Recipe: Meh Mutate

created by joshmiller

Profile

• Name: Meh Mutate
• ID: 104216
• Shared with: Public
• Parent: None
• Children: None
• Created on: December 15, 2020 at 22:27 PM UTC
• Updated on: December 15, 2020 at 22:27 PM UTC
• Description:

  Supposed to be a faster, smarter mutate tool. Ended up being really laggy. Use at your own risk. Maybe someone will get some value out of it. Based on Maaa and Mutate No Wiggle.

Code

-- Smart Mutate by joshmiller
-- A faster, smarter mutate tool. Based on Maaa and Mutate No Wiggle.


-- MAIN
prompt = dialog.CreateDialog("Smart Mutate")
prompt.Select = dialog.AddCheckbox("Use Selection", false)
prompt.Orange = dialog.AddCheckbox("Orange Guard (No orange->blue)", true)
prompt.Malek = dialog.AddCheckbox("MALEK only for helices", true)
prompt.Sheets = dialog.AddCheckbox("YFWTVI only for sheets", true)
prompt.Shake = dialog.AddCheckbox("Shake", true)
prompt.Wiggle = dialog.AddCheckbox("Wiggle", true)
prompt.NoCys = dialog.AddCheckbox("Exclude Cys", true)
prompt.NoGly = dialog.AddCheckbox("Exclude Gly in Helix/Sheet", false)
prompt.NoPro = dialog.AddCheckbox("Exclude Pro in Helix/Sheet", false)
prompt.NoAla = dialog.AddCheckbox("Exclude Ala in Helix/Sheet", false)
prompt.NoST = dialog.AddCheckbox("Exclude S/T in Helices", false)
prompt.Iters = dialog.AddSlider("Iterations", 5, 1, 25, 0)
prompt.Cancel = dialog.AddButton("Cancel", 0)
prompt.Advanced = dialog.AddButton("Advanced", 1)
prompt.OK = dialog.AddButton("OK", 2)

advanced = dialog.CreateDialog("Smart Mutate - Advanced")
advanced.Inst = dialog.AddLabel("Use duplicate letters to increase chance for including")
advanced.IncludeAll = dialog.AddTextbox("Always Include", "")
advanced.ExcludeAll = dialog.AddTextbox("Always Exclude", "")
advanced.IncludeSheet = dialog.AddTextbox("Include in Sheets", "")
advanced.ExcludeSheet = dialog.AddTextbox("Exclude in Sheets", "")
advanced.IncludeHelix = dialog.AddTextbox("Include in Helices", "")
advanced.ExcludeHelix = dialog.AddTextbox("Exclude in Helices", "")
advanced.IncludeLoop = dialog.AddTextbox("Include in Loops", "")
advanced.ExcludeLoop = dialog.AddTextbox("Exclude in Loops", "")
advanced.Back = dialog.AddButton("Back", 1)

selectedOranges = {} -- map res index to SS, either H E L
selectedBlues = {} -- map res index to SS, either H E L

helixAllowed = "arndceqghilkmfpstwyv"
sheetAllowed = "arndceqghilkmfpstwyv"
loopAllowed = "arndceqghilkmfpstwyv"
helixAAs = ""
sheetAAs = ""
loopAAs = ""
helixAAsOrange = ""
sheetAAsOrange = ""
loopAAsOrange = ""

oranges = "acgilmfpwyv"

individualBestAAs = {}
individualBestScores = {}
bestSeq = ""
bestScore = -99999

function charInString(target, s)
    for c in string.gmatch(s, ".") do
        if target == c then
            return true
        end
    end
    return false
end

function doMain()
    
    useSelected = prompt.Select.value
    for i = 1, structure.GetCount() do
        if structure.IsMutable(i) and (not useSelected or selection.IsSelected(i)) then
            individualBestAAs[i] = structure.GetAminoAcid(i)
            individualBestScores[i] = current.GetSegmentEnergyScore(i)
			bestSeq = bestSeq .. individualBestAAs[i]
            if structure.IsHydrophobic(i) then
                selectedOranges[i] = structure.GetSecondaryStructure(i)
            else
                selectedBlues[i] = structure.GetSecondaryStructure(i)
            end
        end
    end
    
    helixAllowed = helixAllowed .. advanced.IncludeAll.value
    sheetAllowed = sheetAllowed .. advanced.IncludeAll.value
    loopAllowed = loopAllowed .. advanced.IncludeAll.value
    helixAllowed = helixAllowed .. advanced.IncludeHelix.value
    sheetAllowed = sheetAllowed .. advanced.IncludeSheet.value
    loopAllowed = loopAllowed .. advanced.IncludeLoop.value
    
    
    helixExclude = advanced.ExcludeHelix.value
    sheetExclude = advanced.ExcludeSheet.value
    loopExclude = advanced.ExcludeLoop.value
    
    if prompt.Malek.value then
        helixExclude = helixExclude .. "rndcqghifpstwyv"
    end
    if prompt.Sheets.value then
        sheetExclude = sheetExclude .. "arndceqghlkmps"
    end
    if prompt.NoCys.value then
        helixExclude = helixExclude .. "c"
        sheetExclude = sheetExclude .. "c"
        loopExclude = loopExclude .. "c"
    end
    if prompt.NoPro.value then
        helixExclude = helixExclude .. "p"
        sheetExclude = sheetExclude .. "p"
    end
    if prompt.NoGly.value then
        helixExclude = helixExclude .. "g"
        sheetExclude = sheetExclude .. "g"
    end
    if prompt.NoAla.value then
        helixExclude = helixExclude .. "a"
        sheetExclude = sheetExclude .. "a"
    end
    if prompt.NoST.value then
        helixExclude = helixExclude .. "st"
    end

    for c in string.gmatch(helixAllowed, ".") do
        if not charInString(c, helixExclude) then
            helixAAs = helixAAs .. c
            if charInString(c, oranges) then
                helixAAsOrange = helixAAsOrange .. c
            end
        end
    end
    
    for c in string.gmatch(sheetAllowed, ".") do
        if not charInString(c, sheetExclude) then
            sheetAAs = sheetAAs .. c
            if charInString(c, oranges) then
                sheetAAsOrange = sheetAAsOrange .. c
            end
        end
    end
    
    for c in string.gmatch(loopAllowed, ".") do
        if not charInString(c, loopExclude) then
            loopAAs = loopAAs .. c
            if charInString(c, oranges) then
                loopAAsOrange = loopAAsOrange .. c
            end
        end
    end
	
	print("Helix choices are " .. helixAAs)
	print("Sheet choices are " .. sheetAAs)
	print("Loop choices are " .. loopAAs)

    for ii = 1, prompt.Iters.value do
        oneIter()
    end
    
-- try restoring each individual seg to their best scoring AA, note overall score
    for index,SS in pairs(selectedOranges) do
        structure.SetAminoAcid(index, individualBestAAs[index])
    end
    
    for index,SS in pairs(selectedBlues) do
        structure.SetAminoAcid(index, individualBestAAs[index])
    end
    
    structure.ShakeSidechainsAll(1)
    structure.WiggleAll(1)
    
    if current.GetScore() > bestScore then
        return
    end

-- finally, restore to the best overall score, if it wasn't the individual sums 
    pointer = 1
	print("Best sequence was " .. bestSeq)
    for index,SS in pairs(selectedOranges) do
        structure.SetAminoAcid(index, string.sub(bestSeq, pointer, pointer))
        pointer = pointer + 1
    end
    
    for index,SS in pairs(selectedBlues) do
        structure.SetAminoAcid(index, string.sub(bestSeq, pointer, pointer))
        pointer = pointer + 1
    end
    
end

function oneIter()
    orangeGuard = prompt.Orange.value
    aaSeq = ""
    
    for index,SS in pairs(selectedOranges) do
        if "H" == SS then
            if orangeGuard then
                SelectableAAs = helixAAsOrange
            else
                SelectableAAs = helixAAs
            end
        elseif "E" == SS then
            if orangeGuard then
                SelectableAAs = sheetAAsOrange
            else
                SelectableAAs = sheetAAs
            end
        else
            if orangeGuard then
                SelectableAAs = loopAAsOrange
            else
                SelectableAAs = loopAAs
            end
        end
        AAindex = math.random(string.len(SelectableAAs))
        newAA = string.sub(SelectableAAs, AAindex, AAindex)
        aaSeq = aaSeq .. newAA
        structure.SetAminoAcid(index, newAA)
        if current.GetSegmentEnergyScore(index) > individualBestScores[index] then
            individualBestAAs[index] = newAA
            individualBestScores[index] = current.GetSegmentEnergyScore(index)
        end
    end
    
    for index,SS in pairs(selectedBlues) do
        if "H" == SS then
            SelectableAAs = helixAAs
        elseif "E" == SS then
            SelectableAAs = sheetAAs
        else
            SelectableAAs = loopAAs
        end
        
        AAindex = math.random(string.len(SelectableAAs))
        newAA = string.sub(SelectableAAs, AAindex, AAindex)
        aaSeq = aaSeq .. newAA
        structure.SetAminoAcid(index, newAA)
    end

-- Shake and Wiggle if desired
    if prompt.Shake.value then
        if prompt.Select.value then
            structure.ShakeSidechainsSelected(1)
        else
            structure.ShakeSidechainsAll(1)
        end
    end
    
    if prompt.Wiggle.value then
        if prompt.Select.value then
            structure.WiggleSelected(1)
        else
            structure.WiggleAll(1)
        end
    end
    
    
-- Save Scores
    for index,SS in pairs(selectedOranges) do
        if current.GetSegmentEnergyScore(index) > individualBestScores[index] then
            individualBestAAs[index] = newAA
            individualBestScores[index] = current.GetSegmentEnergyScore(index)
        end
    end
    
    for index,SS in pairs(selectedBlues) do
        if current.GetSegmentEnergyScore(index) > individualBestScores[index] then
            individualBestAAs[index] = newAA
            individualBestScores[index] = current.GetSegmentEnergyScore(index)
        end
    end
    
    if current.GetScore() > bestScore then
        bestSeq = aaSeq
        bestScore = current.GetScore()
    end
end


function ShowPrompt()
    local buttonClick = dialog.Show(prompt)
    if buttonClick == 1 then
        if dialog.Show(advanced) then
            ShowPrompt()
        end
    end
    if buttonClick == 2 then
        doMain()
    end
end

ShowPrompt()