Recipe: MicroIdealize 4.0

created by spvincent

Profile

• Name: MicroIdealize 4.0
• ID: 102027
• Shared with: Public
• Parent: None
• Children:
  • MicroIdealize 4.0 test
  • MicroIdealize 4.0 Loop
  • MicroIdealize_Sketchbook
  • MicroIdealize 5.0.1bis
• Created on: April 30, 2016 at 17:20 PM UTC
• Updated on: April 30, 2016 at 17:20 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

worst_first = true

score_type = 1
original_slow_filters_setting = 0

kDefaultWiggle = 12

sphere = {}
kSphereRadius = 10

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 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 GoSegment ( start_idx , end_idx )

    save.Quickload ( kOriginalStructureOrNewBest )

    if ( start_idx > 1 ) then
         structure.InsertCut ( start_idx )
    end

    if ( end_idx < n_residues ) then
        structure.InsertCut ( end_idx  )
    end

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

    if ( start_idx > 1 ) then
         structure.DeleteCut ( start_idx )
    end

    if ( end_idx < n_residues ) then
        structure.DeleteCut ( end_idx )
    end

    SphereSelect ( start_idx , end_idx )

    structure.WiggleSelected ( kDefaultWiggle )     

    score = GetScore ()

    if ( score > best_score ) then

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

    end
 
end

function Coprime ( n )

    local primes = {2,3,5,7,11,13,17,19,23,29,31,37,41,43,47,53,59,61,67,71,73,79,83,89,97,101}
    
    i = #primes
   -- find the highest prime < 70% of the residue count and which is coprime with the number of residues

    while ( i >= 1 ) do
        if ( primes [ i ] < n*0.7 and n % primes [ i ]  ~= 0 ) then
           return primes [ i ] 
       end

       i = i - 1

    end

    return 1

end


function pseudorandom ( score )

    -- Returns a pseudorandom number >= 0 and < 1.
    -- Based on the fractional part of the  score

    if ( score >= 0 ) then
      return  score % 1
     else
      return (-score ) % 1
    end

end

function Go ()

    local inc 

    max_possible_residue = max_residue - idealize_length + 1
    n_possible_segs = max_possible_residue - min_residue + 1
 
    r = pseudorandom ( best_score )
    start_idx = min_residue + n_possible_segs *  r
    start_idx = start_idx - start_idx % 1

    inc = Coprime ( n_possible_segs  )

    for  i = 1 , n_possible_segs do
         
       print ( start_idx .. "-" .. start_idx + idealize_length - 1 .. "  (" .. i .. "/" .. n_possible_segs .. ")" )
       GoSegment ( start_idx , start_idx + idealize_length - 1 )

        start_idx = start_idx + inc
        if ( start_idx >  max_possible_residue ) then
            start_idx =  start_idx - n_possible_segs
        end
        
     end

end

function ShellSort ( ids , sequence_scores , n )

    -- Adapted from Numerical Recipes in C

    local  inc = 1

    repeat
      inc = inc * 3 + 1
    until inc > n

    repeat

        inc = inc / 3
        inc = inc - inc % 1

        for i = inc + 1 , n do

            v = sequence_scores [ i ]
            w = ids [  i ]

            j = i
            flag = false

            while ( flag == false and sequence_scores [ j - inc ]  > v ) do

                sequence_scores [ j ] = sequence_scores [ j - inc ]
                ids [ j ] = ids [ j - inc ]

                j = j - inc

                if ( j <= inc ) then
                  flag = true
                end

            end

          sequence_scores [ j ] = v
           ids [ j ] = w

        end

    until inc <= 1

end

function GoWorstFirst ()

    ideality_scores = {}
    sequence_scores = {}
    ids = {}

    max_possible_residue = max_residue - idealize_length + 1
    n_possible_segs = max_possible_residue - min_residue + 1

    for i = min_residue , max_residue do
        ideality_scores [ i ] = current.GetSegmentEnergySubscore ( i , "ideality" )
--print ( i .. "  " .. r3 ( ideality_scores [ i ] ) )
    end

    idx = 1
    for i = min_residue , max_residue - idealize_length + 1 do

        total = 0

        for j = i , i + idealize_length - 1 do
            total = total + ideality_scores [ j ]
        end

        sequence_scores [ idx ] = total
        ids [ idx ] = i
--print ( idx .. "  " .. ids [ idx ] .. "  " .. r3 ( sequence_scores [ idx ] ) )
      
        idx = idx + 1
  
    end

    ShellSort ( ids , sequence_scores , max_possible_residue - min_residue + 1 )

    for  i = 1 , n_possible_segs do
 
--print ( i .. "  " .. ids [ i ] .. "  " .. r3 ( sequence_scores [ i ] ) )
        
       print (  ids [ i ] .. "-" ..  ids [ i ] + idealize_length - 1 .. "  (" .. i .. "/" .. n_possible_segs .. ")" )
       GoSegment ( ids [ i ] , ids [ i ]  + idealize_length - 1 )

    end

end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "MicroIdealize 4.0" )

    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.worst_first = dialog.AddCheckbox ( "Worst first" , worst_first )  

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

    dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 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
        worst_first  = dlog.worst_first.value

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

end


function main ()

    print (  "MicroIdealize 4.0" )

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

    n_residues = structure.GetCount ()

    original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()

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

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

    print ( "Length " .. idealize_length )

    if ( worst_first == false ) then
        Go ()
      else
        GoWorstFirst ()
    end

    cleanup ()

end

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

    behavior.SetSlowFiltersDisabled ( original_slow_filters_setting )
 
end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

Added a "Worst First" option which is enabled by default. If checked, segment sequences are sorted according to the sum of their ideality scores and the worst ones are processed first. This enables you to run the script and kill it after a few iterations (typically 10) when the script is no longer producing gains in the reasonable expectation that the script has gained whatever points is going to.

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

[angeltrouble]

Thank you so much, this recipe is fantastic.
I was reluctant to use cuts when aligning / setting up proteins because I never seemed to be able to solve the ideality issues without it blowing up, but not anymore!

[Bruno Kestemont]

in the options "Score type" 1 or 2

[LociOiling]

Score type 1 is normal scoring for puzzles without filters.

Score type 2 is for puzzles with filters. Score type 2 means filters are disabled during wiggle, but enabled before current.GetEnergyScore is called.

Score type 2 is selected by default if the recipe detects a filter bonus.