Recipe: QuakeR v4

created by GaryForbis

Profile

• Name: QuakeR v4
• ID: 100444
• Shared with: Public
• Parent: None
• Children:
  • QuakeR v4m
  • QuakeR v4 (COPY)
  • QuakeR v4 (COPY)
• Created on: December 28, 2014 at 07:35 AM UTC
• Updated on: December 28, 2014 at 07:35 AM UTC
• Description:

  QuakeR v3.0 updated to scriptV2 with band to Beta Carbon when hydrophobic.

Code

--QuakeR - a randomized Quake
recipeTitle='QuakeR v4.0'
--[[
Based on "Quake" by Grom

v2.51 -- update 2011-01-15 rav3n_pl
v3.0 -- update 2011-04-18 rav3n_pl
v4.0 -- updated 27 Dec 2014 GaryForbis
  converted to script v2
  band hydrophobes to beta carbon
  clean up on early exit

]]

function floor3(x)--cut at 3rd decimal place
    return tostring(x-x%0.001)
end

function Score()
    local s=0
    if normal==true then
        s=current.GetEnergyScore()
    else
        for i=1,segCnt do
            s=s+current.GetSegmentEnergyScore(i)
        end
    end
    return s
end

function ScoreRB()
    local s=0
    if normal==true then
        s=recentbest.GetEnergyScore()
    else
        for i=1,segCnt do
            s=s+recentbest.GetSegmentEnergyScore(i)
        end
    end
    return s
end

function SaveBest()
  local sRB=ScoreRB()
  if sRB>bestScore then     
    print("Gained another "..floor3(sRB-bestScore).." points.")
    bestScore=sRB
    save.Quicksave(4)  -- under normal conditions retain pose even as recording improvement
    recentbest.Restore()
    save.Quicksave(3)
    save.Quickload(4)
  end
  return Score()-bestScore
end

function Wiggle(how, iters, minppi) --score conditioned recursive wiggle/shake
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end

    if iters>0 then
        iters=iters-1
        local sp=Score()
        if how == "s" then structure.ShakeSidechainsAll(1)
            elseif how == "wb" then structure.WiggleAll(2,true,false)
            elseif how == "ws" then structure.WiggleAll(2,false,true)
            elseif how == "wa" then structure.WiggleAll(2,true,true)
        end
        if Score()-sp > minppi then return Wiggle(how, iters, minppi) end
    end
end

function qStab()
    behavior.SetClashImportance(0.1)
    Wiggle("s",1)
    if fastQstab==false then 
        behavior.SetClashImportance(0.4)
        Wiggle("wa",1)
        behavior.SetClashImportance(1)
        Wiggle("s",1)
    end
    behavior.SetClashImportance(1)
    Wiggle()
    return SaveBest()
end

function Fuze1(ci1,ci2)
    behavior.SetClashImportance(ci1)
    Wiggle("s",1)
    behavior.SetClashImportance(ci2)
    Wiggle("wa",1)
end
function Fuze2(ci1,ci2)
    behavior.SetClashImportance(ci1)
    Wiggle("wa",1)
    behavior.SetClashImportance(1)
    Wiggle("wa",1)
    behavior.SetClashImportance(ci2)
    Wiggle("wa",1)
end
function FuzeEnd()
    behavior.SetClashImportance(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    SaveBest()
end
function reFuze(scr)
    local s=ScoreRB()
    if s<scr then 
        recentbest.Restore()
    else
        scr=s
    end
    return scr
end
function Fuze()
    local scr=Score()
    Fuze1(0.3,0.6) FuzeEnd()
    scr=reFuze(scr)
    Fuze2(0.3,1) SaveBest()
    scr=reFuze(scr)
    Fuze1(0.05,1) SaveBest()
    scr=reFuze(scr)
    Fuze2(0.7,0.5) FuzeEnd()
    scr=reFuze(scr)
    Fuze1(0.07,1) SaveBest()
    reFuze(scr)
end

function bandstr(str) --set all band strength
    for i=1, band.GetCount() do
        band.SetStrength(i, str)
    end
end

function calcBandAtom()
  bandAtom={}
  for x = 1,segCnt do
    if (structure.GetAminoAcid(x) == 'g') or not structure.IsHydrophobic(x) then
      bandAtom[x] = 2 -- center for Glycine and Hydophiles
    elseif x == segCnt then
      bandAtom[x] = 6 -- beta carbon for terminal segment
    else
      bandAtom[x] = 5 -- beta carbon
    end
  end
end

function QuakeR()
  math.randomseed(os.time()) math.random() math.random() math.random()
  calcBandAtom()
  --freeze.UnfreezeAll()
  selection.SelectAll()
  StartingScore=Score()
  bestScore=StartingScore
  recentbest.Save()
  save.Quicksave(3)
  print("Starting "..recipeTitle..tostring(qLoops).." passes. Start score: "..floor3(StartingScore))
  for x=1, qLoops do
    print("Pass "..tostring(x).." of "..tostring(qLoops))
    local start=math.floor(math.random(segCnt/10)) --first band somewhere in first 10% of protein
    local len=math.floor(math.random(segCnt/2-5))+10
    local step=math.floor(math.random(segCnt/2-5))+10
    local loss=math.abs(math.floor(Score()*maxLoss/100))
    band.DeleteAll()
    print("Bands from segment "..tostring(start).." of length "..tostring(len)
           .." every "..tostring(step).." segments.")
    print("Pulling until loss of "..tostring(loss).." points.")
    for x=start,segCnt, step do
      for y=start+len, segCnt, step do
        band.AddBetweenSegments(x,y,bandAtom[x],bandAtom[y]) 
      end
    end
    behavior.SetClashImportance(pullingCI)
    recentbest.Save()
    local gain
    for str=minBS,maxBS,0.07 do--search enough band strength to move
      bandstr(str)
      repeat
        structure.WiggleAll(1,true,false)
        gain=SaveBest()
        if gain > 0 then
          recentbest.Restore()
        end
      until gain<=0
      if gain<-loss then 
        break 
      end
    end
    band.DeleteAll()
    behavior.SetClashImportance(1)
    recentbest.Save() --after pulling
    print("Stabilizing...")
    if qStab() > doFuze then
      print("Fuzing....")
      Fuze()
    end
    SaveBest()
    save.Quickload(3) --load best state
    print("Current score: "..floor3(Score()).." Total gain: "..floor3(Score()-StartingScore))
  end
  print("Total QuakeR gain: "..floor3(Score()-StartingScore))
  return true
end

function CleanUp(err)
  if err:find('Cancelled')~=nil then
    print "QuakeR Cancelled"
  else
    print(err)
  end
  behavior.SetClashImportance(1)
--  band.DeleteAll()
  SaveBest()
  save.Quickload(3)
  print("Total QuakeR gain: "..floor3(bestScore-StartingScore))
end
  
segCnt=structure.GetCount()
while structure.GetSecondaryStructure(segCnt)=="M" do segCnt=segCnt-1 end

--- VVVVVVVVVV OPTIONS

normal=(current.GetExplorationMultiplier()==0)
qLoops=50  -- <<<OVER THERE! do more! much more!
minBS=0.3 --starting minimum bands strength
maxBS=1.0 --maximum band strength
maxLoss=1 --minimum percentage loss when pulling. ie 5% of 10000 is 500pts
pullingCI=1.0 --clash importance while pulling
fastQstab=false --true for 1s1w as stabilize (faster)
doFuze=-10 --run fuze when score after qstabilize is close to best. 

xpcall(QuakeR,CleanUp)

Comments

[GaryForbis]

I didn't add a dialogue box for the options. Let me know if you'd like me to do so.

This version:
converted to script v2
band hydrophobes to beta carbon
clean up on early exit

I also did a few small modifications to the logic.

[GaryForbis]

This script put me into a local minimum at AWP well below optimal. It was hard to get out of it.

I've not run QuakeR for 50 turns in ages so don't know if this is an artifact of banding to beta carbons.

Don't use this script excessively until end game.