Recipe: Mutate No Wiggle 1.3.2 -- Brow42

created by bertro

Profile

• Name: Mutate No Wiggle 1.3.2 -- Brow42
• ID: 102991
• Shared with: Public
• Parent: Mutate No Wiggle 1.3.1 -- Brow42
• Children:
  • Mutate No Wiggle 1.3.3 -- Brow42 thr ok loops
  • Mutate No Wiggle 1.3.2 -- Brow42 (SG)
• Created on: January 13, 2019 at 14:06 PM UTC
• Updated on: January 13, 2019 at 14:06 PM UTC
• Description:

  Brute Force Mutator, but doesn't wiggle, stabilize, or fuze. Keeps best AA for each spot. Good for slow design puzzles. Has options for restricting mutations. 1.2.1 bans alanines. 1.3 re-allows p,g,a,t for loops.

Code

--[[
 * Mutate No Wiggle -- Brow42
  * Original Author: Brow42

  * Version 1.0 Sept 6 2014

  * Brute-force mutator without the wiggle...for
  * puzzles where wiggle is too slow.
  
  * Also has options to restrict which amino acids
  * are mutated, and to what.  For example, prolines
  * and glycines won't be added, and cysteines won't
  * be touched.
  
  * Automatically does all mutables from worst to best
  * scoring, but range can be set manually, or via
  * selection/freeze before you run the script.
  
  * This script uses strings instead of tables for AAs.
  *
  * Version 1.02 -- Republished under new id
  *
  * Version 1.1 Oct 31 2014 Brow42
  *
  * Added pause to allow GUI to function. Added timing info
  * Added option to remove unwanted residues (from Googol30)
  * Added trap for User Cancel
  *
  * Version 1.1.1 May 14 2015 Brow42
  *
  * Allowed mutation of locked segments as requested by LociOling
  *
  * Version 1.2 May 18 2015 Brow 42
  *
  * Added options to quickly select only hydrophillics for bonding
  * Added more options to select/exclude polar and aliphatic AAs
  * Rearranged menus to accomodate more options
  * More error checking, such as empty mutate lists
  *
  * Version 1.21 July 30 2015
  *
  * Added option to eliminate alanines
  *
  * Version 1.3 Nov 23 2015
  *
  * Added option to allow aa's in loops
  * Recoded so each SS has it's own allow/deny.
  *
  * Version 1.3.1 Nov 30 2015
  *
  * Bug fix to aas array.
  *
  * Version 1.3.2 Jan 13 2019
  * Wbertro
  * Added threonine
  
--]]
NSeg = structure.GetCount()
title = "Brute Force Mutate No-Wiggle 1.3.1"

options = { cok=true, pok=true, gok=true, aok=true, tok=true, keepc=false, keepp=false, keepg = false, keept = false,
    keephydro=false, charged=true, rings=true, custom="", range="", removeaa=false,
    lockedok=true, philliconly=false, phobiconly=false, phillic=true, phobic=true,
    anyloop=false}

-- Gah. All the options have to be in the dialog, so these options are not in the options table
guitext_template = "%0.2f seconds every %d mutations"
pause = 5
delay = 0.1
options["gui"] = guitext_template:format(delay,pause)

-- Menu Button Enums
OKAY=1
CANCEL=0
SELECT=2
ABOUT=3
AASELECT=4
CLEAR=5
ALL=6
REPEAT=-1
function MainMenu()
    local d = dialog.CreateDialog(title)
    if options.custom == '' then
        d["label1"] = dialog.AddLabel("AA Selection shortcuts (or use button below).")
        d["philliconly"] = dialog.AddCheckbox("Hydrophilic (blue) only (no phobics).",options.philliconly)
        d["phobiconly"] = dialog.AddCheckbox("Hydrophobic (orange) only (no phillics).",options.phobiconly)
    else
        d["label1"] = dialog.AddLabel("AAs have been selected on the AA Allowed page.")
    end
    d["lable2"] = dialog.AddLabel("Don't change these AAs:")
    d["keepc"] = dialog.AddCheckbox("cysteine",options.keepc)
    d["keepp"] = dialog.AddCheckbox("proline",options.keepp)
    d["keepg"] = dialog.AddCheckbox("glycine",options.keepg)
    d["keept"] = dialog.AddCheckbox("threonine",options.keept)
    d["range"] = dialog.AddTextbox("Where:",options.range)
    d["removeaa"] = dialog.AddCheckbox("Remove AAs not marked allowed or don't change",options.removeaa)
    d["keephydro"] = dialog.AddCheckbox("Preserve Hydrophobicity",options.keephydro)
    d["gui"] = dialog.AddTextbox("GUI Saver: Wait",options.gui)
    d["ok"] = dialog.AddButton("OK",OKAY)
    d["cancel"] = dialog.AddButton("Cancel",CANCEL)
    d["where"] = dialog.AddButton("Select",SELECT)
    d["aaselect"] = dialog.AddButton("Allow AA",AASELECT)
    local rc = dialog.Show(d)
    for u,v in pairs(options) do
        pcall(function() options[u] = d[u].value end) -- using scoping so I don't have to pass any variable names
    end
    if options.philliconly and options.phobiconly then
        ErrorMessage("Don't check both phillic-only and phobic-only!","AA Selection")
        rc = REPEAT
    end
    segs,err = RangeToList(ParseRange(options.range))
    if err ~= "" then ErrorMessage(err,"Range Input") rc = REPEAT end
    err = ParseWait(options.gui)
    if err then ErrorMessage(err,"GUI Saver Delay Parameters") rc = REPEAT end

    -- change how allowed AA panel looks
    if options.philliconly then
        options.cok = false
        options.pok = false
        options.gok = false
        options.aok = false
        options.tok = false
        options.phobic = false
        options.rings = false
    end
    if options.phobiconly then
        options.charged = false
        options.phillic = false
    end

    return rc, MainMenu
end

function AASelect()
    local d = dialog.CreateDialog(title)
    if options.custom == '' then
        d["label1"] = dialog.AddLabel("Include these as allowed AA (previous page overrides):")
        d["cok"] = dialog.AddCheckbox("cysteine",options.cok)
        d["pok"] = dialog.AddCheckbox("proline",options.pok)
        d["gok"] = dialog.AddCheckbox("glycine",options.gok)
        d["aok"] = dialog.AddCheckbox("alanine",options.aok)
        d["tok"] = dialog.AddCheckbox("threonine",options.tok)
        d["anyloop"] = dialog.AddCheckbox("But allow ala, pro, gly in loops anyways",options.anyloop)
        d["charged"] = dialog.AddCheckbox("charged hydrophillics",options.charged)
        d["phillic"] = dialog.AddCheckbox("other (polar) hydrophillics",options.phillic)
        d["rings"] = dialog.AddCheckbox("rings (aromatic) hydrophobics: phen, tryp, tyr",options.rings)
        d["phobic"] = dialog.AddCheckbox("other (aliphatic, branched, not c,p,g) hydrophobics", options.phobic)
        d["label2"] = dialog.AddLabel("Or, specify AA (overrides all checkboxes):")
    else
        dialog.AddLabels(d,{"AAs have been selected below.","Clear to see options again."})
    end

    d["custom"] = dialog.AddTextbox("AAs",options.custom)
    d["ok"] = dialog.AddButton("Accept",REPEAT)
    if options.custom ~= '' then
        d["clear"] = dialog.AddButton("Clear",CLEAR)
    else
        d["all"] = dialog.AddButton("Allow All",ALL)
    end
    d["help"] = dialog.AddButton("About",ABOUT)
    local rc = dialog.Show(d)
    
    if rc == CANCEL then return rc end
    
    if rc == CLEAR then
        options.custom = ''
        return REPEAT, AASelect
    end
    
    if rc == ALL then
        options.cok = true
        options.pok = true
        options.gok = true
        options.aok = true
        options.tok = true
        options.charged = true
        options.rings = true
        options.phillic = true
        options.phobic = true
        options.phobiconly = false
        options.philliconly = false
        return REPEAT, MainMenu
    end
    
    for u,v in pairs(options) do
        pcall(function() options[u] = d[u].value end) -- using scoping so I don't have to pass any variable names
    end
    
    if options.custom ~= "" and options.custom:find("[^"..all_aa..all_aa:upper().."]") then
        ErrorMessage("You gave something other than one of the 20 AAs.")
        return REPEAT, AASelect
    end

    return rc, MainMenu
end
-- ================================== Begin New Dialog Library Functions
-- Add a wall of text from a table
function dialog.AddLabels(d,msg,nlabels) -- pass in # of existing autolabels
    local nlabels = nlabels or #(d._Order or {}) -- default, valid if never delete dialog elements
    if type(msg) == 'string' then
        msg = { msg }
    end
    for i = 1,#msg do
        d['autolabel'..tostring(i+nlabels)] = dialog.AddLabel(msg[i])
    end
end
-- Create but don't display a wall of text and 1 or 2 buttons
function dialog.CreateMessageBox(msg,title,buttontext1,buttontext0,buttontext2)
    title = title or ''
    local d = dialog.CreateDialog(title)
    dialog.AddLabels(d,msg)
    buttontext1 = buttontext1 or 'Ok'
    d.button = dialog.AddButton(buttontext1,1)
    if buttontext2 ~= nil then d.button2 = dialog.AddButton(buttontext2,2) end
    if buttontext0 ~= nil then d.button0 = dialog.AddButton(buttontext0,0) end
    return d
end
-- Display a dialog box
function dialog.ShowMessageBox(msg,title,buttontext1,buttontext0,buttontext2)
    return dialog.Show(dialog.CreateMessageBox(msg,title,buttontext1,buttontext0,buttontext2))
end
-- Display a box AND print to the output
function ErrorMessage(msg,title)
    if type(msg) == 'string' then
        msg = { msg }
    end
    for i = 1,#msg do
        print(msg[i])
    end
    return dialog.ShowMessageBox(msg,title)
end
-- ======================================= End Dialog Functions
function About()
    local rc = dialog.ShowMessageBox( {
        "This recipe mutates all mutables to all amino acids",
        "keeping the best score for each segment. It does this",
        "from worst score to best score. NO WIGGLE IS DONE.",
        "",
        "Skipping wiggle allows this to work on puzzles with",
        "very slow wiggle, but probably won't find the same",
        "combination as one of the regular mutation scripts.",
        "",
        "You can control which segments are mutated, and to",
        "what types of amino acids. In particular, you can",
        "prevent prolines and glycines from being added. You",
        "can also prevent cysteines from being mutated to save",
        "bridges. You can restrict mutations to the same",
        "hydrophobicity."
        },title,"Back")
    if rc == CANCEL then return CANCEL end -- cancel script
    return REPEAT, AASelect
end

-- Turn selection or frozen into ranges and range string
RETURN=REPEAT
function Where()
    local d = dialog.CreateDialog(title)
    dialog.AddLabels(d,
        {"Have you selected segments to muate with","the selection or freeze tool?"})
    d.select = dialog.AddButton("Selection",1)
    d.freeze = dialog.AddButton("Freeze",2)
    d.nope = dialog.AddButton("Nope",RETURN)
    -- 0 is window close (cancel script)
    local rc = dialog.Show(d)
    if rc == CANCEL or rc == RETURN then return rc, MainMenu end
    local tmp = {selection.IsSelected, freeze.IsFrozen}
    UserSelect = tmp[rc] -- pretty name because it shows up in the GUI
    
    local appending = false
    local s
    local range
    local list = {}
    for i = 1, NSeg do
        s = UserSelect(i)
        if s then
            if appending then range[2] = i
            else
                range = {i,i}
                list[#list+1] = range
                appending = true
            end
        else
            if appending then appending = false end
        end
    end
    for i = 1,#list do
        if list[i][1] == list[i][2] then list[i] = tostring(list[i][1])
        else list[i] = tostring(list[i][1]).."-"..tostring(list[i][2]) end
    end
    options.range = table.concat(list," ")
    return REPEAT, MainMenu
end

-- sort by score, also filter by mutability
function SortSegments(segs)
    local scores = {}
    local keys = {}

    for j = 1,#segs do
        i = segs[j]
        ss = structure.GetSecondaryStructure(i):upper()
        if structure.IsMutable(i) and (options.lockedok or not structure.IsLocked(i) and
          ( ss=='E' or ss=='H' or ss=='L') ) then
            s = current.GetSegmentEnergyScore(i) - current.GetSegmentEnergySubscore(i,'reference')
            scores[s] = i -- scores map to segments
            keys[#keys+1] = s -- keys are scores
        end
    end
    table.sort(keys)

    for i = 1,#keys do
        keys[i] = scores[keys[i]] -- replace score with segment
    end
    return keys
end

-- Turn a range string into a list of ranges (allows negatives, skips non-numerica)
function ParseRange(str)
    local ranges = {}
    local index
    while true do
        local a,b,x = str:find("(%-?%d+)") -- next number
        local c,d,y,z = str:find("(%d+)%s*%-%s*(%d+)") -- next range
        if a and ( c == nil or a < c ) then
            x = tonumber(x)
            ranges[#ranges+1] = { x, x }
            index = b+1
        elseif c then
            y = tonumber(y)
            z = tonumber(z)
            ranges[#ranges+1] = { y, z }
            index = d+1
        else
            break
        end
        str = str:sub(index+1,str:len())
    end
    return ranges
end

-- Parse the GUI Saver text options
function ParseWait(str)
    local numpat = "(%-?%d*%.?%d*)"
    local notnumpat = "[^%d-.]*"
    local _,_,a,b = str:find(notnumpat..numpat..notnumpat..numpat)
    if options.gui == '' then
        pause,delay = 0,0
        return
    end
    options["gui"] = guitext_template:format(delay,pause)
    local errstate = a == '' or a == nil or b == '' or b == nil
    if errstate ~= false then return
        {"To give the GUI a chance to draw, you can wait a",
         "certain amount of time after a fixed number of",
         "mutations. Just specify either 0 seconds or 0 mutations",
         "to go as fast as possible."
         }
    end
    a,b = tonumber(a),tonumber(b) -- doesn't seem like this can crash on any input matching numpat
    errstate = a == '' or a == nil or b == '' or b == nil -- Something a little goofy having to check this twice
    if errstate ~= false then
        return
        {"To give the GUI a chance to draw, you can wait a",
         "certain amount of time after a fixed number of",
         "mutations. Just specify either 0 seconds or 0 mutations",
         "to go as fast as possible."
         }
    end
    if a < 0 or b < 0 then
        return {"Looks like you entered a negative number.","Zero or greater only please."}
    end
    if a < 0.01 and b > 0 then
        return {"Did I say zero? Actually, 0.01 seconds is the","shortest delay."}
    end
    -- all good
    pause,delay = b,a
    options["gui"] = guitext_template:format(delay,pause)

    return
end

-- Turn list of ranges into a list of segments
function RangeToList(ranges)
    if #ranges == 0 then ranges = {{1,NSeg}} end
    local list = {}
    local err = ""
    for i = 1,#ranges do
        local a,b = unpack(ranges[i])
        if a < 1 or a > NSeg then return list,tostring(a).." is out of range." end
        if b < 1 or b > NSeg then return list,tostring(b).." is out of range." end
        for j = a,b do list[j] = true end
    end
    local list2 = {}
    for u,v in pairs(list) do list2[#list2+1] = u end
    table.sort(list2)
    return list2,err
end

-- =================== Begin Main ==========================
print(title)
print (puzzle.GetName(),current.GetScore())

-- different classes of AAs
charged = "rkdeh"
philic = "qnst" -- excluding charged
phobic = "cmailvpg" -- excluding rings
rings = "fwy"

all_aa = charged..philic..phobic..rings

Menu = MainMenu -- user will see variable name

aas = ''

while aas == '' do
    repeat
        rc,Menu = Menu()
        if rc == CANCEL then print ("User exit.") return end
        if rc == SELECT then Menu = Where end
        if rc == ABOUT then Menu = About end
        if rc == AASELECT then Menu = AASelect end
        if rc == CANCEL then return end -- cancels from child dialogs
    until rc == OKAY

    if options.custom ~= "" then
        aas = options.custom
    else
        if options.phillic and not options.phobiconly then aas = aas..philic end
        if options.phobic and not options.philliconly then aas = aas..phobic end
        if options.charged and not options.phobiconly then aas = aas..charged end
        if options.rings and not options.philliconly then aas = aas..rings end
        if not options.cok then aas = aas:gsub('c','') end
        if not options.pok then aas = aas:gsub('p','') end
        if not options.gok then aas = aas:gsub('g','') end
        if not options.aok then aas = aas:gsub('a','') end
        if not options.tok then aas = aas:gsub('t','') end
    end

    if aas == '' then
        ErrorMessage("You've excluded all the AAs from your mutation list!","AA Selection")
    end
end

aas = { H= aas, E=aas, L=aas }

if options.custom == '' and options.anyloop then
    print ("Re-enabling p,g,a for loops if they were disabled in general...")
    if not options.pok then aas['L'] = aas['L']..'p' end
    if not options.gok then aas['L'] = aas['L']..'g' end
    if not options.aok then aas['L'] = aas['L']..'a' end
    if not options.tok then aas['L'] = aas['L']..'t' end
end

if delay == 0 or pause == 0 then
    print ("No delay between mutations.")
else
    print ("Waiting "..options.gui)
    print ("Maximum possible mutation rate:",pause/delay,"Mutations/second")
end

print("Allowed AAs:")
print (" Helix:",aas['H']:upper())
print ("Sheet:",aas['E']:upper())
print (" Loop:",aas['L']:upper())

-- okay add in the subtypes, for checking type later
philic = philic..charged
phobic = phobic..rings

-- build preserve  list from the checkboxes
preserve = ""
if options.keepc then preserve = preserve.."c" end
if options.keepp then preserve = preserve.."p" end
if options.keepg then preserve = preserve.."g" end
if options.keept then preserve = preserve.."t" end


start = current.GetScore()
order = SortSegments(segs)

start_time = os.time()
n_mutations = 0

speedcheck_n = 100 -- every 100 mutations (5 segments?)
speedcheck_s = 120 -- every 2 minutes
lastspeedcheck_s = start_time
lastspeedcheck_n = 0
function PrintSpeedCheck(force)
    local t = os.time() -- probably won't wrap around
    local dt = t - start_time
    if force or t-lastspeedcheck_s > speedcheck_s or n_mutations-lastspeedcheck_n > speedcheck_n then
        lastspeedcheck_s = t
        lastspeedcheck_n = n_mutations
        print ("Average mutation rate:",n_mutations/dt,"mutations/second")
    end
end

function Main()
    for i = 1,#order do
        recentbest.Save()
        s = current.GetScore()
        iSeg = order[i] -- Not Local
        origaa = structure.GetAminoAcid(iSeg) -- Not Local
        if preserve:find(origaa) == nil then -- skip AAs in keep list
            first_mutation = true -- first mutation this segment
            ss = structure.GetSecondaryStructure(iSeg):upper()
            for j =1,aas[ss]:len() do
                aa = aas[ss]:sub(j,j)
                hydrook = not options.keephydro or 
                    (structure.IsHydrophobic(iSeg) and phobic:find(aa) ~= nil) or 
                    (not structure.IsHydrophobic(iSeg) and philic:find(aa) ~= nil)
                if hydrook then -- if correct type, else skip
                    structure.SetAminoAcid(iSeg,aa)
                    n_mutations = n_mutations + 1
                    if first_mutation and options.removeaa == true and aas[ss]:find(origaa) == nil then -- if removing non-allowed AAs
                        recentbest.Save() -- forget the original score of the unwanted aa, use this one
                    end
                    first_mutation = false
                end
                -- GUI pause here
                if delay > 0 and pause > 0 and n_mutations > 0 and n_mutations % pause == 0 then
                    t = os.clock()
                    repeat
                        dt = os.clock() - t -- watch out, clock() can wrap to 0
                    until dt > delay or dt < 0
                end
                PrintSpeedCheck(false)
            end
            recentbest.Restore()
            print( i, "of", #order, "Segment #", iSeg, origaa, "->", structure.GetAminoAcid(iSeg), "change", current.GetScore()-s )
        else
            print( i, "of", #order, "Segment #", iSeg, origaa, "skipped" )
        end
    end
end

function OnError(errmsg)
    if string.find(errmsg,"Cancelled") then
        print("User cancel. Loading recent best.")
        recentbest.Restore()
    else -- it's a real error, not a cancel
        print(errmsg)
    end
    return errmsg
end

rc, err = xpcall(Main,OnError)

if rc == true then
    print("Final score",current.GetScore(), current.GetScore()-start)
    PrintSpeedCheck(true)
end

Comments

[bertro]

Added threonine