Recipe: IdealizeWalker

created by marsfan

Profile

• Name: IdealizeWalker
• ID: 103643
• Shared with: Public
• Parent: None
• Children:
  • IdealizeWalker (COPY)
  • IdealizeWalker crbest
  • IdealizeWalker (COPY)
• Created on: June 26, 2020 at 03:23 AM UTC
• Updated on: June 26, 2020 at 03:23 AM UTC
• Description:

  Selects each group of secondary structures (helix or sheet) and the surrounding loops one at a time. For each selected, idealizes the peptide bonds and then runs wiggle.

Code

segCount = structure.GetCount()
disableFilters = true
shakeOut = false
previouslySelected = {}
startScore = 0

function previouslySelected.Set()
    previouslySelected.Data = {}
    for segment = 1, segCount do
        if selection.IsSelected(segment) then
            previouslySelected.Data[#previouslySelected.Data + 1] = segment
        end
    end
end

function previouslySelected.Restore()
    selection.DeselectAll()
    for segment = 1, #previouslySelected.Data do
        selection.Select(previouslySelected.Data[segment])
    end
end

function setFiltersDisabled(state) -- Set filters state, but only if user has asked the script to control filters
    if disableFilters then
        behavior.SetFiltersDisabled(state)
    end
end

function getScore() -- Calculate the score, enable/disable filters if asked to
    local score = 0
    setFiltersDisabled(false)
    score = current.GetEnergyScore()

    setFiltersDisabled(true)
    return score
end

function settingsMenu() -- Show settings
    local settings = dialog.CreateDialog("Settings")
    local userChoice = 0
    settings.shake = dialog.AddCheckbox("Shake out after First Wiggle?", shakeOut)
    settings.filters = dialog.AddCheckbox("Disable Filters?", disableFilters)
    settings.ok = dialog.AddButton("OK", 1)
    settings.cancel = dialog.AddButton("Cancel", 0)
    userChoice = dialog.Show(settings)

    -- Update settings from dialog
    shakeOut = settings.shake.value
    disableFilters = settings.filters.value

    return userChoice
end

function findFirstNonLoop() -- Find the firt segment in the protein that is not a loop
    for segment = 1, segCount do
        local ss = structure.GetSecondaryStructure(segment)
        if ss == "E" or ss == "H" then
            return segment
        end
    end
    return nil
end

function findSSRange(startSegment, searchBackwards)
    -- Determine the range of segements where the protein SS stays the same as the provided starting segment
    -- Optionally allows the user search backwards instead of forwards.
    searchBackwards = searchBackwards or false
    -- Find starting segemnt SS
    local startSS = structure.GetSecondaryStructure(startSegment)
    if searchBackwards then
        -- Look through the protein (moving backwards), untill the SS type changes, then return the range where it did not
        for segment = startSegment, 1, -1 do
            if structure.GetSecondaryStructure(segment) ~= startSS then
                return {startSegment, segment + 1}
            end
        end
        return {1, startSegment}
    else
        -- Look through the protein (moving forwards), untill the SS type changes, then return the range where it did not
        for segment = startSegment, segCount do
            if structure.GetSecondaryStructure(segment) ~= startSS then
                return {startSegment, segment - 1}
            end
        end
        return {startSegment, segCount}
    end
end

function findSSLoopRange(ssRange)
    local totalRange = {}
    -- Look for end of loop before SS. But if SS range starts at protein start, set start of range to 1
    if ssRange[1] == 1 then
        totalRange[1] = 1
    else
        for segment = ssRange[1] - 1, 1, -1 do
            if structure.GetSecondaryStructure(segment) ~= "L" then
                totalRange[1] = segment + 1
                break
            elseif segment == 1 then
                totalRange[1] = 1
            end
        end
    end

    -- Look for end of loop after SS, but if SS range ends at protein stop, set end of range to protein length
    if ssRange[2] == segCount then
        totalRange[2] = segCount
    else
        for segment = ssRange[2] + 1, segCount do
            if structure.GetSecondaryStructure(segment) ~= "L" then
                totalRange[2] = segment - 1
                break
            elseif segment == segCount then
                totalRange[2] = segCount
            end
        end
    end
    return totalRange
end

function findAllRanges()
    local startSS = findFirstNonLoop()
    local regions = {startSS}
    local i = 1
    while true do
        regions[i] = findSSLoopRange(findSSRange(regions[i]))
        if regions[i][2] ~= segCount then
            regions[i + 1] = regions[i][2] + 1
        else
            break
        end
        i = i + 1
    end
    return regions
end

function main()
    -- Set the list of segments the user has already selected
    previouslySelected.Set()
    -- Save new recent best
    recentbest.Save()
    -- Get the starting score
    startScore = getScore()
    -- Show the settings dialog
    userChoice = settingsMenu()

    if userChoice > 0 then
        -- Find all of the regions that we will idealize
        regions = findAllRanges()
        -- Iterate through all of the found regions.
        for i = 1, #regions do
            -- Select the region
            selection.DeselectAll()
            selection.SelectRange(regions[i][1], regions[i][2])
            -- Idealize the region
            structure.IdealizeSelected()
            -- Wiggle and Shake the region
            structure.WiggleAll(25, true, true)
            if shakeOut then
                structure.ShakeSidechainsAll(2)
                structure.WiggleAll(25, true, true)
            end
            print("Finished Region "..i.." of "..#regions..".")
            -- Update the score, possibly including filters, so recentbest is correct
            getScore()
            recentbest.Restore()

        end
    end
    cleanup("Recipe Done")
end

function pause()
    x = dialog.CreateDialog('x')
    x.button = dialog.AddButton('OK', 1)
    dialog.Show(x)
end

function cleanup(errorMsg)
    errorMsg = errorMsg or "" -- Make the argument optional, default is an empty string
    if string.find(errorMsg, "Cancelled") then
        print("User Cancelled")
    else
        print(errorMsg)
    end
    recentbest.Restore()
    previouslySelected.Restore()
    print("Total Gain: " .. getScore() - startScore)
    setFiltersDisabled(false)


end

xpcall(main, cleanup)