Recipe: Gary Rebuild Worst 3.1

created by Bruno Kestemont

Profile

• Name: Gary Rebuild Worst 3.1
• ID: 102513
• Shared with: Public
• Parent: Gary Rebuild Worst lua v2
• Children:
  • Gary Rebuild Worst 3.1 BP
• Created on: January 10, 2018 at 19:26 PM UTC
• Updated on: January 10, 2018 at 19:26 PM UTC
• Description:

  Rebuilding Worst Delta . Need 5 to reset delta. Based upon Walkin Rebuild but focuses on most impacted. Leaves secondary structure as is. Converted to lua v2 in order to make further improvements possible.

Code

--Gary Rebuild worst delta
--A modified version of Walkin Rebuild V4
--Now converted to Lua v2 by Susume
--V3 with dialog including new Min4Change by Bruno Kestemont 25/10/2017
--v3.1 cleanup with MovieSteps()

----------------------------------------
-- BEGIN V1 TO V2 CONVERSION LIBRARY
----------------------------------------

-- "lua v1 in v2" library by rav3n_pl
--just add it in front of your v1 code and use v2 and v1 code in v2 scripts :)

-- print(arg1[,...,argN]) no change :)

function  are_conditions_met()
    return current.AreConditionsMet()
end
function band_add_segment_segment(sgi1, sgi2)
    band.AddBetweenSegments(sgi1, sgi2)
end
function band_delete(bndIdx)
    if bndIdx~= nil then 
        band.Delete(bndIdx)
    else
        band.DeleteAll()
    end
end
function  band_disable(bndIdx)
    if bndIdx~=nil then
        band.Disable(bndIdx)
    else
        band.DisableAll()
    end
end
function  band_enable(bndIdx)
    if bndIdx~=nil then
        band.Enable(bndIdx)
    else
        band.EnableAll()
    end
end
function band_set_length(bndIdx, len)
    band.SetGoalLength(bndIdx, len)
end
function band_set_strength(bndIdx, str)
    band.SetStrength(bndIdx, str)
end
function get_band_count()
    return band.GetCount()
end
function  deselect_all()
    selection.DeselectAll()
end
function deselect_index(sgn)
    selection.Deselect(sgn)
end
function  select_all()
    selection.SelectAll()
end
function select_index(sgn)
    selection.Select(sgn)
end
function select_index_range(sg1,sg2)
    selection.SelectRange(sg1,sg2)
end
function do_freeze(bbone,schain)
    freeze.FreezeSelected(bbone,schain)
end
function do_unfreeze_all()
    freeze.UnfreezeAll()
end
function  do_global_wiggle_all(iters)
    structure.WiggleAll(iters,true,true)
end
function do_global_wiggle_backbone(iters)
    structure.WiggleAll(iters, true,false)
end
function do_global_wiggle_sidechains(iters)
    structure.WiggleAll(iters,false,true)
end
function do_local_rebuild(iters)
    structure.RebuildSelected(iters)
end
function do_local_wiggle(iters)
    structure.LocalWiggleSelected(iters,true,true)
end
function do_mutate(iters)
    structure.MutateSidechainsSelected(iters)
end
function do_shake(iters)
     structure.ShakeSidechainsSelected(iters)
end
function do_sidechain_snap(sgn, snap)
    rotamer.SetRotamer(sgn, snap)    
end
function get_sidechain_snap_count(sgn)
    return rotamer.GetCount(sgn)
end
function load_structure()
    save.LoadSecondaryStructure()
end
function save_structure()
    save.SaveSecondaryStructure()
end
function quickload(slot)
    save.Quickload(slot)
end
function  quicksave(slot)
    save.Quicksave(slot)
end
function get_exploration_score()
    return current.GetExplorationMultiplier()
end
function get_ranked_score()
    return current.GetScore()
end
function get_score()
    return current.GetEnergyScore()
end
function get_segment_distance(sg1,sg2)
    return structure.GetDistance(sg1,sg2)
end
function get_aa(sn)
    return structure.GetAminoAcid(sn)
end
function get_segment_count()
    return structure.GetCount()
end
function get_ss(sn)
    return structure.GetSecondaryStructure(sn)
end
function is_hydrophobic(sn)
    return structure.IsHydrophobic(sn)
end
function replace_aa(aa)
    for i=1,structure.GetCount() do
        if selection.IsSelected(i) then
            structure.SetAminoAcid(i, aa)
        end
    end
end
function replace_ss(ss)
    for i=1,structure.GetCount() do
        if selection.IsSelected(i) then
            structure.SetSecondaryStructure(i,ss)
        end
    end
end
function  get_segment_score(sg)
    return current.GetSegmentEnergyScore(sg)
end
function  get_segment_score_part(score_part,sg)
    return current.GetSegmentEnergySubscore(sg,score_part)
end
function reset_puzzle()
    puzzle.StartOver()
end
function restore_abs_best()
    absolutebest.Restore()
end
function restore_credit_best()
    creditbest.Restore()
end
function reset_recent_best()
     recentbest.Save()
end
function restore_recent_best()
    recentbest.Restore()
end
function  set_behavior_clash_importance(ci)
    behavior.SetClashImportance(ci)
end

-----------------------------------
-- END V1 TO V2 CONVERSION LIBRARY
-----------------------------------

CG303={}
game={}
gary={

 -- sort a table of talbes on element y
  -- of the embedded tables
  BubbleSort = function(x, y)
    s=gary.CopyScores(x)
    for i=1,#s - 1 do
      for j =#s, i + 1, -1 do
        if s[i][y] < s[j][y] then
          s[j], s[i] = s[i], s[j]
        end
      end
    end
    return s
  end,

  CopyScores = function(x)
    copy={}
    for i=1, #x do
      copy[i]={x[i][1], x[i][2]}
    end
    return copy
  end,

  GetSegScores = function()
    -- set of segment # and score at seg #
    local scores={}
    for i=1, game.segCount do --fill score table
      scores[i]={i, get_segment_score(i)}
    end
    return scores
  end,

  GetBadRange = function(segW,maxLen)
    -- get a set of segments up to maxLen with scores worst than segW
    local segWScore=get_segment_score(segW)
    local worstFound=true
    local len=1
    local segS=segW
    local segE=segW
    while (len<maxLen) and worstFound do
      worstFound=false
      if segS>1 then
        if get_segment_score(segS-1) < segWScore then
          segS=segS-1
          worstFound=true
          len=len+1
        end
      end
      if (segE<game.segCount) and (len<maxLen) then
        if get_segment_score(segE+1) < segWScore then
          segE=segE+1
          worstFound=true
          len=len+1
        end
      end
    end
    return segS, segE
  end,

  ZeroScores = function()
    -- set of segment # and score at seg #
    local scores={}
    for i=1, game.segCount do --fill score table with zeroes
      scores[i]={i, 0}
    end
    return scores
  end,

  AddScores = function(s1,s2)
    -- s1 and s2 need to be same size and order
    -- no test is performed
    local delta={}
    for i=1, #s1 do
      delta[i]={s1[i][1],s1[i][2] + s2[i][2]}
    end
    return delta
  end,

  SubtractScores = function(s1,s2)
    -- s1 and s2 need to be same size and order
    -- no test is performed
    local delta={}
    for i=1, #s1 do
      delta[i]={s1[i][1], s1[i][2] - s2[i][2]}
    end
    return delta
  end
}

function CG303.detect_ligand(flag)
 --[[
 ligand puzzle detection
 normally, segments have a secondary structure of "E", "H" or "L"
 and they always have a spatial distance of about 3.75 to 3.85 to their next index neighbour.
 a ligand is more far away.

 this function should respond true if this is a ligand puzzle, and false if it is not.
 if flag is nil, ligand auto-detection is enabled, distance of last two segments is checked
 if flag is not nil, ligand auto-detection is disabled, result is flag

 It also returns the last segment index which is no ligand
 ]]--

 local flag=flag

 local LastPos=get_segment_count() -- fetch very last segment index number

 if flag==nil then
   -- print("Detecting if there is a ligand.")
   local ss=get_ss(LastPos)
   flag=not(ss=="L" or ss=="H" or ss=="E" )
   -- if last segment's ss is neither "L" nor "H" nor "E"
   flag=flag or (get_segment_distance(LastPos-1,LastPos)>=3.9)
   -- or distance to second last segment is bigger or equal than 3.9
 end -- if

 local os="This should "
 if flag then
   LastPos=LastPos-1
  else
   os=os.."not "
 end -- if flag
 print(os,"be a ligand puzzle.")

 return flag,LastPos
end -- function

function Round(x)--cut all afer 3-rd place
    return x-x%0.001
end

function SelectSphere(sg, radius,nodeselect)
    if nodeselect~=true then deselect_all() end
    for i=1, game.segCount do
        if get_segment_distance(sg,i)<radius then select_index(i) end
    end
end

function AllLoop()
    do_unfreeze_all()
    select_all()
    replace_ss("L")
end

mingain = 0.05 --minimum gain per 2 wiggle iterations
buddies = 2 -- how many segments asida should be wiggled too (n, n+1 then n, n-1) 
            -- ie worst segment is no 44 and buddies set to 1 then
            -- willging seg 43+44; later seg 44+45 

function wig()
  local change=false
  ss=get_score(true)
  repeat
    sc=get_score(true)
    do_local_wiggle(4)
    se=get_score(true)
    wg=se-sc
  until wg<mingain
  es=get_score(true)
  if es<ss then 
    restore_recent_best()
  else
    change=true
  end
  deselect_all()
  return change
end

function wiggle(s)
        local change=false
    deselect_all()
    do_unfreeze_all()
    if s+1<=game.segCount then select_index(s+1)end
    if s-1>=1 then select_index(s-1)end 
    do_freeze(true, true)
    deselect_all()
    select_index(s)
    if wig() then change=true end
        
    if buddies > 0 then --select buddies
        for b=1, buddies do
            deselect_all()
            do_unfreeze_all()
            if s+b+1<=game.segCount then select_index(s+b+1)end
            if s-1>=1 then select_index(s-1)end 
            do_freeze(true, true)
            deselect_all()
            if s+b>game.segCount then select_index_range(s,game.segCount)
            else select_index_range(s,s+b)end
            if wig() then change=true end
            
            deselect_all()
            do_unfreeze_all()
            if s+1<=game.segCount then select_index(s+1)end
            if s-b-1>=1 then select_index(s-b-1)end 
            do_freeze(true, true)
            deselect_all()
            if s-b<1 then select_index_range(1,s)
            else select_index_range(s-b,s)end
            if wig() then change=true end
            deselect_all()
            do_unfreeze_all()
        end
    end
  return change
end

function Gibaj(jak, iters, minppi) --score conditioned recursive wiggle/shake
    if jak==nil then jak="wa" end
    if iters==nil then  iters=8 end
    if minppi==nil then minppi=0.04 end
    
    if iters>0 then
        iters=iters-1
        local sp=get_score(true)
        if jak == "s" then do_shake(1)
        elseif jak == "wb" then do_global_wiggle_backbone(25)
        elseif jak == "ws" then do_global_wiggle_sidechains(25)
        elseif jak == "wa" then do_global_wiggle_all(25) 
        end
        local ep = get_score(true)
        local ig=ep-sp
        if ig > minppi then Gibaj(jak, iters, minppi) end
    end
end

function BlueFuse(locally)
    reset_recent_best()
    if locally ~=true then select_all() end
    set_behavior_clash_importance(.05)
    do_shake(1)
    set_behavior_clash_importance(1)
    Gibaj()
    set_behavior_clash_importance(.07)
    do_shake(1)
    set_behavior_clash_importance(1)
    Gibaj()
    restore_recent_best()
    set_behavior_clash_importance(.3)
    do_global_wiggle_all(1)
    set_behavior_clash_importance(1)
    Gibaj()
    restore_recent_best()
end

function Lws(mingain)   --score conditioned local wiggle,
  local change=false
  set_behavior_clash_importance(1)
  if mingain==nil then mingain=1 end
  repeat --wiggles selected segments
    local ss=get_score(true)
    do_local_wiggle(4)
    local se=get_score(true)
    local wg=se-ss
    if wg<0 then
      restore_recent_best()
    else
      change=true
    end
  until wg<mingain 
  return change
end

function AfterRebuild(lws, bf,locally)
    if lws==nil then lws=true end
    if bf==nil then bf=true end
    reset_recent_best()
    set_behavior_clash_importance(1)
    Gibaj("s",1)
    Gibaj("ws",1)
    Gibaj("s",1)
    Gibaj("ws",1)
    if lws then Lws(4) end
    if bf then BlueFuse(locally) end
    select_all()
    Gibaj()
end

function Rebuild(maxIters)--local rebuild until any change
    if maxIters==nil then maxIters=5 end
    local s=get_score(true)
    local i=0
    repeat
        i=i+1
        if i>maxIters then break end--impossible to rebuild!
        do_local_rebuild(i)
    until get_score(true)~=s 
    if get_score(true)==s then return false else return true end
end

function LocalRebuild(ss,se,maxiters,sphere, lws, bf)
  local change=false
  deselect_all()
  select_index_range(ss,se)
  local sc=get_score(true)
  local ok=Rebuild(maxIters)
  if ok then
    for s=ss, se do
      SelectSphere(s,sphere,true)
    end
    AfterRebuild(lws,bf,true)
  end

  local gain =get_score(true)-sc
  if gain>0+Min4Change then
    quicksave(3)
    print("Gained: ",get_score(true)-sc," NewScore: ",get_score(true))
    change=true
  elseif gain<0+Min4Change then
    quickload(3)
  else
    print("Failed")
  end
  return change
end

function Build(sSeg, eSeg, backward, len, maxiters, loopmode, sphere, lws, bf)
    if backward then
        for i=eSeg, sSeg,-1 do
            local ss=i-len+1
            if ss>sSeg then
                LocalRebuild(ss,i,maxiters,sphere, lws, bf)
            end
        end
    else
        for i=sSeg, eSeg do
            local se=i+len-1
            if se<game.segCount then
                LocalRebuild(i,se,maxiters,sphere, lws, bf)
            end
        end
    end
end

function gary.RebuildDelta(maxLen, maxiters, sphere, lws, bf, minChange, initRebuilds)
  local sscore = get_score(true)
  local rebuilds=initRebuilds
  print("Gary Rebuild Delta started. Score: ",Round(sscore))
  print("delta calculated after ",initRebuilds," good rebuilds")
  reset_recent_best()
  
  for j= 1, 1000 do
	  quicksave(3)
	  do_unfreeze_all()
	  deselect_all()

	  local oscores=gary.GetSegScores()
	  local delta=gary.BubbleSort(oscores,2)
	  local i=#delta
	  local segW=delta[i][1]
	  local segS, segE = gary.GetBadRange(segW,maxLen)
	  repeat
		if segS~=segE then
		  print("Working on sgmnts ",segS,"-",segE," with delta ", delta[i][2])
		else
		  print("Working on sgmnt ",segS," with delta ", delta[i][2])
		end
		local oldScore=get_score(true)
		if LocalRebuild(segS,segE,maxiters,sphere, lws, bf) then --if enough gain
		  SaveBigSteps()
		  if get_score(true) - oldScore > minChange then
			minChange=minChange / minChangeDelta
			if rebuilds>2 then
			  rebuilds=rebuilds-1
			  print("Need ", rebuilds," more.")
			  i=i-1
			else
			  rebuilds=initRebuilds
			  for x=segS,segE do
				oscores[x][2]=get_segment_score(x)
			  end
			  nscores=gary.GetSegScores()
			  delta=gary.BubbleSort(gary.SubtractScores(nscores,oscores),2)
			  i=#delta
			end
		  else
			i=i-1
		  end
		  if i > 0 then
			segW=delta[i][1]
			segS, segE = gary.GetBadRange(segW,maxLen)
		  end
		else
		  minChange=minChange * minChangeDelta
		  if segS < segE then
			segS, segE=gary.GetBadRange(segW,segE-segS)
		  else 
			i=i-1
			if i > 0 then
			  segW=delta[i][1]
			  segS, segE = gary.GetBadRange(segW,maxLen)
			end
		  end
		end
	  until i==0
	  print("Total rebuild gain: ",Round(get_score(true)-sscore))
	  OldMin4Change= Min4Change
	  Min4Change=Min4Change * minChangeDelta *0.9
	  print("Changing gain condition to "..Round(Min4Change).. " from "..Round(OldMin4Change))
	  
  end
end
  
function ReBuild(sSeg, eSeg, backward, minLen, maxLen, maxiters, loopmode, sphere, lws, bf)
    local sscore = get_score(true)
    print("Walking Rebuild started. Score: ",Round(sscore))
    do_unfreeze_all()
    deselect_all()
    if loopmode then
        save_structure()
        AllLoop()
    end
    reset_recent_best()
    quicksave(3)
    for i=minLen, maxLen do
        Build(sSeg, eSeg, backward, i, maxiters, loopmode, sphere, lws, bf)
    end
    
    print("Total rebuild gain: ",Round(get_score(true)-sscore))
    if loopmode then load_structure() end
end

function get_parameters ()

  local dlog = dialog.CreateDialog ( "Gary Rebuild Worst" )

  dlog.sSeg = dialog.AddSlider ( "From seg" , sSeg , 1 , eSeg-1 , 0 )
  dlog.eSeg = dialog.AddSlider ( "To seg" , eSeg , 2 , eSeg , 0 )
  

  dlog.initRebuilds = dialog.AddSlider ( "Init Rebuilds" , initRebuilds , 1 , 20 , 0 )  
  dlog.backward=dialog.AddCheckbox ( "Backward " , backward ) 

  dlog.minLen = dialog.AddSlider ( "Min len 2 rebuild" , minLen , 1 , 2 , 0 )
  dlog.maxLen = dialog.AddSlider ( "Max len 2 rebuild" , maxLen , 2 , 8 , 0 )
  dlog.maxiters = dialog.AddSlider ( "Max nb rebuilds" , maxiters , 2 , 8 , 0 )  
  dlog.loopmode=dialog.AddCheckbox ( "Loopmode " , loopmode )  
  dlog.sphere = dialog.AddSlider ( "Sphere" , sphere , 2 , 20 , 0 ) 
  dlog.lws=dialog.AddCheckbox ( "lws " , lws )
  dlog.bf=dialog.AddCheckbox ( "bf " , bf )
  dlog.minChange = dialog.AddSlider ( "Min Change" , minChange , 0.1 , 5 , 1 ) 
  dlog.minChangeDelta = dialog.AddSlider ( "Min Change Delta" , minChangeDelta , 0.01 , 1.99 , 2 )
  dlog.Min4Change = dialog.AddSlider ( "Min gain 2 save" , Min4Change , 0 , 100 , 0 )
  
  dlog.ok = dialog.AddButton ( "OK" , 1 )
  dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

  if ( dialog.Show ( dlog ) > 0 ) then
	  sSeg = dlog.sSeg.value
	  eSeg = dlog.eSeg.value
	  initRebuilds = dlog.initRebuilds.value  
	  backward= dlog.backward.value
	  minLen = dlog.minLen.value
	  maxLen = dlog.maxLen.value
	  maxiters = dlog.maxiters.value 
	  loopmode=dlog.loopmode.value
	  sphere = dlog.sphere.value
	  lws=dlog.lws.value
	  bf=dlog.bf.value
	  minChange = dlog.minChange.value 
	  minChangeDelta = dlog.minChangeDelta.value
	  Min4Change=dlog.Min4Change.value	  
	  
    return true
  else
     return false
   end

end

--START Movie store big steps

--SLOTS:
--[[
50-100 used to record each big steps for movie at the end
]]--
SlotStepStart=50 -- New 4/11/2014
SlotStep=SlotStepStart


	StepScore= get_score(true)
	
function StoreBigStep()
	StepScore= get_score(true)
	save.Quicksave(SlotStep)
	SlotStep=SlotStep+1
end	

function SaveBigSteps() -- in order to be able to display big steps afterwards in undos
	local s= get_score(true)
	local g= s-StepScore

	if s >0 and ( (s <7000 and g>500) or (s <9000 and g>200) or (s <10000 and g>100) or (s >10000 and g>50)) then
		StoreBigStep()
	end
end

function MovieSteps()
	undo.SetUndo(true)
	print("See remembering of big steps in undos")
	for i= SlotStepStart, SlotStep do
		save.Quickload(SlotStep)
	end
	--save.Quickload(3)
	
end

--END Movie store big steps

--[[ options
ReBuild(sSeg, eSeg, backward, minLen, maxLen, maxiters, loopmode, sphere, lws, bf)
sSeg- start segment to rebuild
eSeg- end segment to rebuild
backward- start from end
minLen- minimum sgmnts len to rebuild (may be even 1)
maxLen- maximum len to rebuild (over 7 seems useless)
maxiters- maximum tries to rebuild
loopmode- work in all-loop mode
sphere- sphere size for shake/wiggle after rebuild
lws- LWS sphere around (min gain 2pts, not LWSing totally)
bf- BlueFuze sphere around
minChange- minimum change to accept as a change
initRebuilds- Rebuilds needed to calcualte delta.
]]--


game.isLigand, game.segCount=CG303.detect_ligand()

sSeg=1
eSeg=game.segCount
backward=false
minLen=1
maxLen=2
maxiters=5
loopmode=true
sphere=9
lws=true
bf=true
minChange=0.5
minChangeDelta=.99
initRebuilds=5
Min4Change = 0 -- new fo sketchbook (BK)
--ReBuild(sSeg, eSeg, backward, minLen, maxLen, maxiters, loopmode, sphere, lws, bf)



function Cleanup(err) -- NEW BK
    print("Restoring CI, best result, filter and structures")
    CI(1)
	undo.SetUndo(true)
    MovieSteps()
	save.Quickload(3)
	--MovieSteps()
    print(err)
end

function main()
	if get_parameters () then
		gary.RebuildDelta(maxLen, maxiters, sphere, lws, bf, minChange, initRebuilds)
	end
end

xpcall(main,Cleanup)

Comments

[Bruno Kestemont]

With dialogs including a limit acceptable points per round
Cleanup & store big steps

[AtOneMent]

Rebuild delta.
Number of good rebuilds and others.

It would be nice to see a description of what they are/do. If there is already a description, please include the link to it.

Pretty please!

[Bruno Kestemont]

For most of the recipes, you have the explanations in comments in the code of the recipe. Please open the code and read there.
Most of the terminology used here is standard to many recipes.
bf= blue fuze
lws = local wiggle strategy
delta is often the loss accepted for a rebuild before to shake and wiggle it
minimum gain is linked to the minimum gain accepted to go on with a solution etc.