Recipe: nspc - Rotamer check

created by nspc

Profile

• Name: nspc - Rotamer check
• ID: 106448
• Shared with: Public
• Parent: None
• Children: None
• Created on: April 03, 2022 at 17:05 PM UTC
• Updated on: April 03, 2022 at 17:05 PM UTC
• Description:

  Set best rotamers subscore in selected sidechains, ignoring other subscore like clash.

Code

-- Functions Utils --

function GetUnlockedAndLockedSegments()

    local count = structure.GetCount()
    local lockeds = {}
    local unlockeds = {}
    
    for i = 1, count do
        if structure.IsLocked(i) then
            lockeds[#lockeds+1] = i
        else
            unlockeds[#unlockeds+1] = i
        end
    end
    
    return lockeds, unlockeds
end


function IsNearLocked(index, lockeds, lockedsCount)

    minDistance = 10000 -- like a max value

    for i = 1, lockedsCount do
        local distance = structure.GetDistance(index, lockeds[i])
        
        if (distance < minDistance) then
            minDistance = distance;
        end
    end
    
    return minDistance <= parameters.minDistance
end

function DetectInterface()

    print ("Auto detect segment near target..")

    selection.DeselectAll()

    local lockeds, unlockeds = GetUnlockedAndLockedSegments()
    local lockedCount = #lockeds
    local unlockedsCount = #unlockeds
    
    local selectedCount = 0
    
    for i = 1, unlockedsCount do
        local segmentIndex = unlockeds[i]

        if IsNearLocked(segmentIndex, lockeds, lockedCount) then
            selection.Select(segmentIndex)
            selectedCount = selectedCount + 1
        end
    end
    
    print ("Selected segments count " .. selectedCount)
end

function IsAValidSegmentSelected()
    local count = structure.GetCount()
    
    for seg = 1, count do
        if selection.IsSelected(seg) and structure.IsLocked(seg) == false then
        return true;
        end
    end
    
    return false;
    
end

function PrintScore(score)
    return string.format("%.4f", score)
end

-- Parameters --

parameters = {}
function GetParameters()
    local dialogBox = dialog.CreateDialog("nspc - Rotamer")
    
    dialogBox.ok = dialog.AddButton("OK" , 1)
    dialogBox.cancel = dialog.AddButton("Cancel" , 0)
    
    dialogBox.margin1 = dialog.AddLabel("  ")
    
    dialogBox.description1 = dialog.AddLabel("Set best rotamer subscore in selected sidechains,")
    dialogBox.description2 = dialog.AddLabel("ignoring other subscores.")
    dialogBox.description3 = dialog.AddLabel(" ")
    dialogBox.description4 = dialog.AddLabel("This can help to find bad rotamers")
    dialogBox.description5 = dialog.AddLabel("in binder designs that can cause binder fail.")

    dialogBox.margin2 = dialog.AddLabel("  ")
    
    dialogBox.disableFilters = dialog.AddCheckbox("Force Disable Filters", false)
    
    dialogBox.autoSelectDesc = dialog.AddLabel("You can auto select sidechains near binder :")
    
    dialogBox.autoSelectionNearTarget = dialog.AddCheckbox("Auto selection near target", false)
    
    dialogBox.minDistance = dialog.AddSlider("Min dist with target", 9, 5, 15, 1)

    if (dialog.Show(dialogBox ) == 1) then
        parameters.minDistance = dialogBox.minDistance.value;
        parameters.disableFilters = dialogBox.disableFilters.value;
        parameters.autoSelectionNearTarget = dialogBox.autoSelectionNearTarget.value;
        return true
    end
    
    return false
end


-- Main Functions --

function Cleanup()
    print ("Cleanup")
    
    if (parameters.disableFilters == true) then
        behavior.SetFiltersDisabled(false)
    end
end

function ErrorHandler(errorMessage)
    if errorMessage ~= nil then
        if string.find(errorMessage, "Cancelled") then
            print( "User cancel" )
            Cleanup();
        else
            print(errorMessage)
        end
    end
end

function SetBestRotamers()

    save.Quicksave(3)

    for seg = 1, structure.GetCount() do
        save.Quicksave(4)
        
        if selection.IsSelected(seg) then
            local startScore = current.GetSegmentEnergySubscore(seg, "sidechain")
        
            local maxScore = startScore
            local bestRotamer = 1;
                    
            print("Working on segment " .. seg .. " : current score : " .. PrintScore(startScore))
            
            for rot = 1, rotamer.GetCount(seg) do
                rotamer.SetRotamer(seg, rot)
                local currentScore = current.GetSegmentEnergySubscore (seg, "sidechain")
                if  currentScore > maxScore then
                    maxScore = currentScore;
                    bestRotamer = rot;
                end
            end
            
            if (maxScore > startScore) then
                rotamer.SetRotamer(seg, bestRotamer)
                save.Quicksave(4)
            
                print("Increased rotamer score to " .. PrintScore(maxScore))
            else    
                save.Quickload(4)
                
                print("No score change")
            end
            
            print("-----")
            print(" ")
        end
    end
    
    -- load starting protein and just after new one
    save.Quicksave(2)
    
    save.Quickload(3)
    save.Quickload(2)
end

function Main()

    if (GetParameters() == false) then
        return 
    end
    
    if (parameters.disableFilters == true) then
        behavior.SetFiltersDisabled(true)
    end

    print ("Start recipe Rotamer")
    
    if (parameters.autoSelectionNearTarget == true) then
        DetectInterface()
    elseif (IsAValidSegmentSelected() == false) then
        print ("No Valid segment selected")
        print ("Use auto selection option or select some segments before start")
    end
    
    SetBestRotamers();

    Cleanup();
end

xpcall(Main, ErrorHandler)

Comments

[nspc]

This recipe is a tool to set all selected rotamers in the best "ideality" position, ignoring other subscores.
It is only to check rotamers, it is not a tool that realy improve them automatically in the puzzle.

In binder puzzles, If thistool result have too mush clashes, and can't be resolve with wiggle, maybe those sidechains can cause problem in lab.
So maybe we have to choose a different sidechain in some situation.

It is a tool that cans help during Hand Folding