Recipe: Idealize 3.0

created by spvincent

Profile

• Name: Idealize 3.0
• ID: 100708
• Shared with: Public
• Parent: None
• Children:
  • Idealize 3.1
  • Single Segment Idealise 1.0
  • Idealize 3.0 (COPY) no score
• Created on: February 21, 2015 at 02:47 AM UTC
• Updated on: February 21, 2015 at 02:47 AM UTC
• Description:

  See first comment

Code

kFallApartThreshold  = 800    -- If Idealize results in a loss greater than this, skip the subsequent wiggle as the protein has probably exploded

n_residues = 0
min_residue = 1
max_residue =  999

ss_starts = {}
ss_ends  = {}
ss_types  = {}

kOriginalStructureOrNewBest = 8

kWiggleDuration = 10

score_type = 1
original_slow_filters_setting = 0

function r3 ( i )

    -- printing convenience

    return i - i % 0.001

end

function GetScore ()

    if ( score_type == 1 ) then

        score = current.GetEnergyScore () 

    elseif ( score_type == 2 ) then

        behavior.SetSlowFiltersDisabled ( false )
        score = current.GetScore () 
        behavior.SetSlowFiltersDisabled ( 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 GetStructures ()

    curr_type = 'x'

    for i = 1, n_residues do

        ss_type = structure.GetSecondaryStructure ( i )

        if ( ss_type ~= curr_type ) then
    
             -- start of a new struct

              curr_type = ss_type
   
              ss_starts [ #ss_starts + 1 ] = i
              if ( i > 1 ) then
                  ss_ends [ #ss_ends + 1 ] = i -1
              end
              ss_types [ #ss_types + 1 ] = curr_type

        end
    end    -- for i
   
    ss_ends [ #ss_ends + 1 ] = n_residues

end

function IdealizeSection ( s_idx , e_idx , ss_type )

    if ( ( s_idx > max_residue ) or ( e_idx < min_residue ) ) then
       return
    end

    start_idx = math.max ( s_idx , min_residue )
    end_idx = math.min ( e_idx , max_residue )

    save.Quickload ( kOriginalStructureOrNewBest )
    selection.DeselectAll ()

    selection.SelectRange ( start_idx , end_idx )
    print ( "Idealizing " ..  start_idx .. "-" ..  end_idx .. " (" .. ss_type .. ")" )

    structure.IdealizeSelected ()
    score_after_idealize = GetScore ()

    selection.SelectAll ()

    if ( ( curr_best_score - score_after_idealize ) > kFallApartThreshold ) then
        structure.WiggleAll ( 1, false , true )    -- wiggle sidechains
    end

    if ( math.abs ( score - curr_best_score ) > 1e-3 ) then

        structure.WiggleSelected ( kWiggleDuration )

        score_after_wiggle = GetScore ()
        
        if ( score_after_wiggle > curr_best_score ) then
            curr_best_score = score_after_wiggle
            save.Quicksave ( kOriginalStructureOrNewBest )
            print ( "Improvement to : " .. r3 ( curr_best_score ) )
        end
    
    end

end


function GetParameters ()

    local dlog = dialog.CreateDialog ( "Idealize 3.0" )

    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 )  

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

    dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )  
    dlog.tp = dialog.AddLabel ( "1 = Normal : 2 = Normal for Slow 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

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

end

function main ()

    print ( "Idealize 3.0" )

    n_residues = structure.GetCount ()
    behavior.SetClashImportance ( 1 )

    GetStructures ()

    original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()

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

    if ( max_residue < min_residue ) then
        print ( "Rebuild range error" )
        return
    end

    print  ( "Idealizing structures from " .. min_residue .. " to " .. max_residue )
  
    curr_best_score =  GetScore () 

    print ( "Init score : " .. r3 ( curr_best_score ) )
   
    save.Quicksave ( kOriginalStructureOrNewBest )

     for i = 1 , #ss_starts do

        if ( ss_types [ i ] == "H" ) then
            IdealizeSection ( ss_starts [ i ] , ss_ends [ i ] , "H"  ) 
        end
    
    end
    
    for i = 1 , #ss_starts do

        if ( ss_types [ i ] == "E" ) then
            IdealizeSection ( ss_starts [ i ] , ss_ends [ i ] , "E" ) 
        end
    
    end

    for i = 1 , #ss_starts do

        if ( ss_types [ i ] == "L" ) then
            IdealizeSection ( ss_starts [ i ] , ss_ends [ i ] , "L" ) 
         end
    
    end

    cleanup ()

end

function cleanup ()
   
    behavior.SetClashImportance ( 1.0 )
    save.Quickload ( kOriginalStructureOrNewBest )

    behavior.SetSlowFiltersDisabled ( original_slow_filters_setting )
 
end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

A quick-running script that idealizes secondary structure elements. Useful after running a rebuild script.

The principal change since 2.0 is to add a mode for Slow Filters

Algorithm outline

For each secondary structure element
    Idealize
    If the score drop is significant
         Wiggle Sidechains
    end
    Wiggle
    Record any gain
end

It does helices, sheets, then loops: mostly out of a general sense that it's better not to go through the protein in a linear way.

Min residue, Max residue

Only structures that lie at least partially within this range will be processed: by default the entire protein is used.

Score type

Default is Normal. Normal/Slow Filters is for slow design/symmetry puzzles (for such puzzles the score type defaults to this mode): it sets slow filters off apart from scoring.

[LexieGreen]

This worked really well for me, thank you!