Recipe: Local Mutate 4.1 Neural Mutate

created by Joanna_H

Profile

• Name: Local Mutate 4.1 Neural Mutate
• ID: 108180
• Shared with: Public
• Parent: None
• Children:
  • Local Mutate 4.1 Neural Mutate Fixed
• Created on: January 19, 2023 at 11:50 AM UTC
• Updated on: January 19, 2023 at 11:50 AM UTC
• Description:

  Local Mutate with Neural Mutate instead of standard Mutate

Code

min_residue = 1
max_residue =  999
n_residues = 0
n_mutations = 0

delta_residue = 9
kMaxDelta = 20

best_score = 0

clash_importance_during_modify = 0.09
packing_importance_during_modify = 1.0
hiding_importance_during_modify = 1.0
pairwise_importance_during_modify = 1.0
backboneHbond_importance_during_modify = 1.0
sidechainHbond_importance_during_modify = 1.0

kWiggleIterations = 15 

modify_count = 10

score_type = 1

loss_from_modify = {}

original_residues = {}
new_residues = {}

scores = {}
ids = {}

start_time = 0

wiggle_sidechains_first = false

--    Amino acids. Hydrophobics first.

single_letter_codes = { "g","a","v","l","i","m","f","w","p","s","t","c","y","n","q","d","e","k","r","h"}
three_letter_codes  = { "Gly","Ala","Val","Leu","Ile","Met","Phe","Trp","Pro","Ser","Thr","Cys","Tyr","Asn","Gln","Asp","Glu","Lys","Arg","His"}

        -- Use of quicksave slots

kOriginalStructureOrNewBest = 10
base_primary_sequence = {}
n_sequence_changes = 0

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 () 

    end

    return score

end

function aa1_to_aa3 ( k )

  for  j = 1, 20 do
        if ( k == single_letter_codes [  j ] ) then
            return three_letter_codes [  j  ]
        end
    end

    return "Unk"

end

function get_aa3 ( i )

    k = structure.GetAminoAcid (  i )

    for  j = 1, 20 do
        if ( k == single_letter_codes [  j ] ) then
            return three_letter_codes [  j  ]
        end
    end

    return "Unk"

end

function GetBasePrimarySequence ()

    for i = 1, n_residues do
        base_primary_sequence [ i ] = structure.GetAminoAcid ( i )
    end

end

function GetNumberOfPrimarySequenceChanges ()

    n_changes = 0
    for i = 1, n_residues do
        if ( base_primary_sequence [ i ] ~= structure.GetAminoAcid ( i ) ) then
            n_changes = n_changes + 1
        end
    end

    return n_changes
end


function ShellSort ()

-- Adapted from Numerical Recipes in C

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

    repeat

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

        for i = inc + 1 ,  n_residues do

            v =  scores [  i  ]
            w = ids [ i ]

            j = i

            flag = false 

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

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

            end

            scores [ j ]  = v
            ids [ j ] = w
        end

    until  inc  <= 1

end


function PostModify ( i )

    behavior.SetClashImportance ( 1.0 )
    behavior.SetPackingImportance ( 1.0 )
    behavior.SetHidingImportance ( 1.0 )
    behavior.SetPairwiseImportance ( 1.0 )
    behavior.SetBackboneHBondImportance ( 1.0 )
    behavior.SetSidechainHBondImportance ( 1.0 )
 
    selection.SelectAll ()
    if ( wiggle_sidechains_first == true ) then
        structure.WiggleSelected ( 1 , false , true )    -- sidechains
    end
 
    score_before_wiggle = GetScore ()
   
    structure.WiggleSelected ( kWiggleIterations )        
    score_after_wiggle = GetScore ()

end


function MutateResidue ( i  )

    local	j
    local 	k

    save.Quickload ( kOriginalStructureOrNewBest )

     for  j = 1 , n_residues do
        scores [ j ] = structure.GetDistance ( i , j )
        ids [ j ] = j
    end 

    ShellSort ()

    selection.DeselectAll ()
    for j = 1 , modify_count do
        selection.Select ( ids [ j ] )
    end

    behavior.SetClashImportance ( clash_importance_during_modify )
    behavior.SetPackingImportance ( packing_importance_during_modify )
    behavior.SetHidingImportance ( hiding_importance_during_modify )
    behavior.SetPairwiseImportance ( pairwise_importance_during_modify )
    behavior.SetBackboneHBondImportance ( backboneHbond_importance_during_modify )
    behavior.SetSidechainHBondImportance ( sidechainHbond_importance_during_modify )
 
    structure.NeuralNetMutateSidechainsSelected ()  

    score = GetScore ()
    table.insert ( loss_from_modify , best_score - score )

    n_mutations = GetNumberOfPrimarySequenceChanges ()

 --   print ( "Hid " .. r3 ( scores [ modify_count ] ) .. " lim " .. r3 ( best_score - score ) .. "  nc " .. n_mutations )
    print (  "      lom " .. r3 ( best_score - score ) .. "  nc " .. n_mutations )


    for k = 1, n_residues do
        if ( base_primary_sequence [ k ] ~= structure.GetAminoAcid ( k ) ) then
            print ( "         " .. k .. "  "  .. aa1_to_aa3 (  base_primary_sequence [ k ] ) .. " -> " .. aa1_to_aa3 ( structure.GetAminoAcid ( k ) ) )
        end
    end


    if ( math.abs ( score - best_score ) > 0.5 ) then
        PostModify ( i )

        score = GetScore ()
        if ( score > best_score ) then

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

    end

end

function MutateAll ()

    n = 1

    for start_idx = 1 , delta_residue do

        i = min_residue - 1 + start_idx
        
        while ( i <= max_residue ) do

            print ( get_aa3 (i) .. " " .. i .. " (" .. n .. "/" .. max_residue - min_residue + 1 .. ")" )

            MutateResidue ( i )
            i = i + delta_residue
            n = n + 1
        end

    end

end

function GetOptionalParameters ()

    local dlog = dialog.CreateDialog ( "Options" )

    dlog.pidm = dialog.AddSlider ( "Packing importance" , packing_importance_during_modify , 0 , 3.0 , 2 )  
    dlog.hidm = dialog.AddSlider ( "Hiding importance" , hiding_importance_during_modify , 0 , 3.0 , 2 )  
    dlog.widm = dialog.AddSlider ( "Pairwise importance" , pairwise_importance_during_modify , 0 , 3.0 , 2 )  
    dlog.bidm = dialog.AddSlider ( "Backbone hbond importance" , backboneHbond_importance_during_modify , 0 , 3.0 , 2 )  
    dlog.sidm = dialog.AddSlider ( "Sidechain hbond importance" , sidechainHbond_importance_during_modify , 0 , 3.0 , 2 )  

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

    if ( dialog.Show ( dlog ) > 0 ) then
    
        packing_importance_during_modify = dlog.pidm.value
        hiding_importance_during_modify = dlog.hidm.value
        pairwise_importance_during_modify = dlog.widm.value
        backboneHbond_importance_during_modify = dlog.bidm.value
        sidechainHbond_importance_during_modify = dlog.sidm.value
 
        return true
      else
        return false
    end

end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "Local Mutate 4.1 Neural Mutate" )

    dlog.min_residue = dialog.AddSlider ( "Min residue" , min_residue , 1 , n_residues , 0 )  
    dlog.max_residue = dialog.AddSlider ( "Max residue" , max_residue , 1 , n_residues , 0 )  
    dlog.delta_residue = dialog.AddSlider ( "Delta residue" , delta_residue  , 1 , kMaxDelta , 0 )  
    dlog.cidm = dialog.AddSlider ( "Clash importance" , clash_importance_during_modify , 0 , 1.0 , 2 )  
    dlog.modify_count = dialog.AddSlider ( "Modify count" , modify_count , 1 , 40 , 0 )
   
    dlog.ok = dialog.AddButton ( "OK" , 1 )
    dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
    dlog.other_options = dialog.AddButton ( "Other options" , 2 )

    return_code = dialog.Show ( dlog )

    if ( return_code > 0 ) then
    
        min_residue = dlog.min_residue.value
        max_residue = dlog.max_residue.value
        delta_residue = dlog.delta_residue.value
        clash_importance_during_modify = dlog.cidm.value
        modify_count = dlog.modify_count.value
 
    end
    
    return return_code

end

function main ()

    band.DisableAll ()
    n_residues = structure.GetCount ()
 
    -- Trim off locked terminal sequences as a UI convenience
    
    min_residue = 1
    while ( ( structure.IsLocked ( min_residue ) == true ) and ( min_residue <= n_residues ) ) do
      min_residue = min_residue + 1
    end
    
    max_residue = n_residues
    while ( ( structure.IsLocked ( max_residue ) == true ) and ( max_residue >= 1 ) ) do
      max_residue = max_residue - 1
    end  

    save.Quicksave ( kOriginalStructureOrNewBest )
    GetBasePrimarySequence ()

    repeat
       dialog_code = GetParameters ()
       if ( dialog_code == 2 ) then
           GetOptionalParameters ()
       end
    until ( dialog_code < 2 )

    if ( dialog_code == 0 ) then
        return
    end

    print ( "Local Mutate 4.1 Neural Mutate" )
 
    max_residue = math.min ( n_residues , max_residue )
    min_residue = math.max ( 1 , min_residue )

    print  ( "Mutate range " .. min_residue .. " to " .. max_residue )
    if ( max_residue < min_residue ) then
        print ( "Mutate range error." )
        return
    end
 
    print  ( "Delta " .. delta_residue )
    
    print ( "Clashing importance " .. r3 ( clash_importance_during_modify ) )
    print ( "Packing importance " .. r3 ( packing_importance_during_modify ) )
    print ( "Hiding importance " .. r3 ( hiding_importance_during_modify ) )
    print ( "Pairwise importance " .. r3 ( pairwise_importance_during_modify ) )
    print ( "Backbone Hbond importance " .. r3 ( backboneHbond_importance_during_modify ) )
    print ( "Sidechain Hbond importance " .. r3 ( sidechainHbond_importance_during_modify ) )
    
    print  ( "CI on modify " .. r3 ( clash_importance_during_modify ) )
    print  ( "Modify count " .. modify_count )
    print  ( "" )

    best_score = GetScore ()
    print (  "Start  score : " .. r3 ( best_score ) )

    for i = 1 , n_residues do
        original_residues [ i ] = structure.GetAminoAcid ( i )
    end

    if ( ( math.abs ( packing_importance_during_modify ) - 1 > 1e-3 ) or 
         ( math.abs ( hiding_importance_during_modify ) - 1 > 1e-3 ) or 
         ( math.abs ( pairwise_importance_during_modify ) - 1 > 1e-3 ) or 
         ( math.abs ( backboneHbond_importance_during_modify ) - 1 > 1e-3 ) or 
         ( math.abs ( sidechainHbond_importance_during_modify ) - 1 > 1e-3 ) ) then 
       print ( "" )
       print ( "MAKE SURE Recipe Score Modding IS CHECKED" )
       print ( "" )
    end
    
    start_time = os.time ()

    MutateAll ()

    cleanup ()

end

function cleanup ()
   
    print ( "Cleaning up" )
   
    behavior.SetClashImportance ( 1.0 )
    behavior.SetPackingImportance ( 1.0 )
    behavior.SetHidingImportance ( 1.0 )
    behavior.SetPairwiseImportance ( 1.0 )
    behavior.SetBackboneHBondImportance ( 1.0 )
    behavior.SetSidechainHBondImportance ( 1.0 )

    save.Quickload ( kOriginalStructureOrNewBest )

    selection.SelectAll ()
    band.EnableAll ()

    if ( #loss_from_modify > 1 ) then
        table.sort ( loss_from_modify )
        mid_pt = math.ceil ( #loss_from_modify / 2 )
        print ( "Median loss from modify " .. r3 ( loss_from_modify [ mid_pt ] ) )
     end

    for i = 1 , n_residues do
        new_residues [ i ] = structure.GetAminoAcid ( i )
    end

    for i = 1 , n_residues do
        if ( new_residues [ i ] ~= original_residues [ i ] ) then
            print ( i .. " : " .. aa1_to_aa3 ( original_residues  [ i ]  ) .. " -> " .. aa1_to_aa3 ( new_residues  [ i ] ) )
        end
    end

    end_time = os.time ()
    print ( "Elapsed time : " .. os.difftime ( end_time , start_time ) .. " secs" )

end

--main ()
xpcall ( main , cleanup )

Comments

[Joanna_H]

Whoops… Accidently pressed publish, not even sure if this is gonna work effectively yet.