Recipe: Cut and Wiggle 1.5

created by spvincent

Profile

• Name: Cut and Wiggle 1.5
• ID: 101906
• Shared with: Public
• Parent: None
• Children:
  • Cut and Wiggle 1.5longslider
• Created on: February 22, 2016 at 01:49 AM UTC
• Updated on: February 22, 2016 at 01:49 AM UTC
• Description:

  See first comment

Code

-- Adapted from Karen CH's script

min_residue = 1
max_residue =  999
n_residues = 0

fragment_length = 5
clash_importance_during_modify = 0.3

score_type = 1
original_slow_filters_setting = 0

curr_best_score = 0

kLowCI = 0.3

        -- Use of quicksave slots

kOriginalStructureOrNewBest = 10


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 DoesPuzzleHaveSlowFilters ()

    init_setting = behavior.GetSlowFiltersDisabled ()
 
    if ( init_setting == false ) then
       score_without_sf = current.GetScore () 
       behavior.SetSlowFiltersDisabled ( true )
       score_with_sf = current.GetScore () 
     else
       score_with_sf = current.GetScore () 
       behavior.SetSlowFiltersDisabled ( false )
       score_without_sf = current.GetScore () 
    end

    behavior.SetSlowFiltersDisabled ( init_setting )
 
    if ( math.abs ( score_without_sf - score_with_sf ) >1e-3 ) then
        return true
      else
        return false
    end

end

function Go ()

    n_iterations_without_improvement = 0
    n = 0

    while true do

        for j = 0 , fragment_length - 1 do

            n = n + 1
            undo.SetUndo ( false )

            save.Quickload ( kOriginalStructureOrNewBest )

            for i = min_residue + j , max_residue , fragment_length do
                structure.InsertCut ( i )
            end

            selection.SelectRange ( min_residue , max_residue )

            behavior.SetClashImportance ( kLowCI )
            structure.WiggleSelected ( 1 )

            behavior.SetClashImportance ( 1.0 )
            structure.WiggleSelected ( 10 )

             for i = min_residue + j , max_residue , fragment_length do
                structure.DeleteCut ( i )
            end

            undo.SetUndo ( true )

            behavior.SetClashImportance ( kLowCI )
            structure.WiggleSelected ( 1 )

            behavior.SetClashImportance ( 1.0 )
            structure.WiggleSelected ( 10 )

            score = GetScore ()

            print ( "n " .. n .. " " .. r3 ( score ) )

            if ( score > curr_best_score ) then
                save.Quicksave ( kOriginalStructureOrNewBest )
                curr_best_score = score
                print ( "Improvement to " .. r3 ( score ) )
                n_iterations_without_improvement = 0
              else
                n_iterations_without_improvement = n_iterations_without_improvement + 1
            
            end

            if ( n_iterations_without_improvement >= fragment_length ) then
              return
            end

        end

    end

end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "Cut and Wiggle 1.5" )

    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.fragment_length = dialog.AddSlider ( "Fragment length" , fragment_length  , 1 , 10 , 0 )  
    dlog.cidm = dialog.AddSlider ( "Clash importance" , clash_importance_during_modify , 0 , 1.0 , 2 )  

    if ( DoesPuzzleHaveSlowFilters () == true ) then
        score_type = 2
    end

    dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )  
    dlog.tp2 = 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
        fragment_length = dlog. fragment_length.value
        clash_importance_during_modify = dlog.cidm.value
 
        score_type = dlog.score_type.value

        return true
      else
        return false
    end

end

function main ()

    print ( "Cut and Wiggle 1.5" )

    band.DisableAll ()
    n_residues = structure.GetCount ()
 
    save.Quicksave ( kOriginalStructureOrNewBest )
    behavior.SetClashImportance ( 1.0 )

    original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()

    if ( GetParameters () == false ) then
        return
    end

    print  ( "Range " .. min_residue .. " to " .. max_residue )
    print  ( "Fragment length " .. fragment_length  )
    print  ( "Clash importance low " .. r3 ( clash_importance_during_modify ) )

    if ( score_type == 1 ) then
        print (  "Score type : Normal" )
     elseif ( score_type == 2 ) then
        print (  "Score type : Normal/Slow Filters" )
    end

    curr_best_score = GetScore ()
    print ( "Start score " .. r3 ( curr_best_score ) )
    print  ( "" )

    Go ()

    cleanup ()

end

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

    selection.SelectAll ()
    band.EnableAll ()

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

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

KarenCH's Cut and Wiggle script revamped. Functional changes include:

1) The ability to selectively work on part of the protein.
2) Minimize undo graph activity.
3) Turn off filters when working on a design puzzle.

The default settings work well: changing the size from 5 to something else often wrings out a few extra points.

I've usually used this as an endgame script: others think it should be used earlier as it loosens things up.