Recipe: Fibonacci Wiggle V3.1

created by TurtleByte

Profile

• Name: Fibonacci Wiggle V3.1
• ID: 104732
• Shared with: Public
• Parent: Fibonacci Wiggle V3
• Children: None
• Created on: April 11, 2021 at 04:55 AM UTC
• Updated on: April 11, 2021 at 04:55 AM UTC
• Description:

  Local wiggle sections of either increasing or decreasing size. ; Originally by Crashguard303. Translated to LuaV2 by joshmiller using LociOiling's MacroScanner.

Code

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-- Fibonacci Wiggle
--
-- Local wiggles segemnts of either increasing or decreasing size using
-- fibonacci numbers
--
-- V0 Originally by Crashguard303. 
-- V1 Translated to LuaV2 by joshmiller using LociOiling's MacroScanner. 
-- V2 Modification and simplification by PieThrower.
-- V3 Generated fib numbers based on size of protein, added versioning - TurtleByte
-- V3.1
--    Fixed bug where 1 was not in list of fib numbers
--    Fixed bug that allowed fib number generation to go past protein length
--    Added loop to repeat until gain < minGain, minGain set by user
--    Freeze segments re-enabled, controlled via dialog option
--    Localized and renamed Foldit functions
--    TurtleByte 4/10/2021
--------------------------------------------------------------------------------

--[[ TODO
- figure out what freezing was supposed to do
- add more verbose cleanup
- add more/better logging
]]--

--------------------------------------------------------------------------------

local shakeAll = structure.ShakeSidechainsAll
local wiggleSelected = structure.LocalWiggleSelected 

local deselectAll = selection.DeselectAll
local selRange = selection.SelectRange
local freezeSelected = freeze.FreezeSelected
local unfreezeAll = freeze.UnfreezeAll
local score = current.GetEnergyScore 

local isInc = false
local doFreeze = true
local shakeIters = 1
local wiggleIters = 25
local protLen = structure.GetCount()
local fiboNums = {1}
local fiboNumsStr = "1 "
local initialScore = score()
local bestScore = score()
local minGain = 0.001

-- Generate list of fib numbers up to the protein size
function fib()     
    if protLen == 0 then 
        fiboNums = {0}
        fiboNumsStr = "0"
    elseif protLen == 1 or protLen == 2 then 
        fiboNums = {1}
        fiboNumsStr = "1"
    else
        local fib, fib1, fib2 = 0, 1, 1
        while fib < protLen do 
            fib = fib1 + fib2
            fib1 = fib2
            fib2 = fib
            if fib <= protLen then 
                table.insert(fiboNums, fib) 
                fiboNumsStr = fiboNumsStr..fib.." "                
            end
        end
    end
end
    
function getParameters()
    dlg = dialog.CreateDialog("Fibonacci Wiggle")
    dlg.isInc = dialog.AddCheckbox("Small to Large", false)
    dlg.doFreeze = dialog.AddCheckbox("Do Freezes", true)
    dlg.wiggleIters = dialog.AddSlider("Wiggle Iterations", 10, 1, 25, 0)
    dlg.shakeIters = dialog.AddSlider("Shake Iterations", 1, 0, 10, 0)
    dlg.minGain = dialog.AddSlider("Min Gain", 0.001, 0.001, 1, 3)
    dlg.ok = dialog.AddButton("OK", 1)
    dlg.cancel = dialog.AddButton("Cancel", 0)

    if dialog.Show(dlg) > 0 then
        isInc = dlg.isInc.value
        doFreeze = dlg.doFreeze.value
        wiggleIters = dlg.wiggleIters.value
        shakeIters = dlg.shakeIters.value
        minGain = dlg.minGain.value
        return true
    else
        print("Program Cancelled")
    end
    return false
end

function freeze(len) 
    if len / 2 > 2 then
        for seg = math.floor (len / 2), protLen, len do
            deselectAll ()
            selRange ( seg, math.min (seg + len / 2 - 1, protLen) )
            freezeSelected ( true, true )
        end
    end
end

function wiggleLength (len)
    print("running with length", len)
    
    local currentScore, bestWiggleScore = score(), score()
    while true do
        if doFreeze then freeze(len) end

        for seg = 1, protLen, len do
            deselectAll ()
            selRange ( seg, math.min (seg + len - 1, protLen) )
            wiggleSelected ( wiggleIters )
        end
        
        if doFreeze then unfreezeAll () end
        
        if shakeIters > 0 then 
            structure.ShakeSidechainsAll ( shakeIters )
        end
        
        currentScore = score()
        if currentScore > bestWiggleScore then
            local gain = currentScore - bestWiggleScore
            bestWiggleScore = currentScore
            if gain < minGain then break end
        end
    end
end

function cleanup ()
    print("Script complete. Score changed by", score() - initialScore)
    print("Ending score:", score())
end

function main ()
    if not getParameters() then return false end

    fib()
    print("Protein length : "..protLen)
    print("Fib numbers : " .. fiboNumsStr)
    print("Starting score :", initialScore)
    print()

    local currentScore = score()
    while true do
        deselectAll()
        unfreezeAll()
        if isInc then
            for i = 1, #fiboNums do
                wiggleLength(fiboNums[i])
            end
        else
            for i = #fiboNums, 1, - 1 do
                wiggleLength(fiboNums[i])
            end
        end
        currentScore = score()
        if currentScore > bestScore then
            local gain = currentScore - bestScore
            bestScore = currentScore
            if gain < minGain then break end
        end
    end
end

xpcall(main, cleanup)

Comments

[TurtleByte]

V3.1
Fixed bug where 1 was not in list of fib numbers
Fixed bug that allowed fib number generation to go past protein length
Added loop to repeat until gain < minGain, minGain set by user
Freeze segments re-enabled, controlled via dialog option
Localized and renamed Foldit functions