Recipe: Blue Fuse 2020b

created by marsfan

Profile

• Name: Blue Fuse 2020b
• ID: 103547
• Shared with: Public
• Parent: Blue Fuse 2020
• Children:
  • Blue Fuse 2020b (COPY) edit 0.99 of CI
  • Blue Fuse 2020c (COPY) - Just shakes
• Created on: June 16, 2020 at 03:53 AM UTC
• Updated on: June 16, 2020 at 03:53 AM UTC
• Description:

  Updated version of Blue Fuse v1.1 by Vertex, January 2010 - see https://fold.it/portal/recipe/2052

  Changes in May 27, 2020 version: Added support for disabling filters before wiggling and shaking, script now repeats untill there is no more gain, now does 25 iterations of wiggle and 2 iterations of shake.

  June 15, 2020 Changes: ; Added ability to scale CI values so CI never exceeds user set CI. ; Added a menu that allows the user to control the number of wiggle iterations, shake iterations, wheter or not to scale CI values, whether or not to repeat untill no score change, whether or not to disable filters when wiggling/shaking, and display a help menu. ; Added a cleanup routine to reset the CI, restore recent best, and re-enable filters if the user presses cancel

Code

--
--  Blue Fuse 2020a - 21 March 2020 - see notes at end
--

-- Global settings values. changed by user setting the GUI
wiggleIterations = 25
shakeIterations = 2
scaleCI = true
repeatFuse = true
filterOnRun = true
ciScaleFactor = 1


-- New dialog function to add a gap in a dialog
dialog.AddNewline = function()
    return dialog.AddLabel("")
end


function enableFilters(state)
    if filterOnRun then
        behavior.SetFiltersDisabled(not state)
    end
end

function fuse()
        enableFilters(true)
        startScore = current.GetEnergyScore ()      -- Get the current energy score.
        print ( "starting score = " .. startScore ) -- print the starting score

        enableFilters(false)
        behavior.SetClashImportance ( 0.05 * ciScaleFactor)        -- Set the clashing importance.
        structure.ShakeSidechainsAll ( shakeIterations)          -- Shake all sidechains.
        behavior.SetClashImportance ( 1.00  * ciScaleFactor )        -- Reset the clashing importance.
        structure.WiggleAll ( wiggleIterations )                   -- Global wiggle all segments.
        enableFilters(true)
        print ( "after first shake/wiggle, score = " .. current.GetEnergyScore () )
        enableFilters(false)
        behavior.SetClashImportance ( 0.07 * ciScaleFactor)        -- Set the clashing importance.
        structure.ShakeSidechainsAll ( shakeIterations )          -- Shake all sidechains.
        behavior.SetClashImportance ( 1.00 * ciScaleFactor)        -- Reset the clashing importance.
        structure.WiggleAll ( wiggleIterations )                   -- Global wiggle all segments.
        enableFilters(true)
        print ( "after second shake/wiggle, score = " .. current.GetEnergyScore () )


        recentbest.Restore ()                       -- Load the recent best pose.
        print ( "after restoring recent best, score = " .. current.GetEnergyScore () )
        enableFilters(false)
        behavior.SetClashImportance ( 0.3 * ciScaleFactor)         -- Set the clashing importance.
        structure.WiggleAll (shakeIterations)                   -- Global wiggle all segments.
        behavior.SetClashImportance ( 1.00 * ciScaleFactor )        -- Reset the clashing importance.
        structure.WiggleAll ( wiggleIterations )                   -- Global wiggle all segments.
        enableFilters(true)
        print ( "after final wiggle, score = " .. current.GetEnergyScore () )

        recentbest.Restore ()                       -- Load the recent best pose.

        finalScore = current.GetEnergyScore ()      -- Get the current energy score.
        print ( "final score = " .. finalScore )    -- print the final score
        gain = finalScore - startScore              -- calculate the gain
        print ( "gain = " .. gain )                 -- print the gain
        print ( "Blue Fuze 2020b complete" )
        return gain

end

function makeGUI()
    local options = dialog.CreateDialog("Blue Fuse 2020b")
    options.wiggleIterations = dialog.AddTextbox("Wiggle Iterations", tostring(wiggleIterations))
    options.shakeIterations = dialog.AddTextbox("Shake Iterations", tostring(shakeIterations))
    options.scaleCI = dialog.AddCheckbox("Scale CI To Current Value", scaleCI)
    options.repeatFuse = dialog.AddCheckbox("Repeat Until Gain = 0", repeatFuse)
    options.filterOnRun = dialog.AddCheckbox("Disable filters",filterOnRun)
    options.OK = dialog.AddButton("OK", 1)
    options.help = dialog.AddButton("Help", 2)
    options.cancel = dialog.AddButton("Cancel", 0)
    return options
end

function textToValidNumber(text)
    -- Try to convert text to a number
    converted = tonumber(text)
    -- Check that number converted properly, is not nan, is an integer, and is greater than 1
    -- If any of the tests fail, return a boolean false
    if converted and (converted == converted) and (converted%1 == 0) and (converted >=0) then
        return converted
    else
        return false
    end
end

function showBadNumber(invalidSetting)
    local badNumberDialog = dialog.CreateDialog("Invalid Value")
    badNumberDialog.label = dialog.AddLabel("The value for "..invalidSetting.." is invalid")
    badNumberDialog.label2 = dialog.AddLabel("Please set it to a positive integer.")
    badNumberDialog.button = dialog.AddButton("OK", 1)
    dialog.Show(badNumberDialog)
end

function updateSettingsVars(optionMenu)
    valuesAreGood = true
    wiggleIterationsCheck = textToValidNumber(optionMenu.wiggleIterations.value)
    shakeIterationsCheck = textToValidNumber(optionMenu.shakeIterations.value)
    scaleCI  = optionMenu.scaleCI.value
    repeatFuse = optionMenu.repeatFuse.value
    filterOnRun = optionMenu.filterOnRun.value
    if not wiggleIterationsCheck then
        valuesAreGood=false
        showBadNumber("Wiggle Iteraions")
    else
        wiggleIterations = wiggleIterationsCheck

    end
    if not shakeIterationsCheck then
        valuesAreGood = false
        showBadNumber("Shake Iterations")
    else
        shakeIterations = shakeIterationsCheck
    end
    return valuesAreGood

end


function showHelp()
    local helpMenu = dialog.CreateDialog("Blue Fuse 2020b Help")

    helpMenu.wiggleHelp = dialog.AddLabel("Wiggle Iterations: How many cycles of wiggle to run")
    helpMenu.WiggleHelp2 = dialog.AddLabel("each time script starts wiggling protein.")
    helpMenu.space1 = dialog.AddNewline()
    helpMenu.shakeHelp = dialog.AddLabel("Shake Iterations: How many cycles of shake to run")
    helpMenu.shakeHelp2 = dialog.AddLabel("each time script starts shaking protein.")
    helpMenu.space2 = dialog.AddNewline()
    helpMenu.scaleHelp = dialog.AddLabel("Scale CI to Current Value: Scale defualt CI  values")
    helpMenu.scaleHelp2 = dialog.AddLabel("so that max CI is never greater than currently set")
    helpMenu.scaleHelp3 = dialog.AddLabel("CI value. Useful if you want to fuse, but keep CI")
    helpMenu.scaleHelp4 = dialog.AddLabel("below a specific value. ")
    helpMenu.space3 = dialog.AddNewline()
    helpMenu.repeatHelp = dialog.AddLabel("Repeat Until Gain = 0: Repeat Blue Fuse 2020b until")
    helpMenu.repeatHelp2 = dialog.AddLabel("no more score gain.")
    helpMenu.space4 = dialog.AddNewline()
    helpMenu.filterHelp = dialog.AddLabel("Disable Filters: Disable filters when wiggling and")
    helpMenu.filterHelp2 = dialog.AddLabel("shaking to speed up script.")
    helpMenu.OK = dialog.AddButton("OK", 0)
    dialog.Show(helpMenu)
end


function main()
    recentbest.Save ()                          -- Save the current pose as the recent best pose.
    existingCI = behavior.GetClashImportance()
    print ( "Blue Fuze 2020b" )
    -- Keep looping so that we can re-draw GUI if user makes a mistake, or presses help
    while true do
        options = makeGUI()
        selection = dialog.Show(options)

        -- Check if user pressed cancel, if not, update the settings to what the user input.
        if (selection == 0) then
            break
        else
            if updateSettingsVars(options) then
                if (selection == 1) then
                    if scaleCI then
                        ciScaleFactor = existingCI
                    else
                        ciScaleFactor = 1
                    end

                    if repeatFuse then
                        repeat
                            fuse()
                        until(gain <= 0)
                    else
                        fuse()
                    end
                    break
                elseif (selection == 2) then
                    showHelp()
                end
            end
        end
    end
end

function cleanup(err)
    if string.find(err, "Cancelled") then
        print("User Cancelled")
    else
        print(err)
    end
    recentbest.Restore()
    behavior.SetFiltersDisabled(false)
    behavior.SetClashImportance(existingCI)

end

--
--  original: Blue Fuse v1.1 by Vertex 3 January 2010 - https://fold.it/portal/recipe/2052
--
--  BlueFuse 2020a - LociOiling - 21 March 2020
--  + converted to Foldit Lua interface V1 to V2
--  + added printing scores and gain
--  + dropped "select_all", not needed with ShakeSidechainsAll and WiggleAll
--
-- BlueFuse 2020b - marsfan - 27 May 2020
--  + Added ability to disable filters to improve performance
--  + Script now repeats untill no more gain
--  + Wiggle Iterations changed to 25
--  + Shake Iterations changed to 2
--
--  BlueFuse 2020b2 - marsfan - 16 June 2020
--  + Added ability to scale clash importance settings
--  + Added quicksaving so that pressing cancel reverts to recent best score.
--  + Added GUI to enable/disable repeat, enable/disable scaling of CI, and set iteration counts.
--  + Add built in help for options
--
--  Some potential improvements:
--
--  TODO: round the score to three decimals
--  TODO: repeat the process if there's a gain
--  TODO: try different values for clashing importance
--  TODO: try a different number of iterations for
--  TODO: add a dialog to control settings
--


xpcall(main, cleanup)

Comments

[Formula350]

You sure that you want 25 Iters of SHAKE and only 2 of Wiggle?

That seems opposite of what most people would want.

:)
-Form

[marsfan]

Good catch. I check, and that is just a typo in the description. Fixed

[marsfan]

Checked, not check.