Recipe: Migi Irradiator v1.0

created by Migi

Profile

• Name: Migi Irradiator v1.0
• ID: 103409
• Shared with: Public
• Parent: None
• Children: None
• Created on: April 14, 2020 at 17:20 PM UTC
• Updated on: April 14, 2020 at 17:20 PM UTC
• Description:

  Randomly mutates 1-2 segments and then fuzes, and keeps the result if the score didn't drop too much (or increased). The maximum allowable score drop slowly goes to zero over time. Don't use this recipe to gain points, use it to drift away from your current fold, either if you want to get out of a local optimum, if you want to let multiple instances diverge, or just if you want to explore the solution space a bit.

Code

--[[ 
  * Irradiator

  * Original Author: Migi
  * Version 1.0 April 10, 2020

  * Randomly mutates 1 or 2 amino acids, then fuzes.
  * Keeps mutations if they score "well enough" (but can lose score!)
  * Use this early on to let it "explore" the space of probabilities,
  * or when stuck in a local optimum (similar to Jolter),
  * or just if you want to let your solution "drift" from where it started.
]]--

version = '1.0'

print ( 'Irradiator v'..version )

math.randomseed(os.time())

initialClashImportance = behavior.GetClashImportance()
initialFiltersDisabled = behavior.GetFiltersDisabled()

nSegments = structure.GetCount ( )
mutableSegments = {}
mutableTo = {}
chains = {"g";"a";"v";"c";"p";"t";"s";"i";"l";"n";"d";"m";"h";"q";"e";"f";"k";"y";"r";"w"}
hydrophobicities = {0,41,76,49,-46,13,-5,99,97,-28,-55,74,8,-10,-31,100,-23,63,-14,97}

aaLetterToChainIndex={}
for k,v in pairs(chains) do
    aaLetterToChainIndex[v]=k
end

maxDrop = 100
settleTime = 7
scriptStartTime = os.time() -- updated again after config is set
quickSaveSlot = 33

curTriedMutation = ""

function showOptionsDialog()
    local dlog = dialog.CreateDialog ( "Irradiator Options" )
    dlog.text1 = dialog.AddLabel ( "Initial allowable score drop (at each step):" )
    dlog.maxDrop = dialog.AddSlider ( "Max score drop" , maxDrop , 0 , 500 , 0 )
    dlog.text2 = dialog.AddLabel ( "Allowable score drop slowly goes to zero, after" )
    dlog.settleTime = dialog.AddSlider ( "this many hours" , settleTime, 0 , 30 , 1 )
    
    dlog.ok = dialog.AddButton ( "OK" , 1 )
    dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
    
    if dialog.Show ( dlog ) then
        maxDrop = dlog.maxDrop.value
        settleTime = dlog.settleTime.value
        
        return true
    else
        return false
    end
end

function getScore()
    behavior.SetFiltersDisabled(false)
    score = current.GetScore ()
    behavior.SetFiltersDisabled(true)
    return score
end

function getCurMaxDrop()
    local timeD = os.difftime ( os.time () , scriptStartTime )
    local x = timeD / (settleTime * 60.0 * 60.0)
    if x >= 0.0 and x < 1.0 then
        return (1.0 - x) * (1.0 - x) * maxDrop
    else
        return 0.0
    end
end

function mutateRandomly(mutableSegment)
    local curAASegment = mutableSegments[mutableSegment]
    local curAA = structure.GetAminoAcid(curAASegment)
    local curAAIndex = aaLetterToChainIndex[curAA]
    while true do
        local randomAAIndex = mutableTo[mutableSegment][math.random(#(mutableTo[mutableSegment]))]
        local hydrophobicityDiff = math.abs(hydrophobicities[curAAIndex] - hydrophobicities[randomAAIndex])
        local randomAA = chains[randomAAIndex]
        if math.random() >= (hydrophobicityDiff / 150.0) and structure.CanMutate(curAASegment, randomAA) then
            structure.SetAminoAcid(curAASegment, randomAA)
            return curAASegment .. " to " .. randomAA
        end
    end
end

function main()
    save.Quicksave ( quickSaveSlot )
    local currentScore = getScore()
    
    showOptionsDialog()

    scriptStartTime = os.time()

    local curMaxDrop = maxDrop

    print( "Settings:" )
    print( "Initial max score drop: " .. maxDrop )
    print( "Settle time: " .. settleTime .. " hours" )
    print( "Initial score: " .. currentScore )
    
    print( "Calculating which segments can be mutated..." )

    selection.DeselectAll()
    
    for ii = 1, nSegments do
        local frzback, frzside = freeze.IsFrozen ( ii )
        if structure.IsMutable( ii ) and not frzside then
            local tt = {}
            for jj = 1, #chains do
                if structure.CanMutate ( ii, chains [ jj ] ) then
                    table.insert(tt, jj)
                end
            end
            if #tt == 0 then
                print( "Sidechain " .. ii .. " is supposedly mutable but CanMutate() always returns false?")
            elseif #tt == 1 then
                print( "Sidechain " .. ii .. " is supposedly mutable but only has 1 valid AA. Skipping...")
            else
                selection.Select(ii)
                table.insert(mutableSegments, ii)
                table.insert(mutableTo, tt)
            end
        end
    end

    numMutableSegments = #mutableSegments
    
    if numMutableSegments == 0 then
        print( "None found. Stopping script..." )
        return 0
    end
    
    print( "Done. Starting script..." )
    
    while true do
        local mutatedSegment = math.random(numMutableSegments)
        local bestSegment = 0
        local bestSegmentDist = 9999999.9
        if math.random() < 0.5 then
            for ii = 1, numMutableSegments do
                local accepted = true
                if ii == mutatedSegment then
                    accepted = false
                elseif ii == mutatedSegment-1 or ii == mutatedSegment+1 then
                    if math.random() < 0.85 then
                        accepted = false
                    end
                elseif ii == mutatedSegment-2 or ii == mutatedSegment+2 then
                    if math.random() < 0.8 then
                        accepted = false
                    end
                elseif ii == mutatedSegment-3 or ii == mutatedSegment+3 then
                    if math.random() < 0.75 then
                        accepted = false
                    end
                elseif ii == mutatedSegment-4 or ii == mutatedSegment+4 then
                    if math.random() < 0.7 then
                        accepted = false
                    end
                else
                    if math.random() < 0.3 then
                        accepted = false
                    end
                end
                if accepted then
                    local dist = structure.GetDistance(mutableSegments[mutatedSegment], mutableSegments[ii])
                    if dist < bestSegmentDist then
                        bestSegmentDist = dist
                        bestSegment = ii
                    end
                end
            end
        end
        
        curTriedMutation = mutateRandomly(mutatedSegment)
        if bestSegment ~= 0 then
            curTriedMutation = curTriedMutation .. " and " .. mutateRandomly(bestSegment)
        end
        
        behavior.SetFiltersDisabled(true)
        behavior.SetClashImportance ( 0.2 + math.random()*0.3 )
        structure.WiggleAll( 20 )
        behavior.SetClashImportance ( 0.7 + math.random() * 0.2 )
        structure.ShakeSidechainsAll( 1 )
        structure.WiggleAll( 20 )
        behavior.SetClashImportance ( 0.8 + math.random() * 0.2 )
        structure.MutateSidechainsSelected( 1 )
        behavior.SetClashImportance ( 1.0 )
        structure.WiggleAll( 20 )
        
        local s = getScore()
        
        if s >= currentScore - curMaxDrop then
            currentScore = s
            curMaxDrop = getCurMaxDrop()
            print( "Accepted mutation: " .. curTriedMutation )
            print( "New working score: " .. s .. ", new max drop: " .. curMaxDrop )
            save.Quicksave ( quickSaveSlot )
        else
            print( "Rejected mutation: " .. curTriedMutation .. ". Score: " .. s )
            save.Quickload( quickSaveSlot )
        end
    end
end

function ErrorHandler(errmsg)
    if string.find(errmsg, "Cancelled") then
        print( "Recipe stopped. Restoring last accepted fold." )
        print( "Run time: " .. os.difftime ( os.time () , scriptStartTime ) .. " seconds" )
        behavior.SetClashImportance(initialClashImportance)
        behavior.SetFiltersDisabled(initialFiltersDisabled)
        save.Quickload( quickSaveSlot )
    else
        print( "ERROR: " .. errmsg )
    end
end

xpcall( main, ErrorHandler )