
             ( structure.GetDistance ( i , j ) < kMaxSphereDistance ) ) then
            SphereSegList [ i ] = true
        end
    end
  end

end

function SelectSphere ()

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

end


function get_parameters ()

  local dlog = dialog.CreateDialog ( "Loop explorer" )

  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.weight_difference = dialog.AddCheckbox ( "Weight according to difference" , weight_by_difference )  
  dlog.ok = dialog.AddButton ( "OK" , 1 )
  dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

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

end

function NudgeWiggle ()

    selection.SelectAll ()

    score_in_kTemp = GetScore ()
    save.Quicksave ( kTemp)

    behavior.SetClashImportance ( 0.7 )
    structure.WiggleSelected ( 1 )
    behavior.SetClashImportance ( 1 )
    structure.WiggleSelected ( 6 )

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

end


function rebuild_section ( start_idx , end_idx ) 

    save.Quickload ( kOriginalStructureOrNewBest )

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

    structure.RebuildSelected ( 1 )

    score_after_rebuild_shake = GetScore ()
 
    SelectSphere ()
    structure.ShakeSidechainsSelected ( 1 )

    score_after_rebuild_shake = GetScore ()
 
    selection.SelectAll ()
  
    structure.WiggleSelected ( 10 )
    score_after_wiggle = GetScore ()

    if ( score_after_wiggle - score_after_rebuild_shake  < 10 ) then
  
        --    The wiggle got stuck and didn't achieve anything

        NudgeWiggle ()
        score_after_wiggle = GetScore ()
    end

    if ( weight_by_difference  == true ) then

        FindDifferenceValues ( curr_differences , min_residue , max_residue )
   
        dh = ComputeDifferenceHeuristic ( start_idx , end_idx )
   
        wd = ComputeWeightedDifference ( score_after_wiggle , dh )
      else
        wd = best_score - score_after_wiggle
        dh = 1
    end

    if ( score_after_wiggle > best_score ) then
   
        best_score = score_after_wiggle
        save.Quicksave ( kOriginalStructureOrNewBest )

        print ( "rb : " .. rb .. " Improvement to " .. r3 ( score_after_wiggle ) )
        --print ( "  dh " , r3 ( dh ) )

    elseif ( wd < math.max ( best_post_rebuild_weighted_score_delta_1 , best_post_rebuild_weighted_score_delta_2 ) ) then

      if ( best_post_rebuild_weighted_score_delta_1 >  best_post_rebuild_weighted_score_delta_2  ) then
          slot = kPostRebuild_1
          best_post_rebuild_weighted_score_delta_1 = wd
        else
          slot = kPostRebuild_2
          best_post_rebuild_weighted_score_delta_2 = wd
      end

      save.Quicksave ( slot )

      print ( "rb : " .. rb .. " Storing " .. r3 ( score_after_wiggle ) .. " in quicksave " .. slot  )
      --print ( "  dh " , r3 ( dh ) )
      --print ( "  wd " , r3 ( wd ) )
     
  else
     print ( "rb : " .. rb )
     --print ( "rb : " .. rb .. " dh " , r3 ( dh ) )
   end

end

function main()

    band.DisableAll ()
    n_residues = structure.GetCount ()

    rb = 0
    save.Quicksave ( kOriginalStructureOrNewBest )

    behavior.SetClashImportance ( 1 )

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

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

    if ( max_residue <= min_residue ) then
        print ( "Rebuild  range error." )
        print ( "Max residue (" .. max_residue .. ") must be greater than or equal to Min residue (" ..  min_residue .. ")" )
        return
    end

    print  ( "Rebuilding " .. min_residue .. " to " .. max_residue )

    ConstructListOfResiduesWithinRange ( min_residue , max_residue )

    cos_worst_allowable_angle = math.cos ( math.rad ( kWorstAllowableAngle ) )

    FindResidueClosestToMidRebuild  ( min_residue , max_residue )

    FindDifferenceValues ( init_differences , min_residue , max_residue )

    store_next_post_rebuild_in_1 = true

    while true do
         rb = rb + 1
         rebuild_section ( min_residue , max_residue ) 
    end

    save.Quickload ( kOriginalStructureOrNewBest )
    band.EnableAll ()

end

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

     band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

Repeatedly rebuilds, shakes and wiggles a selected area, storing the most promising results in Quicksave slots.

This script is not intended to improve your score in itself, although it may have that happy side effect. Its intended use is as a late game script to explore new configurations of an existing loop,which can then be loaded, inspected, and the rebuilder of your choice used to hammer away at the new loop and hopefully produce a better score.

Min residue: max residue

Used to define the area (not necessarily a loop, despite the name of the script) to be rebuilt. A likely candidate would be one 8-12 residues in length with an appearance that displeases you or which you have cause to think may be stuck in a local minimum.

Weight according to difference

If unchecked, new configurations are saved according to best score in two Quicksave slots (11 and 12 by default). If checked a weighting function (based on differences between the position of each side chain between the new configuration and the original) is applied such that new configurations that are significantly different from the original will be preferred, even though their score may be lower.