Recipe: V2 Acid Tweaker R v1.1g

created by jeff101

Profile

• Name: V2 Acid Tweaker R v1.1g
• ID: 47301
• Shared with: Public
• Parent: V2 Acid Tweaker R v1.1f
• Children:
  • V2 Acid Tweaker R v1.1h
  • Acid Tweaker R v1.1g V2(COPY)
  • V2 Acid Tweaker R & BWF v1.0
• Created on: November 23, 2013 at 04:16 AM UTC
• Updated on: November 23, 2013 at 04:16 AM UTC
• Description:

  Acid Tweaker v1.1g, added AA names, minimum rotamer # option, round down the scores

Code

-- modified for foldit V2
 --Acid Tweaker R v1 - randomatic acid tweaker
-- by rav3n_pl based on
-- Acid Tweaker v1.0 by Steven Pletsch
-- Acid Tweaker v1.1a , added options for the order of segment processing
-- Acid Tweaker v1.1c , added gui, added option to reorder processing, fixed V1 to V2 conversion bug
-- Acid Tweaker v1.1d, added a few more SetNote lines
-- Acid Tweaker v1.1e, modified usableAA function to support puzzles with ligands
-- Acid Tweaker v1.1f, added reverse option, maximum rotamer # option
-- Acid Tweaker v1.1g, 11/19/13 jeff101 adapted V2 Acid Tweaker R v1.1f to
--                     add minimum rotamer # option, AA names, rounding down for scores

-- last updated 11/19/13 356pm

--option to easy set start and end of AT work to
ATgui=true   -- display gui
ATstart=1 --1st segment
ATend=nil --end of protein if nil
ATpass1=false
ATpass2=false
ATpass3=true
AToption=12 -- set sorting option according to table below
ATalternate=false
ATreverse=false
ATminrotamer=1 -- 1 to 999
ATmaxrotamer=999  -- 1 to 999

-- process segments in order according to 2nd argument where
--  0 - random
--  1 - segment number
--  2 - segment score
--  3 - clashing score
--  4 - packing score
--  5 - hiding score
--  6 - bonding score
--  7 - backbone score
--  8 - sidechain score
--  9 - reference score
-- 10 - disulfide score
-- 11 - other score
-- 12 - number of sidechain snap locations

function trunc3(res)
return res-res%0.001 -- round res down to nearest 0.001's place
end

function Wiggle(how, iters, minppi)
  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=current.GetScore()
    if how == "s" then structure.ShakeSidechainsSelected(1)
      elseif how == "wb" then structure.WiggleSelected(2,true,false)
      elseif how == "ws" then structure.WiggleSelected(2,false,true)
      elseif how == "wa" then structure.WiggleSelected(2,true,true)
    end
    local ep = current.GetScore()
    local ig=ep-sp
    if how~="s" then
      if ig > minppi then Wiggle(how, iters, minppi) end
    end
  end
end

function SelectSphere(sg, radius,nodeselect)
  if nodeselect~=true then selection.DeselectAll() end
  for i=1,segCount do
      if structure.GetDistance(sg,i)<radius then selection.Select(i) end
  end
end

function SaveBest()
  local s=current.GetScore()
  local g=s-bestScore
  if g>0 then
    print(string.format("Gained another %.3f pts. Current score: %.3f",g,trunc3(s)))
    bestScore=s
    save.Quicksave(3)
  end
end

function usableAA(sn)
  local usable=false

  if structure.GetSecondaryStructure(sn)=="M" then return false end -- added for puzzles with ligands

  if #useThat>0 then
    for i=1,#useThat do
      if sn==useThat[i] then
        usable=true
        break
      end
    end
  else
    if #useOnly > 0 then
      for i=1,#useOnly do
        local ss=useOnly[i][1]
        local se=useOnly[i][2]
        for s=ss,se do
          if s==sn then
            usable=true
            break
          end
        end
      end
    else
      usable=true
      if #doNotUse>0 then
        for i=1,#doNotUse do
          local ss=doNotUse[i][1]
          local se=doNotUse[i][2]
          for s=ss,se do
            if s==sn then
              usable=false
              break
            end
          end
          if usable==false then break end
        end
      end

      if #skipAA>0 then
        local aa=structure.GetAminoAcid(sn)
        for i=1,#skipAA do
          if aa==skipAA[i] then
            usable=false
            break
          end
        end
      end
    end
  end

  local se=segCount
  if ATend~=nil then se=ATend end
  if sn<ATstart or sn>se then usable=false end

  return usable
end

function wiggle_out()
  behavior.SetClashImportance(.6)
  structure.WiggleSelected(1,true,true)
  behavior.SetClashImportance(1.)
  Wiggle()
  Wiggle("s",1)
  selection.SelectAll()
  behavior.SetClashImportance(.6)
  Wiggle()
  behavior.SetClashImportance(1.)
  Wiggle()
  recentbest.Restore()
  structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f (AT(min,max)rotamer=%i,%i)",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore()),ATminrotamer,ATmaxrotamer))
  SaveBest()
end

function sidechain_tweak()
  print("Pass 1 of 3: Sidechain tweak")
  for x=1,#segments do
    i=segments[x]
    if usableAA(i) then
      selection.DeselectAll()
      selection.Select(i)
      aaname=structure.GetAminoAcid(i)
      local ss=current.GetScore()
      g_total_score=current.GetScore()
      behavior.SetClashImportance(0)
      structure.ShakeSidechainsSelected(2)
      behavior.SetClashImportance(1.)
      if(current.GetScore() > g_total_score -1.) then
        recentbest.Restore()
      else
        print(string.format("Try sgmnt: %s%i %i/%i",aaname,i,x,#segments))
        if(current.GetScore() > g_total_score - 30) then
          SelectSphere(i, 12)
          wiggle_out()
        else
          SelectSphere(i, 12)
          selection.Deselect(i)
          behavior.SetClashImportance(.75)
          structure.ShakeSidechainsSelected(2)
          selection.Select(i)
          wiggle_out()
        end
      end
    end
  end
end

function sidechain_tweak_around()
  print("Pass 2 of 3: Sidechain tweak around")
  for x=1,#segments do
    i=segments[x]
    if usableAA(i) then
      selection.DeselectAll()
      for n=1, g_segments do
        g_score[n] = current.GetSegmentEnergyScore(n)
      end
      selection.Select(i)
      aaname=structure.GetAminoAcid(i)
      local ss=current.GetScore()
      g_total_score=current.GetScore()
      behavior.SetClashImportance(0)
      structure.ShakeSidechainsSelected(2)
      behavior.SetClashImportance(1.)
      if(current.GetScore() > g_total_score -1.) then
        recentbest.Restore()
      else
        print(string.format("Try sgmnt: %s%i %i/%i",aaname,i,x,#segments))
        if(current.GetScore() > g_total_score - 30) then
          SelectSphere(i,12)
          wiggle_out()
        else
          selection.DeselectAll()
          for n=1,g_segments do
            if(current.GetSegmentEnergyScore(n) < g_score[n] - 1) then
              selection.Select(n)
            end
          end
          selection.Deselect(i)
          behavior.SetClashImportance(0.1)
          structure.ShakeSidechainsSelected(2)
          SelectSphere(i,12,true)
          wiggle_out()
        end
      end
    end
  end
end

function sidechain_manipulate()
  print("Last pass: Brute force sidechain manipulator")
  ATtime=os.time()
  for x=1,#segments do
    i=segments[x]
    if usableAA(i) then
      selection.DeselectAll()
      rotamers = rotamer.GetCount(i)
      aaname=structure.GetAminoAcid(i)
      save.Quicksave(4)
      if(rotamers > 1) then
        local ss=current.GetScore()
--      print(string.format("Sgmnt: %s%i %i/%i positions: %i (%i)",aaname,i,x,#segments,rotamers,os.difftime(os.time(),ATtime)))
        print(string.format("Sgmnt: %s%i %i/%i positions: %i (processing positions %i-%i)",aaname,i,x,#segments,rotamers,ATminrotamer,math.min(rotamers,ATmaxrotamer)))
        -- below is a 'for x' loop inside another 'for x' loop ... tolerable in LUA ... bad in other languages 11/19/13 jeff101
        for x=ATminrotamer,math.min(rotamers,ATmaxrotamer) do
          save.Quickload(4)
          g_total_score = current.GetScore()
          rotamer.SetRotamer(i,x)
          behavior.SetClashImportance(1.)
          if(current.GetScore() > g_total_score -1.) then
            recentbest.Restore()
--          structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore())))
            structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f (AT(min,max)rotamer=%i,%i)",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore()),ATminrotamer,ATmaxrotamer))
          else
            if(current.GetScore() > g_total_score - 30) then
              SelectSphere(i,12)
              wiggle_out()
            else
              SelectSphere(i,12)
              selection.Deselect(i)
              behavior.SetClashImportance(.75)
              structure.ShakeSidechainsSelected(2)
              selection.Select(i)
              wiggle_out()
            end
          end
        end
      end
    end
    if os.difftime(os.time(),ATtime) > 600 then -- report the time every 10 minutes
      report_time(start_clock,start_time)
      ATtime=os.time()
    end
  end
--structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore())))
  structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f (AT(min,max)rotamer=%i,%i)",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore()),ATminrotamer,ATmaxrotamer))
end

function sidechain_manipulate2()
  print("Last pass: Brute force sidechain manipulator 2")
  nrot=ATminrotamer
  ATtime=os.time()
  repeat
    print(string.format(" \nProcessing rotamer position %i",nrot))
    max_rotamers=0
    for x=1,#segments do
      i=segments[x]
      if usableAA(i) then
        selection.DeselectAll()
        rotamers = rotamer.GetCount(i)
        aaname=structure.GetAminoAcid(i)
        if rotamers>max_rotamers then max_rotamers=rotamers end
        save.Quicksave(4)
        if(nrot <= rotamers) then
          local ss=current.GetScore()
--        print(string.format("  Sgmnt: %s%i %i/%i positions: %i (%i)",aaname,i,x,#segments,rotamers,os.difftime(os.time(),ATtime)))
          print(string.format("  Sgmnt: %s%i %i/%i positions: %i",aaname,i,x,#segments,rotamers))
          save.Quickload(4)
          g_total_score = current.GetScore()
          rotamer.SetRotamer(i,nrot)
          behavior.SetClashImportance(1.)
          if(current.GetScore() > g_total_score -1.) then
            recentbest.Restore()
--          structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore())))
            structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f (AT(min,max)rotamer=%i,%i)",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore()),ATminrotamer,ATmaxrotamer))
          else
            if(current.GetScore() > g_total_score - 30) then
              SelectSphere(i,12)
              wiggle_out()
            else
              SelectSphere(i,12)
              selection.Deselect(i)
              behavior.SetClashImportance(.75)
              structure.ShakeSidechainsSelected(2)
              selection.Select(i)
              wiggle_out()
            end
          end
        end
      end
      if os.difftime(os.time(),ATtime) > 600 then -- report the time every 10 minutes
        report_time(start_clock,start_time)
        ATtime=os.time()
      end
    end
    nrot=nrot+1
  until nrot>max_rotamers or nrot>ATmaxrotamer
--structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore())))
  structure.SetNote(note_number,string.format("(%s) %.3f + Acid Tweaker %.3f (AT(min,max)rotamer=%i,%i)",user.GetPlayerName(),trunc3(AT_starting_score),trunc3(current.GetScore()),ATminrotamer,ATmaxrotamer))
end

function get_segment_scores_array(first,last,snap_count)
  local array1={}
  local seg
  local ix,ix2
  local attr={"clashing","packing","hiding","bonding","backbone","sidechain","reference","disulfides","other"}
  if first==nil then first=1 end
  if last==nil then last=structure.GetCount() end
  if snap_count==nil then snap_count=false else snap_count=true end
  ix2=1
  for seg=first,last do
    array1[ix2]={}
    array1[ix2][1]=seg
    array1[ix2][2]=current.GetSegmentEnergyScore(seg)
    for ix=1,#attr do
      array1[ix2][ix+2]=current.GetSegmentEnergySubscore(seg,attr[ix])
    end
    if snap_count==true then
      array1[ix2][#array1[ix2]+1]=rotamer.GetCount(seg)
    end
    ix2=ix2+1
  end
  return array1
end

function sort_by_column(a,b)
  if a[sort_column]<b[sort_column] then return true else return false end
end

function Acid(l1,l2,l3,sortidx) -- sortidx begins as AToption
  segments={}
  if ATend==nil then ATend=g_segments end
  for i=ATstart, ATend do
    segments[#segments+1]=i
  end
  if sortidx==nil then sortidx=0 end
  if sortidx==0 then
    for i=1,#segments do
      local r=math.random(#segments)
      segments[i],segments[r]=segments[r],segments[i]
    end
  else
    array1=get_segment_scores_array(ATstart,ATend,true)
    -- get_segment_scores_array is a function defined above
    sort_column=sortidx
    table.sort(array1,sort_by_column) 
    -- sort_by_column is a function (above) that uses the variable sort_column
    if ATreverse then
      for i=1,#segments do
          segments[#segments-i+1]=array1[i][1]
      end
    else
      for i=1,#segments do
          segments[i]=array1[i][1]
      end
    end
  end
  recentbest.Save()
  save.Quicksave(3)--in save 3 always best solution. Load in case of crash.
  s1=current.GetScore()
  if l1 then sidechain_tweak() end
  s2=current.GetScore()
  print(string.format("Tweak gain: %.3f",s2-s1))
  if l2 then sidechain_tweak_around() end
  s3=current.GetScore()
  print(string.format("Around gain: %.3f",s3-s2))
  if l3 then
   if ATalternate then
     sidechain_manipulate2()
   else
     sidechain_manipulate()
   end
  end
  s4=current.GetScore()
  print(string.format("Start score: %.3f",trunc3(s1)))
  print(string.format("Tweak gain: %.3f",s2-s1))
  print(string.format("Tweak gain: %.3f",s2-s1))
  print(string.format("Around gain: %.3f",s3-s2))
  print(string.format("Manipulate gain: %.3f",s4-s3))
  print(string.format("Total Acid gain: %.3f",s4-s1))
  print(string.format("End score: %.3f",trunc3(s4)))
end

function report_time(start_clock,start_time,clock_msg,time_msg)
  local seconds,minutes,hours,days
  if clock_msg==nil then clock_msg="CPU time" end
  if time_msg==nil then time_msg="Elasped time" end
  print(string.format("%s",os.date()))
  days,remainder=math.modf((os.clock()-start_clock)/(24*60*60))
  hours,remainder=math.modf(remainder*24)
  minutes,remainder=math.modf(remainder*60)
  seconds,remainder=math.modf(remainder*60)
  print(string.format("%s(%02id:%02ih:%02im:%02is)",clock_msg,days,hours,minutes,seconds))
  days,remainder=math.modf(os.difftime(os.time(),start_time)/(24*60*60))
  hours,remainder=math.modf(remainder*24)
  minutes,remainder=math.modf(remainder*60)
  seconds,remainder=math.modf(remainder*60)
  print(string.format("%s(%02id:%02ih:%02im:%02is)",time_msg,days,hours,minutes,seconds))
end

function Acid_Tweaker_gui()
  ATmenu=dialog.CreateDialog("Acid Tweaker")
  ATmenu.pass1=dialog.AddCheckbox("Pass 1",ATpass1)
  ATmenu.pass2=dialog.AddCheckbox("Pass 2",ATpass2)
  ATmenu.pass3=dialog.AddCheckbox("Pass 3",ATpass3)
  ATmenu.option=dialog.AddSlider("Option",AToption,0,12,0)
  ATmenu.alternate=dialog.AddCheckbox("Alternate",ATalternate)
  ATmenu.reverse=dialog.AddCheckbox("Reverse",ATreverse)
  ATmenu.start=dialog.AddTextbox("First seg",ATstart)
  if ATend==nil then ATend=structure.GetCount() end
  ATmenu.endx=dialog.AddTextbox("Last seg",ATend)
  ATmenu.minrotamer=dialog.AddTextbox("Min rotamer #",ATminrotamer)
  ATmenu.maxrotamer=dialog.AddTextbox("Max rotamer #",ATmaxrotamer)
  ATmenu.run=dialog.AddButton("Run",1)
  rc=dialog.Show(ATmenu)
  if rc==1 then
    ATpass1=ATmenu.pass1.value
    ATpass2=ATmenu.pass2.value
    ATpass3=ATmenu.pass3.value
    AToption=ATmenu.option.value
    ATalternate=ATmenu.alternate.value
    ATreverse=ATmenu.reverse.value
    ATstart=tonumber(ATmenu.start.value)
    ATend=tonumber(ATmenu.endx.value)
    ATminrotamer=tonumber(ATmenu.minrotamer.value)
    ATmaxrotamer=tonumber(ATmenu.maxrotamer.value)
    if ATmaxrotamer<1 or ATmaxrotamer>999 then ATmaxrotamer=999 end
    if ATminrotamer<1 then ATminrotamer=1 end
    if ATminrotamer>ATmaxrotamer then ATminrotamer=ATmaxrotamer end
 -- print(string.format("Just got inputs AT(min,max)rotamer=%i,%i.",ATminrotamer,ATmaxrotamer))
  end
end


--------------VV options below

--g_segments=g_segments-1 -- uncomment for lingard puzzles only!

useThat={ --only segments what have to be used OVERRIDES all below
--18,150,151,205,320,322,359,361,425,432,433 --382
}

useOnly={ --ranges what have to be used OVERRIDES BOTH LOWER OPTIONS
--{12,24},
--{66,66},
}
doNotUse={ --ranges that should be skipped
--{55,58},
--{12,33},
}
skipAA={ --aa codes to skip
'a',
'g',
}

note_number=structure.GetCount()
for seg=structure.GetCount(),1,-1 do
  if structure.GetNote(seg)~="" then break end
  note_number=seg
end
print(string.format("Recording Acid Tweaker results in Note for segment %i",note_number))
AT_starting_score=current.GetScore()



g_segments = structure.GetCount()   -- total number of segments in puzzle
g_total_score = 0   --  recent best to compare to and see if score was improved
g_score = {}    -- array of segment scores for comparisons (total for segment)

if ATgui then Acid_Tweaker_gui() end

segCount=structure.GetCount()
bestScore=current.GetScore()


start_clock=os.clock()
start_time=os.time()

print('V2 Acid Tweaker R v1.1g')
print('    doing puzzle '..puzzle.GetName())
print('    with puzzle ID '..puzzle.GetPuzzleID()..', '..segCount..' segments,')
print('    ATpass1-3='..tostring(ATpass1)..' '..tostring(ATpass2)..' '..tostring(ATpass3)..',') -- use tostring to print booleans as strings
print('    AToption='..tostring(AToption)..', ATalternate='..tostring(ATalternate)..', ATreverse='..tostring(ATreverse)..',')
print('    ATstart-ATend='..ATstart..'-'..ATend..',')
print('and AT(min,max)rotamer='..ATminrotamer..','..ATmaxrotamer..'.\n ')

print(string.format("Initial score: %.3f (%s)",trunc3(current.GetScore()),os.date()))
Acid(ATpass1,ATpass2,ATpass3,AToption) --all 3 passes

print("--------")
report_time(start_clock,start_time)
print("--------")