Recipe: MicroIdealize 1.0

created by spvincent

Profile

• Name: MicroIdealize 1.0
• ID: 48411
• Shared with: Public
• Parent: None
• Children:
  • MicroIdealize 1.1
  • MicroIdealize 1.3 - CW
  • Deep Idealize 2.3
  • Idealize-MicroIdealize 1.0
  • MicroRemix 1.1
  • MicroIdealize 1.0 SFNC
• Created on: March 03, 2014 at 18:25 PM UTC
• Updated on: March 03, 2014 at 18:25 PM UTC
• Description:

  See first comment

Code

kOriginalStructureOrNewBest = 1	  -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot

best_score = 0

idealize_length = 3
min_residue = 1
max_residue = 999

sphere = {}
kSphereRadius = 10

function r3 ( i )

    -- printing convenience

    return i - i % 0.001

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

end

function SphereSelect ( start_idx , end_idx )

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

     for  i = 1 , n_residues do
         for j = start_idx , end_idx do
             if ( structure.GetDistance ( i , j ) < kSphereRadius ) then
                sphere [ i ] = true
             end
        end
    end

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

end


function Go ( sz )

    for i = min_residue - 1 , max_residue - sz do
       
        print ( i + 1 .. "-" .. i + sz )

        save.Quickload ( kOriginalStructureOrNewBest )

        if ( i > 0 ) then
             structure.InsertCut ( i )
        end

        if ( i < n_residues ) then
            structure.InsertCut ( i + sz )
        end

        selection.DeselectAll ()
        selection.SelectRange ( i + 1 , i + sz )
        
        structure.IdealizeSelected ()

        if ( i > 0 ) then
             structure.DeleteCut ( i )
        end

        if ( i < n_residues ) then
            structure.DeleteCut ( i + sz )
        end

        SphereSelect ( i + 1 , i + sz )

        structure.WiggleSelected ( 12 )     

        score  = GetScore ()

        if ( score > best_score  ) then

            best_score =  score
            print ( "Improvement to "..  r3 ( best_score )  )
 
            save.Quicksave ( kOriginalStructureOrNewBest )

        end
 
     end


end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "MicroIdealize" )

    dlog.idealize_length = dialog.AddSlider ( "Idealize length" , idealize_length , 1 , 20 , 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 )  

    dlog.ok = dialog.AddButton ( "OK" , 1 )
    dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

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

end


function main ()

    print (  "MicroIdealize" )

    band.DisableAll ()

    save.Quicksave ( kOriginalStructureOrNewBest )
    best_score = GetScore ()
    print ( "Start score " .. r3 ( best_score ) )

    n_residues = structure.GetCount ()

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

    Go ( idealize_length )

    save.Quickload ( kOriginalStructureOrNewBest )

end

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

    band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

Intended as an endgame script to be used at high WP but may be more generally applicable now Ideality has assumed more importance.

Algorithm outline

For each section (default length 3) in the selected range (default = whole protein)
    Isolate that section with cut points (prevents the structure from blowing apart)
    Idealize the section
    Close cutpoints
    Wiggle