Recipe: QuakeR v5.5 with mutate for binders

created by ZeroLeak7

Profile

• Name: QuakeR v5.5 with mutate for binders
• ID: 104206
• Shared with: Public
• Parent: None
• Children: None
• Created on: December 11, 2020 at 17:13 PM UTC
• Updated on: December 11, 2020 at 17:13 PM UTC
• Description:

  Quaker v5.0 now with mutate + better shake and wiggle ci in Fuze + GUI

Code

--QuakeR - a randomized Quake
recipeTitle='QuakeR v5.5wmfb '
--[[
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
v4.5 -- updated 2019-12-30 ZeroLeak7
v5.0 -- updated 2019-12-31

  -converted to script v2
  -band hydrophobes to beta carbon
  -clean up on early exit
  -better shake and wiggle ci in Fuze and with mutate now
  -updated with a gui
]]

-- Globals
 loop_starts = {}
 loop_ends  = {}
 n_loops = 0
 n_residues = 0
 
 
 function Lockedresidues ()
	selection.SelectAll()
	structure.SetSecondaryStructureSelected("H")
	
	for i=1, structure.GetCount() do

		if structure.GetAminoAcid(i) == "unk" then
		structure.SetSecondaryStructure(i, "H")
		end

		if structure.IsLocked(i) == false then
		
		structure.SetSecondaryStructure(i, "L")
		
	end
	end
end

function GetLoops ()

within_loop = false
for i = 1, n_residues do
if ( structure.GetSecondaryStructure ( i ) == "L" and structure.IsLocked(i) == false ) then
if ( within_loop == false ) then    
-- start of a new loop
within_loop = true    
 n_loops = n_loops + 1
 loop_starts [ n_loops ] = i           
 end
 elseif ( within_loop == true ) then            
 -- end of a loop
 within_loop = false
 loop_ends [ n_loops ] = i -1
 end
 end    -- for i
 if ( within_loop == true ) then
 loop_ends [ n_loops ] = n_residues
 end
 end

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 g=Score()-bestScore
  if g>0 then   
    print("Gained another "..floor3(g).." points.")
    bestScore=Score()
    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(0.21)
	structure.MutateSidechainsSelected(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)
    behavior.SetClashImportance(0.9)
    structure.MutateSidechainsSelected(1)
    Wiggle()
    behavior.SetClashImportance(1)
    Wiggle("wa",1)
    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(1,0.6) FuzeEnd()
    scr=reFuze(scr)
    Fuze2(1,1) SaveBest()
    scr=reFuze(scr)
    Fuze1(1,0.9) SaveBest()
    scr=reFuze(scr)
    Fuze2(1,1) FuzeEnd()
    scr=reFuze(scr)
    Fuze1(1,1) 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(ix,iy,ql,rev)
  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(ql).." passes.")
  print("Start score: "..floor3(StartingScore))
  for x=1, ql do
    print("Pass "..tostring(x).." of "..tostring(ql))
    local step=math.floor(math.random((iy-ix)/10,((iy-ix)/10)+10))
    band.DeleteAll()
    print("Bands from segment "..tostring(ix).." of length "..tostring(step)
           .." every "..tostring(step).." segments.")
    print("Pulling..")
if(rev==true) then
    for x=ix,iy, step do
      for y=ix, iy, step do
       band.AddBetweenSegments(x,y)
      end
      end
       else
   for x=ix,iy, step do
      
   for y=ix+step, iy, step do       
   band.AddBetweenSegments(x,y)      
   end      
   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
        break
    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 GetParameters ()

    local dlog = dialog.CreateDialog ( "QuakeR v5 with mutate for binders" )

    dlog.iterations = dialog.AddSlider ( "normal iter: " , qLoops , 1 , 1000 , 0 )

   dlog.iterationsr = dialog.AddSlider ( "reverse iter:  " , qLoops2 , 1 , 1000 , 0 )
    dlog.ok = dialog.AddButton ( "OK" , 1 )
    dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

    if ( dialog.Show ( dlog ) > 0 ) then
    
        qLoops = dlog.iterations.value
        qLoops2 = dlog.iterationsr.value
 
        return true
      else
        return false
    end

end
function main ()
    if ( GetParameters () == false ) then
      return                -- graceful exit
    end
n_residues = structure.GetCount ()
behavior.SetClashImportance ( 1 )
print("wait! initializing...")
Lockedresidues ()
GetLoops ()    
n_loops = #loop_starts    
print ( n_loops .. " loops" )      
n_loops = #loop_starts
for i = 1 , n_loops  do
print ( "Loop " .. i .. " : (" .. loop_starts [ i ] .. "-" .. loop_ends [ i ] .. ")" )
end
local idx_starts = loop_starts[ 1 ]
local idx_ends = loop_ends[ 1 ]

QuakeR(idx_starts, idx_ends, qLoops,false)
print("reverse QuakeR starts:")
QuakeR(idx_ends, idx_starts, qLoops2,true)

cleanUp()

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=5
qLoops2=5  -- <<<OVER THERE! do more! much more!
minBS=0.3 --starting minimum bands strength
maxBS=1.0 --maximum band strength
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(main,CleanUp)