Recipe: Loop explorer 1.0 With Mutate

created by phallicies

Profile

• Name: Loop explorer 1.0 With Mutate
• ID: 44633
• Shared with: Public
• Parent: Loop explorer 1.0
• Children: None
• Created on: November 17, 2012 at 06:05 AM UTC
• Updated on: November 17, 2012 at 06:05 AM UTC
• Description:

  Added Mutate

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.MutateSidechainsSelected ( 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 )