Recipe: Loop explorer 3.01

created by spvincent

Profile

• Name: Loop explorer 3.01
• ID: 101630
• Shared with: Public
• Parent: None
• Children:
  • gw - Loop explorer 3.01
• Created on: November 23, 2015 at 02:09 AM UTC
• Updated on: November 23, 2015 at 02:09 AM UTC
• Description:

  See first comment

Code

-- Repeatedly rebuild/shake/wiggle a particular segment

-- Constants

kMaxSphereDistance = 13                  -- Residues further than this away won't be shaken

score_type = 1

-- 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

kInvalidScore = -999999
best_post_rebuild_score_1 = kInvalidScore
best_post_rebuild_score_2 = kInvalidScore

post_rebuild = 2
rebuild_threshold = 100

original_slow_filters_setting = 0

-- Quicksave slots

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

--  Performance monitoring

monit = false
monit_r_loss = 0
monit_s1_gain = 0
monit_w1_gain = 0
monit_s2_gain = 0
monit_w2_gain = 0

function r3 ( x )

-- Round to 3 decimal places

  t  = 10 ^ 3

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

end

function GetScore ()

    if ( score_type == 1 ) then

        score = current.GetScore () 

    elseif ( score_type == 2 ) then

        behavior.SetFiltersDisabled ( false )
        score = current.GetScore () 
        behavior.SetFiltersDisabled ( true )

    end

    return score

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 NudgeWiggle ()

    selection.SelectAll ()

    score_in_kTemp = GetScore ()
    save.Quicksave ( kTemp)

    behavior.SetClashImportance ( 0.5 )
    structure.WiggleSelected ( 1 )
    behavior.SetClashImportance ( 1 )
    structure.WiggleSelected ( 6 )

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

end


function RebuildSection ( start_idx , end_idx ) 

    save.Quickload ( kOriginalStructureOrNewBest )

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

    structure.RebuildSelected ( 1 )

    score_after_rebuild = GetScore ()
 
    if ( ( score_after_rebuild > best_score ) or ( best_score - score_after_rebuild > rebuild_threshold ) ) then

        if ( monit ) then
            monit_r_loss = score_after_rebuild - best_score
            monit_s1_gain = 0
            monit_w1_gain = 0
            monit_s2_gain = 0
            monit_w2_gain = 0
        end

        SelectSphere ()
        structure.ShakeSidechainsSelected ( 1 )

        if ( monit ) then
            monit_s1_gain = GetScore () - score_after_rebuild
        end

        if ( post_rebuild >= 2 ) then

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

            if ( score_after_wiggle - score_before_wiggle  < 1 ) then
  
                --    The wiggle got stuck and didn't achieve anything

                NudgeWiggle ()
            end

            if ( monit ) then
                monit_w1_gain = GetScore () - score_before_wiggle
            end

            if ( post_rebuild >= 3 ) then

                score_before_sm = GetScore ()

                SelectSphere ()
                if ( post_rebuild == 3 ) then
                   structure.ShakeSidechainsSelected ( 1 )
                  else
                   structure.MutateSidechainsSelected ( 1 )
                end

                score_after_sm = GetScore ()
 
                if ( monit ) then
                    monit_s2_gain = score_after_sm - score_before_sm
                end

                if ( score_after_sm - score_before_sm  > 1e-3 ) then
  
                    score_before_wiggle = score_after_sm
                    structure.WiggleSelected ( 10 )
                    score_after_wiggle = GetScore ()

                    if ( score_after_wiggle - score_before_wiggle < 1 ) then
  
                        --    The wiggle got stuck and didn't achieve anything

                        NudgeWiggle ()
                    end

                    if ( monit ) then
                        monit_w2_gain = GetScore () - score_before_wiggle
                    end

                end

            end   -- ( post_rebuild >= 3 )

        end   -- ( post_rebuild >= 2 )

        score = GetScore ()

        if ( monit ) then
            print ( rb .. "  " .. 
                      r3 ( monit_r_loss ) .. "   " ..
                      r3 ( monit_s1_gain ) .. "   " ..
                      r3 ( monit_w1_gain ) .. "   " ..
                      r3 ( monit_s2_gain ) .. "   " ..
                      r3 ( monit_w2_gain ) .. "   " ..
                      r3 ( best_score - score ) .. "   " )
        end

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

            print ( "rb : " .. rb .. " Improvement to " .. r3 ( score ) )
  
        elseif ( score > math.min ( best_post_rebuild_score_1 , best_post_rebuild_score_2 ) ) then

            if ( best_post_rebuild_score_1 <  best_post_rebuild_score_2  ) then
                slot = kPostRebuild_1
                best_post_rebuild_score_1 = score
            else
               slot = kPostRebuild_2
               best_post_rebuild_score_2 = score
            end

           save.Quicksave ( slot )

          if ( monit == false ) then
              print ( "rb : " .. rb .. " Storing " .. r3 ( score ) .. " in quicksave " .. slot  )
          end

      else
         print ( "rb : " .. rb )
       end

    else
        print ( "rb : " .. rb .. " bt" )    -- below threshold
    end
end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "Loop explorer 3.1" )

    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.post_rebuild = dialog.AddSlider ( "Post rebuild" , post_rebuild , 1 , 4 , 0 )  
    dlog.pr = dialog.AddLabel ( "1 = Sh : 2 = Sh/W : 3 = Sh/W/Sh/W : 4 = Sh/W/Mu/W"  )

    dlog.rebuild_threshold = dialog.AddSlider ( "Rebuild threshold" , rebuild_threshold , 0 , 1000 , 0 )  
 
    dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )  
    dlog.tp = dialog.AddLabel ( "1 = Normal : 2 = Normal for Filters"  )

    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
       post_rebuild = dlog.post_rebuild.value
       rebuild_threshold = dlog.rebuild_threshold.value
       score_type = dlog.score_type.value
       return true
    else
       return false
   end

end


function main ()

    n_residues = structure.GetCount ()

    rb = 0
    save.Quicksave ( kOriginalStructureOrNewBest )

    behavior.SetClashImportance ( 1 )
    original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()

    print ( "Loop Explorer 3.1" )
 
    if ( GetParameters () == false ) then
      return                -- graceful exit
    end

    best_score = GetScore ()
 
    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

    for i = min_residue , max_residue do

        seg_backbone_frozen, seg_sidechain_frozen = freeze.IsFrozen ( i )

        if ( seg_backbone_frozen == true ) then
            print ( "Backbone frozen" )
            return
        end

    end

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

    print ( "Rebuilding " .. min_residue .. " to " .. max_residue )
    if ( post_rebuild == 1 ) then
        print ( "Post rebuild : Shake" )
    elseif ( post_rebuild == 2 ) then
        print ( "Post rebuild : Shake/Wiggle" )
    elseif ( post_rebuild == 3 ) then
        print ( "Post rebuild : Shake/Wiggle/Shake/Wiggle" )
    elseif ( post_rebuild == 4 ) then
        print ( "Post rebuild : Shake/Wiggle/Mutate/Wiggle" )
    end

    print ( "Threshold " .. r3 ( rebuild_threshold ) )

    ConstructListOfResiduesWithinRange ( min_residue , max_residue )

    store_next_post_rebuild_in_1 = true

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

    cleanup ()

end

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

    if ( best_post_rebuild_score_1 ~= kInvalidScore ) then
        print ( "Loading Quicksave " .. kPostRebuild_1 .. " (" .. r3 ( best_post_rebuild_score_1 ) .. ")" )
        save.Quickload ( kPostRebuild_1 )
    end

    if ( best_post_rebuild_score_2 ~= kInvalidScore ) then
        print ( "Loading Quicksave " .. kPostRebuild_2 .. " (" .. r3 ( best_post_rebuild_score_2 ) .. ")" )
        save.Quickload ( kPostRebuild_2 )
    end

    print ( "Loading start" )
    save.Quickload ( kOriginalStructureOrNewBest )

    if ( score_type == 2 ) then
        behavior.SetSlowFiltersDisabled ( original_slow_filters_setting )
    end

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

(Change from 3.0 : on termination load results in Quicksave slots for easy access via Undo as suggested by Bruno)

Repeatedly rebuilds, shakes and wiggles a selected area (not necessarily a loop, the name's a bit misleading); 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 to explore new configurations of an existing region, 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.

This script never terminates. It's up to the user to stop it after a bit and examine the poses in Quicksave slots 11 and 12 which are loaded on termination prior to restoring the current best pose. Suggest taking the best-looking (not necessarily the higher scoring) of these two poses and proceed from there.

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.

Post rebuild

Specifies the action(s) to be taken after a rebuild. The default is a Shake/Wiggle but other action sequences are provided: they allow the usual trade off between speed and accuracy.

Rebuild threshold

The idea is to reject rebuilds that are too similar to the original. If the score after a rebuild is less than the original score by this value or lower than the rebuild will be rejected. ( "bt" will be printed in the output ). Not entirely sure how well this will works in practise but it struck me as a nice feature when writing the script. Drag slider to zero to effectively remove this feature.

Score type

If set to 2, toggles filters off except when determining the score. For better performance on slow design puzzles.

[drumpeter18yrs9yrs]

I wish after rebuild, it would start off with CI=0.01