Recipe: Electron Density kick-off User WP

created by Bruno Kestemont

Profile

• Name: Electron Density kick-off User WP
• ID: 108261
• Shared with: Public
• Parent: Electron Density kick-off
• Children: None
• Created on: April 27, 2023 at 19:25 PM UTC
• Updated on: April 27, 2023 at 19:38 PM UTC
• Description:

  1. Reduced importance of H-Bonds to get better fit to the cloud. ; 2. Normalise H-Bond importance and cycle W/S to improve score. ; 3. Use your normal polishing tricks after that. ; 4. *Do not* re-run the script once you have made further improvements, like indealise or rebuild. It will only make it worse. This is just to give a good starting position while you get a coffee.

  1st attempt at a script, automating tedious start to electron density puzzles.

  Be gentle.

Code

-- 1st attempt at a script, automating tedious start to electron density puzzles
-- User's wiggel power at start. Default option start with shake tehn wiggle.


recipename= "Electron Density kick-off User WP v0.1"

local ask = dialog.CreateDialog("Electron Density - start of puzzle")
ask.revertWiggleStrength = dialog.AddCheckbox("Wiggle strenth Auto when finished?", false)
ask.StartWithShake = dialog.AddCheckbox("Start with shake", true)
ask.instructionsIterations = dialog.AddLabel("Iters before checking for improvement per cycle")
ask.wiggleIterations = dialog.AddSlider("Wiggle Iters", 7, 1, 20, 0)
ask.shakeIterations = dialog.AddSlider("Shake Iters", 3, 1, 10, 0)
ask.instructionsMinimums = dialog.AddLabel("Minimum improvements to break out of each cycle")
ask.wiggleImprovement = dialog.AddSlider("Wiggle Min", 0.1, 0.01, 20, 3)
ask.shakeImprovement = dialog.AddSlider("Shake Min", 0.01, 0.001, 5, 3)
ask.cycleImprovement = dialog.AddSlider("Cycle Min", 0.1, 0.01, 20, 3)
ask.OK = dialog.AddButton("OK", 1)
ask.Cancel = dialog.AddButton("Cancel", 0)

if (dialog.Show(ask) > 0) then
    StartWithShake=ask.StartWithShake.value
    wiggleIterations = ask.wiggleIterations.value
    shakeIterations = ask.shakeIterations.value
    revertWiggleStrength = ask.revertWiggleStrength.value
    wiggleImprovement = ask.wiggleImprovement.value
    shakeImprovement = ask.shakeImprovement.value
    cycleImprovement = ask.cycleImprovement.value
end

print ("wiggleIterations ="..wiggleIterations)
print ("shakeIterations ="..shakeIterations)
print ("wiggleImprovement ="..wiggleImprovement)
print ("shakeImprovement ="..shakeImprovement)
print ("cycleImprovement ="..cycleImprovement)

-- Set behavior to 'best fit' the cloud
behavior.SetClashImportance(1)
behavior.SetBackboneHBondImportance(0)
behavior.SetSidechainHBondImportance(0)
-- behavior.SetWigglePower("h")

function DoWiggle()
    -- Keeps going while improvement up to dialogue spec wiggles
    local recentBest = recentbest.GetEnergyScore()
    local startingScore = current.GetEnergyScore()
    
    for i=1, 200 do -- 200 to stop infinite loop to an asymptote
        -- Measure the improvement from one wiggle
        local loopStartScore = current.GetEnergyScore()
        structure.WiggleAll(wiggleIterations)
        local loopEndScore = current.GetEnergyScore()
        
        -- Break if we stop making progress
        if (loopEndScore - loopStartScore < wiggleImprovement) then
            break
        end
        -- Let everyone know what's happening
        print ("DoWiggle improvement:"..loopEndScore)
    end
    
    return current.GetEnergyScore() > recentBest
end

function DoShake()
    -- Keeps going while improvement up to 20 shakes
    local recentBest = recentbest.GetEnergyScore()
    local startingScore = current.GetEnergyScore()
    
    for i=1, 200 do -- 200 to stop infinite loop to an asymptote
        -- Measure the improvement from one shake
        local loopStartScore = current.GetEnergyScore()
        structure.ShakeSidechainsAll(shakeIterations)
        local loopEndScore = current.GetEnergyScore()
        
        -- Break if we stop making progress
        if (loopEndScore - loopStartScore < shakeImprovement) then
            break
        end
        -- Let everyone know what's happening
        print ("DoShake improvement: "..loopEndScore)
    end
    
    return current.GetEnergyScore() > recentBest
end

function DoCycle()
    -- Switches back and forth between wiggle and shake while improvement
    local recentBest = recentbest.GetScore()
    local startingScore = current.GetEnergyScore()
    for i=1, 200 do -- 200 to stop infinite loop to an asymptote
        -- Measure improvement from one cycle
        local loopStartScore = current.GetEnergyScore()
        if StartWithShake then
            DoShake()
        end
        DoWiggle()
        if not StartWithShake then
            DoShake()
        end
        local loopEndScore = current.GetEnergyScore()
        -- Break if we stop making progress
        if (loopEndScore - loopStartScore < cycleImprovement) then
            break
        end
        -- Let everyone know what's happening
        print ("DoCycle improvement: "..i.." "..loopEndScore)
    end
    
    return current.GetEnergyScore() > recentBest
end


-- Loose munge to the cloud shape
print ("Do the cloud-fit bit, not worrying about score")
DoCycle()

-- Restore normal behavior
behavior.SetBackboneHBondImportance(1)
behavior.SetSidechainHBondImportance(1)

-- Get some points
print ("Do the get points bit")
DoCycle()


if revertWiggleStrength then
    behavior.SetWigglePower("a")
    print ("Wiggle strength set to Auto")
    else
        print ("Wiggle strength left as user's")
    end
        
print ("Electron density kick-off wiggles and shakes complete.")
print ("Do not re-run once you've improved from here - it will make it worse.")
print ("Over to you.")