Recipe: Idealize 2.0 (NC)

created by spvincent

Profile

• Name: Idealize 2.0 (NC)
• ID: 47961
• Shared with: Public
• Parent: None
• Children:
  • Deep Idealize 2.1
  • Idealize Hard 2.0 (NC)
  • Idealize Repeats 2.0 (NC)
  • Idealize 2.0 (NC) souped up
  • Wiggle Structure with Neighbors
• Created on: January 30, 2014 at 02:38 AM UTC
• Updated on: January 30, 2014 at 02:38 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

kMaxIterations = 10                -- Sanity check for the new wiggle loop

n_residues = 0

ss_starts = {}
ss_ends  = {}

kOriginalStructureOrNewBest = 8

function r3 ( i )

    -- printing convenience

    return i - i % 0.001

end

function GetScore ()

    score = current.GetEnergyScore () 

    return score

end

function get_structures ( starts , ends  )

    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
   
              starts [ #starts + 1 ] = i
              if ( i > 1 ) then
                  ends [ #ends + 1 ] = i -1
              end

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

end

function Wiggle ( step , threshold )

    n_it = 0
    new_score = GetScore ()

    repeat
       
        prev_score = new_score
        structure.WiggleSelected ( step )        
        new_score = GetScore ()
        n_it = n_it + 1

    until ( ( math.abs ( new_score - prev_score ) < threshold ) or ( n_it > kMaxIterations ) )

end

function main ()

    print (  "Idealize 2.0 : New Chapters" )
    curr_best_score =  GetScore () 

    print ( "Init score : " .. r3 ( curr_best_score ) )

    save.Quicksave ( kOriginalStructureOrNewBest )

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

    get_structures ( ss_starts , ss_ends  )

    for i = 1 , #ss_starts do

        save.Quickload ( kOriginalStructureOrNewBest )
        selection.DeselectAll ()
        selection.SelectRange ( ss_starts [ i ] , ss_ends [ i ] )
        print ( "Idealizing " ..  ss_starts [ i ] .. "-" ..  ss_ends [ i ] )

        structure.IdealizeSelected ()
        
        score = GetScore ()

        if ( ( curr_best_score - score ) > kFallApartThreshold ) then
             print ( "Loss exceeded threshold" )
      
        elseif ( math.abs ( score - curr_best_score ) > 1e-3 ) then

            selection.SelectAll ()
            Wiggle ( 6 , 0.1 )

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

    save.Quickload ( kOriginalStructureOrNewBest )

end

function cleanup ()
   
    save.Quickload ( kOriginalStructureOrNewBest )
 
end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

Updated for New Chapters

For each secondary structure element : Idealize then Wiggle

Doesn't Wiggle if Idealize lost too many points as this probably means the protein exploded.

[Bruno Kestemont]

Great !