Recipe: Ebola 4.3

created by Bruno Kestemont

Profile

• Name: Ebola 4.3
• ID: 101746
• Shared with: Public
• Parent: None
• Children:
  • Ebola 4.2.6 repost
  • Ebola 4.3_MS
• Created on: January 05, 2019 at 17:30 PM UTC
• Updated on: January 05, 2019 at 17:30 PM UTC
• Description:

  Interlinked edrw and GAB worst. With a wizard for the options, an ooc (options out of context)

Code

--[[A reset of Ebola concept, By Bruno Kestemont:
A merge of TvdL250beta and GABcut
    Based on Tvdl Rav3n_pl Deep Rebuild v3.x (and Rav3n_pl GAB (both enhanced by BK)
    
    edrw on each zone of x segments, then GAB using always the same zones
    then next zone of y segment, then GAB etc.
    Note: GAB is always started, even if no rebuild gain
    This is different from original Ebola, where GAB was only started if DRW minimum gain.
    To Do: change this
    
    WARNING!
    1) Script uses a lot of save slots
    2) (selected) Best score are always in slot 3
    
Slot attribution:

2= BestScoreNF3Slot = best score (filters disabled)
3 = BestScoreSlot = selected best (could be score or filter or both)
4 = TotalSlot = Fuse or rebuild results (Total)
5 = LocTotalSlot = loctotal (MUST be 5 for edrw)
6-17 used by edrw (initialized) for subscore slots WARNING ! May be more !!!!! then it will bug
18 = BestFilterBonus3 --- This slot to be evaluated !! not sure is not used in edrw BK 11/11/2014
19 = PreferredScoreSlot = preferred see Savebest
20 = BestItelligentSlot = best compromise between filter and score
21 =BestFilterSlot -- BK 11/11/2014 -- Best filter score only
22 =PreferrredFilterSlot -- BK 11/11/2014 -- best filter not on any cost
50-100 gradually used for recipe


GAB Slots

23 = BestGABslot (was 3 in original recipe)
24 = GABrbSlot
25 = GABherSlot
30-49 used to record each big steps for movie at the end


Description:
This is a long run rebuilder. Idea is to rebuild given/found area so many tyimes to found better position.
Each rebuild is scored in different ways and saved if better.
After rebuild finishes script is trying to stabilize each different saved position.
Because some positions are best in more than 1 way sometimes it is only 1 positions to stabilize.
On the best position a fuze is run if it looks promising enough.

Changed by: Timo van der Laan 17-12-2011 till 28-12-2012
Changed by Bruno Kestemont 29-12-2012 till 11-11-2014
added Idealize, remix, filter management... all experimental
]]-- Introduction

--[[ Overview:

This version of Rav3n_pl DRW has several new features.

First of all it is made totally V2 and uses option dialogs.
It has an optimised fuze and qStab, and will run a lot faster as the original.
The main optimalisation is that futile shakes and allready tried rebuilds are skipped.
Another one is that unprommissing fuzes can be skipped.
Features (most have parameters):
1. Can be used in design puzzles, has mutate options for that.
2. It will only recompute the next rebuild if there has been enough gain
3. It will not try to rebuild the exact same segments for a second time
4. It will not try a fuze if the loss is too great depending on the size of the rebuild
5. It will not try to rebuild frozen or locked parts
6. You can specify what parts of the protein to work on.
7. If you want it can keep disulfide bridges intact (thanks Brow42)
8. If the starting score is negative, default is that no wiggles will be done to avoid exploding the protein.
9. If stopped, it will reset CI, best score and secondary structures.
10. You can skip a number of worst parts (handy after a crash)
11. It breaks off rebuild tries if no chance of success.
12. It works on puzzles even if the score is < -1000000 (but will be slower).
13. Fuze and qStab can be suppressed (default if score is negative from the start)
14. You can specify to disable bands when rebuilding and enable them afterwards.
NEW in version 2
15. You can choose which slots will be active (slots = archive of subscores)
"After each rebuild there is a small local shake to remove clashes. After the rebuild phase qstab is run on each slot selected 
and only the best result will be fuzed if the score is high enough.
I always include slot 4 (total score)"
16. You can choose which segment scoreparts count for finding worst
17. It will recognize puzzle properties and set defaults for it
18. Instead of skipping cycles you can specify nr of worst to skip
19. On ED puzzles the other component is given proper weight for finding worst
20. Code has been cleaned up
21. And something special for Auntdeen :-)
2.1.0 Added code for disjunct searching, fixed bridgesaving init.
2.1.1 Changed some max and min slider values and autodetects Layer Filter
2.2.0 Added ligand slot
2.3.0 GRRR Had to change other by Density
2.4.0 Dynamic list of active subscores,
      Puts back the old selection when stopped,
      Added rebuildnumber to the gainslot,
      Added alternative local cleanup after rebuild,
      Resets the original structure if mutated after rebuild for the next rb,
      Sets default mutate settings if a design puzzle.
	  
2.4.0 nc  BK adapted for New Chapter 08/02/2014
2.4.1 nc BK 09/02/2014 optimized for new Chapter (longer but better wiggle)
2.5.0 beta BK 11/11/2014 added filter score management for slots options

EBOLA
3.0 = first merge
3.1 = better score concepts management
3.1.1 = added slot subscore name 17/12/2014 in order to better understand what happens
3.2. Original edrw50 wiggle function + added filter management inside it
3.2.1 Trying to optimize filters versus score
3.2.2 Enable filter on each score computing: NOTE that if you start with filter disabled, it will do everything like this unless the score computing
      more gab generations like in original ebola
3.3  Filter included in slots
3.3.1 Reset options, from fast to slow
3.3.2 Generic Filter Management by BitSpawn
3.4 GAB options
3.4.1 Log cleaning ("recovering" was not correct) + optimize the GAB breeding generations
3.4.2 Filter management default at the start of the recipe, debugged, added FUZE2BEST
3.4.3 trying to fig cut bug (by including save and recentbest in generic filter funtions)
3.4.4 skipping slot RB solutions when cost of total slot points it too high (>100 pts)
trying to fix the bug preferred GAB score ingnored
3.4.5 huge threshold for missed gains (went against the new slot policy)
skipping threshold default changed, changed filter skip default threshold
3.4.6 Trying to fix bug filters default always disabled
3.4.7 Trying to correct the starting fuze problem
3.4.8 Higher Max length limit in order to be able to rebuild a very big part
3.4.9 Higher cost for filters allowed (but still not allowing to looze > 2 pts filter for 1 pt score)
included automatic options for herds and critters
3.5 TOOMUCHFILTERLOSS implemented in order to stop going down too far with herd
3.6 Contextual options
TOOMUCHFILTERLOSS: on the level of critters, not herd
reinitialize UseSegments each starting GAB (onterwise it was cumulative)
3.6.1 debugged contextual options for ED
3.6.2 Use ligand in rebuild and GAB if ligands
3.6.3 Slow Filter cleaning + delete power test + some GAB slower on choice 5 + only GAB compatible
TO DO: not allowing lost = always taking only the best score (for quick run)
3.7: TvdLmaxbonus for fast filter management 29/03/2015
reducing the number of time score is calculated (this is slow)
3.7.1 refinements of scores & NEGATIVEFILTER filter default options + bigger SkipSlotThreshold
3.7.2 started new SaveBest3
3.7.3 added CUTWORST
3.7.4 refinements of NEGATIVEFILTER and ScorePriority
3.7.5 bug score log hopefully fixed
3.7.6 refinement default options, scores, filters and added gabfilterHigh
3.7.7 tvdl filter option implemented (test with prefered score)
3.7.8 still trying to debug the score log
3.7.9 debugged for Marburg
3.8   jeff101 info each generation, and reduced GAB threshold
3.8.1 debugged and added last which
3.8.2 hopefully debugged cut in worst
3.8.3 starting with "backbone" worst till 2 days before the end, 30/11/2015, and other WorstGroups like in parent ER
	contextual option if recipe already used (nskip skipping 2 worst parts to save time ) 3/12/2015
	Most options are in QuickOptions(choice) where choice = velocity
3.8.4 better score log for cycles
	Skip fuze on first days when running on HANDFOLD puzzles
3.8.5 From can be longer than to (first dialog)
	and thus deleted Longest in the "more" options
3.9.0 FILTERPROTECT: No significant filter loss allowed on mutate (it's a loss of time)
	LostFpgain will be the loss allowed for filter if any gain in mutate
	Avoids to calculate filters again and again (hopefully saving time)
3.9.1 Keeps user bands and activated bandflip in DRW (disabling existing bands in rebuild)
	AddBand2UserBands optional on each critter if existing bands between symmetrics (experimental)
	Bands to space are already working (but they must start from an active segment)
3.9.2 Debug bands
3.9.3 Accelerating start (GENERICFILTER problem) and with FILTERON feature
4.0.0 maxLenLimit till full length of the protein, also on min (allows a kind of FSP)
	  GAB option for Band in Space probability
	  designProtect: freezes backbones of non selected (avoids some macro moves)
4.0.1 made a function StatusGen(nrofRuns)
	  Only turning hydrophobics to center
	  AlwUseLigand= false always by default because there is a Foldit bug of false ligands after using auto structure
	  BUG useLigand should also be false in case of the bug.
4.0.2 Fixed turning hydrophobics only for BBS	  
4.0.3 Archiving changed options in note. The idea is to keep track on default options that have been changed, in order to inform other
	players of succesfull options
4.0.5 fixed: bug some options don't change when changing velocity ! (nrskip) and from-to don't change after subdialogs
4.0.6 Added undo disabling  (to save time on old computers) and reset default nb worst on velocity 5
4.1.0 Added remix tool and no rebuild case
4.1.1 Reactivated GAB in all cases
4.1.2 Split idealize and remix for better performance
	  Introduced StartEbolaScoreLater in case of very long run
4.1.3 tvdl filter fixed (hopefully) when priority = score: TvdLFilteractive and ScorePriority==0
4.1.4 if NOREBUILDMODE then GABfilter=-1 always as default (ebola is then mainly used for its remix)
4.1.5 if rebuild =0, not necessarilly only gab + other ways to identify no rebuild mode from description
		fixed uncut worst
4.1.6 small thinks for mutates when not HASMUTABLE
4.1.7 added SUSPECTNOREBUILD in case "no rebuild" is not mentioned in a design puzzle (the user can confirm or still want to rebuild)
		 to ensure that remix and idealize will replace Rebuild in most Design puzzles
4.1.8 filters on on band.commands (in order to prevent unideal loop bug)
4.1.9 oops fixed SUSPECTNOREBUILD
4.2.   higher SkipSlotThreshold
	   jeff101 verbose StatusGen and SaveBigSteps on each sub-loop
	   ContextualOptions() every day (for very long run, user options will be partially erased every day)
	   Auto Pilot Mode after some time: HoursResetOptions
4.2.1 oops fixed previous autopilot
4.2.2  OOPS !! fixed GAB error (it didn't start from rebuild recult but from best result !!!)
4.2.3 Option in case of Sketchbook puzzle
4.2.4 added minppi option in first dialog for SKETCHBOOK
4.2.5 new wiggle
4.2.6 changed defminppi in evaluations TE BE EVALUATED !
4.3 GRRR adapted filter setting to new lua commands: return2GlobalOriginalFilterSetting()

	  NOTE: to verify FILTERON use
	  
	  TO DO: freeze segments (backbone/sidechain) with higher scores, or select only x higher
	  TO DO: duplicated bands for hydrophobics pull on worst hide scores
	 
]]-- Versions

recipename="Ebola 4.3"
defUndo= false
undo.SetUndo(defUndo)

print(recipename)
print("Inspired by Ebola Rebuild by Jean-Bob and L'Alliance Francophone")
print(os.date())

CIfactor=1

function CI(CInr)
    behavior.SetClashImportance(CInr*CIfactor)
end

function CheckCI()
   local ask=dialog.CreateDialog("Clash importance reset to 1")
   ask.l1=dialog.AddLabel("Last change to change it")
   ask.l2=dialog.AddLabel("CI settings will be multiplied by set CI")
   ask.l3=dialog.AddLabel("WAIT for main dialog ! (now adjusting best options to power conditions)")
   ask.continue=dialog.AddButton("Continue",1)
   dialog.Show(ask)
end

if behavior.GetClashImportance() < 0.99 then CI(1) CheckCI() end -- default = 1 it's rare we want something else
CIfactor=behavior.GetClashImportance()

userbands=band.GetCount()
print(userbands..' user-supplied bands.\n ')

function round3(x)--cut all afer 3-rd place
    return x-x%0.001
end

function down(x)
    return x-x%1
end

function Max(x,y)
 if x>y then return x else return y end
end


--ooc parameters
startRecTimeSec= os.time() -- also for HoursRun()
timeLeft=os.difftime(puzzle.GetExpirationTime(),startRecTimeSec)/86400 -- in days
startRecTime=os.clock () -- New BK 11/10/13 to calculate client power for options
LoopOptions=0
function HoursRun(StartTime)
	local StartTime = StartTime or startRecTimeSec -- in seconds
	local result= os.difftime(os.time(),StartTime)/3600 -- in hours
	local minutes = down((result - down(result))*60)
	print(down(result)..":"..minutes.." hours busy with same options")
	return result -- in hours
end

-- START Wiggle Power Setting stuff
function DisplayLongWigglePower ()
	local PowerSetting = behavior.GetWigglePower()
	local result = ""
	if PowerSetting == "l" then result = "Low"
	elseif PowerSetting == "m" then result = "Medium"
	elseif PowerSetting == "h" then result = "High"
	elseif PowerSetting == "a" then result = "Auto"
	end
	return result
end
OriginalWPowerSetting= DisplayLongWigglePower ()
print(OriginalWPowerSetting .. " Wiggle Power")

function CheckWP() -- including Alarm Dialog
	if OriginalWPowerSetting == "Low" or OriginalWPowerSetting == "Auto" then
	   local ask=dialog.CreateDialog("Wiggle Power is ".. OriginalWPowerSetting)
	   ask.l1=dialog.AddLabel("Are you sure ?")
	   ask.continue=dialog.AddButton("Continue",1)
	   ask.stop=dialog.AddButton("Cancel",0)
	   askresult=dialog.Show(ask)
	   if askresult < 1 then return false end
   end
   return true
end

-- STOP Wiggle Power Setting stuff

--START Generic Filter Management by BitSpawn 21/12/2014
--Source: http://fold.it/portal/node/1998917

--identifying filtered puzzles and all properties
OriginalFilterSetting = filter.AreAllEnabled()
PROBABLEFILTER= false
GENERICFILTER=false
FIRSTGENERICFILTER=false -- used if changing GENERICFILTER on the fly
FILTERMANAGE= false
FILTERON=not OriginalFilterSetting -- order to save time in score functions
NEGATIVEFILTER= false -- true= big preference for filter growth (on the cost of score) new 15/4/2015
HASMUTABLE= false
IDEALCHECK= false
PROBABLESYM= false
SEPSIS= false
ELECTRON= false
DISULFIDEBONUS= false -- NOT USED
CENTROID= false
HOTSPOT= false
HANDFOLD=false -- identifies recipes just after a hand fold (necessity to protect the HF design)
NOREBUILDMODE= false
SUSPECTNOREBUILD= false
SKETCHBOOK = false
sym=1


function return2GlobalOriginalFilterSetting()
	if OriginalFilterSetting then -- if true, all filters are default enabled
		filter.EnableAll()	--Enables all filters
	else
		filter.DisableAll()	--Disables all filters
	end

end


function detectfilterandmut() -- new BK 10/10/2013; 13/2/2015; 5/12/2016; 4/1/2019
	local descrTxt=puzzle.GetDescription()
	local puzzletitle=puzzle.GetName()
	if #descrTxt>0 and (descrTxt:find("Sketchbook") or descrTxt:find("Sketchbook")) then
		SKETCHBOOK =true
	end
	if #puzzletitle>0 and puzzletitle:find("Sketchbook") then -- new BK 17/6/2013
		SKETCHBOOK =true
	end
	if #descrTxt>0 and (descrTxt:find("filter") or descrTxt:find("filters") or descrTxt:find("bonus") or descrTxt:find("bonuses") and not descrTxt:find("disabled"))then
		PROBABLEFILTER=true
		FILTERMANAGE=true -- default yes during wiggle (will always be activate when scoring)
		GENERICFILTER=false -- to be evaluated
	end
	if #descrTxt>0 and (descrTxt:find("H-bond networks") or descrTxt:find("Hydrogen Bond Networks") or descrTxt:find("H-bond Networks") 
		or descrTxt:find("H-bond Network") and not descrTxt:find("disabled"))then
		PROBABLEFILTER=true
		FILTERMANAGE=false -- default no
		GENERICFILTER=false -- to be evaluated
	end	
	if #descrTxt>0 and (descrTxt:find("design") or descrTxt:find("designs")) then
		HASMUTABLE=true
		IDEALCHECK=true
		HANDFOLD=true
	end
	if #descrTxt>0 and (descrTxt:find("De-novo") or descrTxt:find("de-novo") or descrTxt:find("freestyle")
		or descrTxt:find("prediction") or descrTxt:find("predictions")) then
		IDEALCHECK=true
		HANDFOLD=true
	end

	if #puzzletitle>0 then
		if (puzzletitle:find("Sym") or puzzletitle:find("Symmetry") or puzzletitle:find("Symmetric")
				or puzzletitle:find("Dimer") or puzzletitle:find("Trimer") or puzzletitle:find("Tetramer")
				or puzzletitle:find("Pentamer")) then
			PROBABLESYM=true
			if puzzletitle:find("Dimer") and not puzzletitle:find("Dimer of Dimers") then sym=2		
			elseif puzzletitle:find("Trimer") or puzzletitle:find("trimer") then sym=3
			elseif puzzletitle:find("Dimer of Dimers") or puzzletitle:find("Tetramer") then sym=4
			elseif puzzletitle:find("Pentamer") then sym=5
			else sym=6
			end
		end
	end
	if #descrTxt>0 and (descrTxt:find("Sym") or descrTxt:find("Symmetry") or descrTxt:find("Symmetric")
			or descrTxt:find("sym") or descrTxt:find("symmetry") or descrTxt:find("symmetric")) then
		PROBABLESYM=true
		if (descrTxt:find("Dimer") or descrTxt:find("dimer") or descrTxt:find("C2 symmetry") or descrTxt:find("twoo symmetric"))
			and not (descrTxt:find("Dimer of Dimers") or descrTxt:find("dimer of dimers")) then sym=2 
		elseif descrTxt:find("Trimer") or descrTxt:find("trimer") or descrTxt:find("C3 symmetry") or descrTxt:find("three symmetric") then sym=3
		elseif (descrTxt:find("Dimer of Dimers") or descrTxt:find("Tetramer") or descrTxt:find("C4 symmetry") or descrTxt:find("four symmetric"))
			and not (descrTxt:find("dimer of dimers") or descrTxt:find("tetramer"))then sym=4 
		elseif descrTxt:find("Pentamer") or descrTxt:find("pentamer") or descrTxt:find("C5 symmetry") or descrTxt:find("five symmetric") then sym=5
		else sym=6
		end
	end
	--print resulting sym info
	if PROBABLESYM then
		print("Symmetric")
		if sym==2 then
			print("Dimer")
		elseif sym==3 then
			print("Trimer")
		elseif sym==4 then
			print("Tetramer")
		elseif sym==5 then
			print("Pentamer")
		elseif sym>5 then
			print("Terrible polymer")
		end
	else print("Monomer")
	end

	if #puzzletitle>0 and puzzletitle:find("Sepsis") then -- new BK 17/6/2013
		SEPSIS=true
		HANDFOLD=true
		--p(true,"-Sepsis")
		print("Sepsis")
	end
	if #puzzletitle>0 and puzzletitle:find("Electron Density") then -- for Electron Density
		--p(true,"-Electron Density")
		ELECTRON=true
		HANDFOLD=true
		print("Electron density")
	end
	if #puzzletitle>0 and puzzletitle:find("Centroid") then -- New BK 20/10/2013
		--p(true,"-Centroid")
		CENTROID=true
		print("Centroid")
	end
	if #puzzletitle>0 and puzzletitle:find("Hotspot") then -- New BK 21/01/2014
	HOTSPOT=true
	print("Hotspot")
	end
	if #puzzletitle>0 and (puzzletitle:find("No Rebuilding!") or puzzletitle:find("No Rebuilding")) then -- New BK 21/01/2014
		NOREBUILDMODE=true
		print("No Rebuild allowed")
	end
	if #descrTxt>0 and (descrTxt:find("Rebuild action has been disabled") or descrTxt:find("No Rebuilding")) then
		NOREBUILDMODE=true
		print("No Rebuild allowed")
	end
	
	return
end
detectfilterandmut()


-- function to copy class/table


function CopyTable(orig)

    local copy = {}

    for orig_key, orig_value in pairs(orig) do

        copy[orig_key] = orig_value  

    end

    return copy

end

-- functions for filters

function FiltersOn()
	if not FILTERON then
		--if filter.AreAllEnabled() then
			filter.EnableAll()
			FILTERON=true
		--end
	end
end

function FiltersOff()
	if FILTERON then
		--if behavior.GetFiltersDisabled()==false then
			filter.DisableAll()
			FILTERON=false
		--end
	end
end

-- function to overload a funtion

function mutFunction(func)

    local currentfunc = func

    local function mutate(func, newfunc)

        local lastfunc = currentfunc

        currentfunc = function(...) return newfunc(lastfunc, ...) end

    end

    local wrapper = function(...) return currentfunc(...) end

    return wrapper, mutate

end

-- function to overload a class

-- to do: set the name of function

classes_copied = 0

myclcp = {}

function MutClass(cl, filters)

    classes_copied = classes_copied+1

    myclcp[classes_copied] = CopyTable(cl)

    local mycl =myclcp[classes_copied]

    for orig_key, orig_value in pairs(cl) do

        myfunc, mutate = mutFunction(mycl[orig_key])

        if filters==true then

            mutate(myfunc, function(...)

                FiltersOn()

                if table.getn(arg)>1 then

                    -- first arg is self (function pointer), we pack from second argument

                    local arguments = {}

                    for i=2,table.getn(arg) do

                        arguments[i-1]=arg[i] 

                    end

                    return mycl[orig_key](unpack(arguments))

                else

                    --print("No arguments")

                    return mycl[orig_key]()

                end

            end)   

            cl[orig_key] = myfunc

        else

            mutate(myfunc, function(...)

                FiltersOff()

                if table.getn(arg)>1 then

                    local arguments = {} 

                    for i=2, table.getn(arg) do

                        arguments[i-1]=arg[i]  

                    end

                    return mycl[orig_key](unpack(arguments))

                else

                    return mycl[orig_key]()

                end

            end)   

            cl[orig_key] = myfunc
        end
    end
end

-- how to use:
--setting default options if filters BK 4/2/2015
--MutClass(structure, false)
--MutClass(band, false)
--MutClass(current, true)

--[[ it does not work well here, better to put it after dialog?
if GENERICFILTER then -- WARNING: TO VERIFY !! (may be it's irreversible for several funtions bellow)
	MutClass(structure, false)
	MutClass(band, false)
	MutClass(current, true)
	MutClass(recentbest, true) -- otherwise, it remembers cut solutions
	MutClass(save, true) -- better to save with full score
end
]]--		
--STOP Generic Filter Management

---COMMON DRW and GAB
FiltersFirst=false -- new BK 11/11/2014 To evaluate (will be true for filtered puzzles depending on options)
GABfilter=5 -- max loss (0-50) for launching GAB after each rebuild (on slots). 70-GABfilter is the min rebuild gain for full GAB after each rebuild session
SkipGAB=false -- not really needed in dialog since we can put GAB threshold at minimum
FUZE2BEST=true -- also fuze the second best solution after stabilizing slots (unless it is too low)
GABfilterHigh=20 -- max gain (if more, continue only with rebuilds - case normal edrw)
onlyGAB=false -- not used yet, but it's envisageable last day may be?

function p(fmt, ...)
	if #arg==0 then print(fmt or '')
	elseif arg==nil then return--print(fmt or '')-- added BK 23/3/13 -- supressed empty lines 11/6/2013
	elseif fmt==nil then return--print('')-- added BK 23/3/13 -- supressed empty lines 11/6/2013
	else print(string.format(fmt, unpack(arg))) end
end

--eDRW START ############################################################
-- Handy shorts module
normal= (current.GetExplorationMultiplier() == 0)
segCnt=structure.GetCount()
segCnt2=segCnt
while structure.GetSecondaryStructure(segCnt2)=="M" do segCnt2=segCnt2-1 end

--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS  SLOTS  SLOTS  SLOTS  SLOTS  SLOTS 
--SelectedSlot=3 -- BK 11/11/2014 -- What we keep depending on options
CurrentHigh=1 -- temporary slot
BestScoreNF3Slot=2 -- -- best score filter disabled
BestScoreSlot=3 -- best score only, at any cost for filter ALWAYS HERE THE BEST ONE from start
TotalSlot=4 -- Fuse or rebuild result MUST BE 4 for edrw
LocTotalSlot= 5 -- MUST BE 5 for edrw
--6-17 used by edrw (initialized) for subscore slots WARNING ! May be more !!!!! then it will bug
--18 = best filter slot   ????

BestFilterBonus3Slot=18 --- WARNING not evaluated, may be used already by edrw !!!!!
PreferredScoreSlot=19 -- -- preferred see Savebest
BestItelligentSlot=20 -- best compromise between filter and score
BestFilterSlot=21 -- BK 11/11/2014 -- Best filter score only
PreferrredFilterSlot=22 -- BK 11/11/2014 -- best filter not on any cost

--GAB Slots

BestGABslot=23 -- (was 3 in original recipe)
GABrbSlot=24
GABherSlot=25
--30-49 used to record each big steps for movie at the end
StartRemixSlot=50
--50-100 gradually used for recipe

--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS  SLOTS  SLOTS  SLOTS  SLOTS  SLOTS 

-- Score functions
-- filter strategy: default FILTERMANAGE
-- FILTERMANAGE default false on normal filter, default (or select) true on PROBABLEFILTER
-- the filters will be disabled on normal, enabled on filtered (unless specified by "false" or "no filter manage")

function ScoreRank(FilterOn)--return total score displayed on the rank, BK (filter on or off depending on argument)
	local CurrentFilterSetting = filter.AreAllEnabled()
	local FilterOn=FilterOn -- or (not CurrentFilterSetting) = BUG !??

	local function return2CurrentOriginalFilterSetting()
		if OriginalFilterSetting then -- if true, all filters are default enabled
			filter.EnableAll()	--Enables all filters
		else
			filter.DisableAll()	--Disables all filters
		end
	end	
	
	if FilterOn then FiltersOn() elseif FilterOn==false then FiltersOff() end
    if energy==true then -- TO DO, energy does not exist here !
        return current.GetEnergyScore()
    else
        return current.GetScore() -- WARNING it's the default of this new function !!!!
    end
	return2CurrentOriginalFilterSetting()
	FILTERON=not CurrentFilterSetting
end 

function Score(pose, FilterOn) -- original tvdl (filters enabled)
	local CurrentFilterSetting = filter.AreAllEnabled()
	local FilterOn=FilterOn
	local function return2CurrentOriginalFilterSetting()
		if OriginalFilterSetting then -- if true, all filters are default enabled
			filter.EnableAll()	--Enables all filters
		else
			filter.DisableAll()	--Disables all filters
		end
	end		
	if FilterOn then FiltersOn()
	elseif FilterOn==false then FiltersOff()
	end -- elseif nil, don't change the filter
    if pose==nil then pose=current end
    local total= pose.GetEnergyScore()
    -- FIX for big negatives

        if total < -999999 and total > -1000001 then total=SegScore(pose) end

    if normal then
        return total
    else
        return total*pose.GetExplorationMultiplier()
    end
	if FilterOn~=nil then
		return2CurrentOriginalFilterSetting()
		FILTERON=not CurrentFilterSetting
	end
end

function Score3() -- best with and without filter NEW fixed version 4/1/2019
	--ScoreNF3=ScoreRank(false) --global
	Score3=ScoreRank(true) --global
	--FilterBonus3=Score3-ScoreNF3 --global
	FilterBonus3=filter.GetBonusTotal()	--Total bonus score of the filters
	ScoreNF3=Score3-FilterBonus3
end


-- for contextual options

Score3() -- NEW It's here that we calculate filter bonus
StartEbolaScore=Score3
StartEbolaScoreLater = StartEbolaScore -- after reset when gain very high
StartEbolaScoreNF=ScoreNF3
StartEbolaFilterBonus=FilterBonus3
WorstGroups="All" --{"All", "Backbone", "Sidechain", "Other"}
--[[
subscores={ --select given score parts for calculating worst/best areas
	{"clashing", "packing", "hiding", "bonding", "backbone", "sidechain", "disulfides", "density", "ideality", "reference"}, -- 1:All
	{"clashing", "packing", "backbone", "ideality"}, -- 2:Backbone 07/02/2014
	{"hiding", "bonding", "sidechain"}, -- 3:Sidechain
	{"density", "reference"}, -- 4:Other
	mode={"All", "Backbone", "Sidechain", "Other"}
}]]--
--if OriginalFilterSetting then filterstatus=" with filters (Filters are disabled !!)" else filterstatus=" with filters (filters enabled)" end
--print(">>>>>>Start Score = "..StartEbolaScore..filterstatus)
print(">>>>>>Start Score = "..round3(StartEbolaScore).." (disabled: "..down(StartEbolaScoreNF).."). Filter="..down(StartEbolaFilterBonus))


function TestPower()
	local RealRecTime=(os.clock()-startRecTime)
	RecTime=RealRecTime*segCnt2*sym
	if PROBABLEFILTER then
		RecTime=RecTime*2
	end
	local Weight=RecTime/RealRecTime
	print("Test time= " ..RealRecTime.."sec. Weight= "..Weight) -- pc performance till now in seconds, for options
end
TestPower()

-- end for contextual options

function SegScore(pose, FilterOn) -- version including symmetry BK 4/1/2019
	local CurrentFilterSetting = filter.AreAllEnabled()
	local FilterOn=FilterOn
	local symmetry = sym or 1 -- global sym
	local function return2CurrentOriginalFilterSetting()
		if OriginalFilterSetting then -- if true, all filters are default enabled
			filter.EnableAll()	--Enables all filters
		else
			filter.DisableAll()	--Disables all filters
		end
	end	
	if FilterOn then FiltersOn()
	elseif not FilterOn then FiltersOff()
	end
    if pose==nil then pose=current end
    local total=8000
    for i=1,segCnt2 do
        total=total+symmetry*pose.GetSegmentEnergyScore(i) -- added sym
    end
	return2CurrentOriginalFilterSetting()
	FILTERON=not CurrentFilterSetting
    return total
end

bestScore3=StartEbolaScore
BestScoreNF3=StartEbolaScoreNF
BestFilterBonus3=StartEbolaFilterBonus

TvdLmaxbonus=StartEbolaFilterBonus
LastFilter=TvdLmaxbonus -- new 23/12/2015
GotMaxFilter=false
ShadowFilter=true
PreferShadowFilter=true -- necessary for first show in dialog

TestSimpleFilterPref= false
ScorePriority=0 -- 0= score first or normal; 1= both filter AND score must rise; 2=Only filter must rise

--Not used anymore:
function FilterBonus(pose) -- changed by BK (independent from score functions)
	local pose=pose or current
	local CurrentFilterSetting = filter.AreAllEnabled()
	local function return2CurrentOriginalFilterSetting()
		if OriginalFilterSetting then -- if true, all filters are default enabled
			filter.EnableAll()	--Enables all filters
		else
			filter.DisableAll()	--Disables all filters
		end
	end	
	FiltersOn()
	TvdLscore=pose.GetEnergyScore()
	FiltersOff()
	TvdLscore2=pose.GetEnergyScore()
	return2CurrentOriginalFilterSetting() FILTERON=not CurrentFilterSetting
	TvdLbonus=TvdLscore-TvdLscore2 -- global
	return TvdLbonus
end

function FilterScore() -- new BK 11/11/2014, 23/12/2015, 4/1/2019 TO DO: user defined "filter" !
	local Thisfilter=TvdLmaxbonus  -- the one given by the user at start
	local filterShadow=0 -- shadow filter
	local filterObserved=0 -- current observed filter
	if GotMaxFilter then -- saves time but it's risky case filter loss !
		Thisfilter=TvdLmaxbonus		
	else
		filterObserved=FilterBonus() -- needed to calculate global TvdLbonus
		if filterObserved==TvdLmaxbonus then
			TvdLmaxbonus=filterObserved
			GotMaxFilter=true
			print("Max bonus achieved !")
		elseif filterObserved>TvdLmaxbonus then
			TvdLmaxbonus=filterObserved
		end
	end
	if ShadowFilter and PreferShadowFilter then -- case official filter or shadow filter choice
		filterShadow=ScoreRank(true)-SegScore(current,true) -- filters enabled
		if filterShadow > filterObserved + 10 or filterShadow < filterObserved - 10 then -- signif. different
			if PreferShadowFilter then
				Thisfilter =filterShadow
			end
			ShadowFilter=true -- will show in first dialog
		else
			Thisfilter= filterObserved
			ShadowFilter=false
		end
	else -- the normal case when we only want to rise the official filter bonus
		Thisfilter= filterObserved
	end
	LastFilter=Thisfilter
	return Thisfilter
end -- new BK 11/11/2014, 29/03/2015, 4/1/2019

--for archiving options by Bruno Kestemont
ChangedOptionsTxt="Ebola non-default options: \n  "
function ChangedOptions(label,before,after) -- archiving the changed options
	local label, before, after = label, before, after -- or "", 0, 0  or "", true, true
	if label== "subscore" then
		ChangedOptionsTxt=ChangedOptionsTxt..after.." "..label.." added "..'\n  ' -- new line
		return after
	else
		if before ==true or before == false then -- boolean
			if not ((before and after) or (not before and not after)) then -- changed boolean option
				if after then 
					ChangedOptionsTxt=ChangedOptionsTxt..label.." turned on \n  " -- new line
				else
					ChangedOptionsTxt=ChangedOptionsTxt..label.." turned off \n  " -- new line
				end
				return after
			end
		elseif before > 0 or after > 0 or before <1 or after < 1 then -- numbers
			if before~= after then -- numbers
				ChangedOptionsTxt=ChangedOptionsTxt..label..": "..after..'\n  ' -- new line
				return after
			end --else return before
		end
		return before -- always return something ! can be after also here if it is the same !
	end
end
--end for archiving options

function TvdLFilterDialog()  -- changed by BK, ONLY if PROBABLEFILTER in text
   local ask=dialog.CreateDialog("Slow filters seem to be active")
   TvdLmaxbonus1=TvdLbonus -- already calculated in last FilterScore
   local ShadowFilterScore= LastFilter -- first calculation before knowing preferences
   --ask.disable=dialog.AddCheckbox("Run with disabled slow filters",TvdLFilteractive)
   if ShadowFilter then
	   ask.l5=dialog.AddLabel("Total current shadow filter: "..ShadowFilterScore)
	   ask.l6=dialog.AddLabel("Improve shadow filter OR filter bonus?")
	   ask.PreferShadowFilter=dialog.AddCheckbox("Improve shadow filter (slow)",false)
   end
   ask.l1=dialog.AddLabel("Current filter bonus: "..TvdLmaxbonus1)
   ask.l2=dialog.AddLabel("If this is not the maximum bonus, change next line")
	if TvdLmaxbonus1<200 then tvdlSupermaxbonus= 200 else tvdlSupermaxbonus=TvdLmaxbonus1/5 end
   if TvdLmaxbonus < 0 then
   	if TvdLmaxbonus < 1000 then ScorePriority= 1 else ScorePriority= 2 end -- 1 filter and score must rise; 2= only filter
	TvdLmaxbonus=0
	NEGATIVEFILTER=true -- for contextual options
	end
   ask.maxbonus=dialog.AddSlider("Set maxbonus/10",TvdLmaxbonus/10,0,tvdlSupermaxbonus,0)
   --ask.l3=dialog.AddLabel("Scores will only be checked for real gains if")
   --ask.l4=dialog.AddLabel("Score with filter off+maxbonus is a potential gain")
   	ask.l7=dialog.AddLabel("Priority to 0=score; 1=both; 2=filter bonus")
	-- WARNING: both is complex (can be both or score or filter)
	ask.ScorePriority=dialog.AddSlider("",ScorePriority,0,2,0)
   ask.continue=dialog.AddButton("Continue",1)
   
   dialog.Show(ask)
	ScorePriority=ChangedOptions("ScorePriority",ScorePriority,ask.ScorePriority.value)
	if ScorePriority==2 then FiltersFirst=true end
	TvdLmaxbonus=ChangedOptions("TvdLmaxbonus",TvdLmaxbonus,10*ask.maxbonus.value)
   if ShadowFilter then
	PreferShadowFilter=ChangedOptions("PreferShadowFilter",PreferShadowFilter,ask.PreferShadowFilter.value)
   end
   --TvdLFilteractive=ask.disable.value
end

BetterRecentBest=false
function FilterOff() -- TO DO: check slots !!!!!!!
    -- Filters off but restore a better recentbest with filter off
    FiltersOff()
    if BetterRecentBest then
        save.Quicksave(99)
        save.Quickload(98)
        recentbest.Save()
        save.Quickload(99)
    end
end

function FilterOn() -- Filter on but remember recent best if better than current
    BetterRecentBest= Score(recentbest) > Score()
    if BetterRecentBest then
        save.Quicksave(99)
        recentbest.Restore()
        save.Quicksave(98)
        save.Quickload(99)
    end
    FiltersOn()
end

TvdLFilteractive=(math.abs(TvdLmaxbonus) > 0.1) -- TvdLmaxbonus is calculated lines 599 & 647
if TvdLFilteractive then PROBABLEFILTER= true end

bestScore=Score()
if TvdLFilteractive and ScorePriority==0 then FilterOff() end -- TO DO verify, may be duplicate, should come after choosing ScorePriority

function RBScore()
    return Score(recentbest)
end


--[[Concepts:
Scores:
1) "Score()" = Score3 = classical (filtered) score
1a) ScoreNF3 = score with filters disabled
2)
3)
4) FilterBonus3 = net macro filter as displayed above the window (negative red or positive blue)
4a) ShadowFilterScore = difference between sum of segment score and macro score (filters enabled)
4b) ShadowFilterScoreNF = difference between sum of segment score and macro score (filters disabled)

Best scores:
1) bestScore = classical absolute best score only
1a) BestScoreNF3 = best score with filters disabled
2) PreferedScore= WHAT WE KEEP depending on options. WARNING !!
3) BestItelligentScore= Score or filter must gain only at no cost (no cost for filter or score)
4) BestFilterBonus3 = best net macro filter as displayed above the window (negative red or positive blue)
4a) bestFScore= classical absolute best filter only
5) preferredFScore= best filter but not at any cost (cost is an option)
6) BestSolution ????


Related slots:
1) BestScoreSlot -- classical best score only, at any cost for filter
1a) BestScoreNF3Slot = best score with filters disabled
2) PreferredScoreSlot -- WHAT WE KEEP depending on options. WARNING !!
3) BestItelligentSlot -- best compromise between filter and score (no cost allowed)
4) BestFilterBonus3Slot= Best filter bonus (red/blue credited as displayed top of screen)
4a) BestFilterSlot -- BK 11/11/2014 -- Best filter score only (any kind of filter selected)
5) PreferrredFilterSlot -- BK 11/11/2014 -- best filter not on any cost
6) BestSlot ?????

Related booleans:
1) improvedscore= 		if bestScore improved
1a) improvedScoreNF3 = best score with filters disabled improved
2) 
3)
4) improvedFilterBonus = classical absolute best filter only
4a) improvedFilter=  	if filter improved
4b) samefilter = same filter score
5a) improvedPfilter= if preferred filter improved
5b) samePfilter= if same preferred filter
6) ????

Related gains
1) g = g3 = bestScore gain (classical absolute gain)
1a) gN3= BestScoreNF3 = best score with filters disabled
2) pg= preferred score gain (gain on last kept)
3a) ig= intelligent score gain (might be zero if only filter rose)
3b) ifg= intelligent filter gain (might be zero if only score rose)
4) fg=fg3= best filter gain (classical absolute gain)
5) pfg= preferred filter gain
6) sg = selected score gain   WARNING error here !

Related costs
1) tfc = total filter cost of bestScore (relative to absolute best filter)
2a) fc= filter cost of preferred score gain (gain & cost on last kept)
2b) sc= score cost on preferred score gain  (gain & cost on last kept)
3) (no short term cost allowed here)
4) tsc= total score cost of this best filter (score relative to absolute best score)
5a) tpfsc= preferred filter score cost (score relative to absolute best score)
5b) LostpFgain = score lost allowed for each pt of preferred filter gain
5c) LostAllowed=pgf*LostpFgain
6a) ssc= selected score cost (score relative to absolute best score)
6b) sfc= selected filter cost (score relative to absolute best filter)




]]--Score Concepts by Bruno Kestemont 15/12/2014

PreferedScore=StartEbolaScore
bestScore=PreferedScore -- init
BestItelligentScore=PreferedScore

LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
--this default is no filter preference (score gain = filter gain)
LostFpgain= 9 -- default filter lost allowed per 10 pt score gain
--this default is quite strong score preference (score gain at almost any filter lost)
-- case only gain iff also at least same filter gain= -10
-- case no filter loss: 0
-- case small filter loss allowed: <10
-- almost full priority to score: 100
-- Remark: I don't allow pure full score priority

defminppi= 0.1 -- default minppi will be changed if only big jumps are wanted
defiter= 2 -- default iteration base for wiggles etc. Will be changed for Sketchbook puzzles: Can be only 2-5-8-11-14 because ((defiter+1)/3) must be integer

minGain = 50 -- force a new round if gain is MORE than this (nothing to do with Sketchbook)

--otherwise, the score collapses !

--[[Strategy for best scores:
SaveBesttvdl reacts like original one: with no filter, it's a normal savebest; with filter, it tries
to identify the max potential score by using the maxbonus given by user.
SaveBest selects which savebest to use according to preferences.

If there is a filter bonus,it depends on the score priority.
If it's 1, it does only a very simple SaveBest3
Otherwise: 
0) calculates the filter bonus and the potential score, like in edrw28.

1) and normal puzzle without bonus:
if bonus declared by user on beginning

]]--


function SaveBesttvdl() -- original tvdl solution (filter must be always off) priority to score
  if (not TvdLFilteractive) or
     (Score()+TvdLmaxbonus>bestScore) then -- if filteractive but potential filtered gain
     if TvdLFilteractive then FilterOn() end
     local g=Score()-bestScore
     if g>defminppi then -- was 0 but I will not save small gains (default 0.02)
        if g>0.01 then print("Gained another "..round3(g).." pts.") end
        bestScore=Score()
		PreferedScore=bestScore -- new
        save.Quicksave(BestScoreSlot)
		save.Quicksave(PreferredScoreSlot)
		WhriteNote()
     end
     if TvdLFilteractive then FilterOff() end
  end
end

function SaveBest() -- By Bruno Kestemont 22/1/2015, 12/4/2015, 2/6/2015 DEFAULT generic - Filter priority included
	local SBScore=-99999
	local tempfilter=-999
	if SKETCHBOOK and not current.AreConditionsMet() then -- we are obliged to take the latest good one !
		print("FAILED CONDITIONS! retrieving older solution")
		--save.Quickload(PreferredScoreSlot) -- it's too close to the condition limit.
		save.Quickload(SlotStep) -- it's the latest big step
		return -- breaking the function
	end
	if ScorePriority<=1 then -- priority to score => normal tvdl
		SaveBesttvdl() return
	else -- scorePriority different than score will be controlled by FiltersFirst
	  if (not TvdLFilteractive) or
		 (Score()+TvdLmaxbonus>bestScore) then -- if potential filtered gain
		if TvdLFilteractive then FilterOn() end
		WhriteNote()
		local SBScore=Score()
		local g=SBScore-bestScore -- since best absolute score
		local pg=SBScore-PreferedScore -- since latest selection
		improvedPscore=false
		if pg>0.01 then improvedPscore=true end
		improvedscore = false
		if g>defminppi then -- classical absolute gain
			bestScore=SBScore
			if g>0.01 then print(">>>Gained another "..round3(g).." pts. Best score= "..round3(bestScore)) end
			save.Quicksave(BestScoreSlot)
			improvedscore = true
		end
		if TvdLFilteractive then -- new 29/03/2015 deactivate this when no filter. Priority to Filter or both
			SaveBestFilter()-- new BK 11/11/2014
			LostFilterAllowed=LostFpgain*g/10
			--selection of solution to go further
			--print("Selecting preferred solution")
			if (improvedscore and (improvedfilter or samefilter))
													or (g>=0 and improvedfilter) then
				print("Well done ! Archiving this best solution")
				BestItelligentScore=SBScore
				PreferedScore=SBScore -- always
				bestScore=SBScore
				save.Quicksave(BestScoreSlot) -- update in case of filter gain on same score
				save.Quicksave(BestItelligentSlot) -- archive for info only
				save.Quicksave(PreferredScoreSlot) -- this case is evident ! All scores reinitialized
				
			elseif improvedfilter and FiltersFirst and improvedPscore then -- case improved filter but lowest score
				-- added condition on improvedPscore, for safety:
				--you can win on filter only once, the second time, you should at least also improve your preferred score
				if g-LostAllowed>0 then -- not at any cost !
					save.Quicksave(PreferredScoreSlot) -- be careful, we loose our best preferred score here !!
					PreferedScore=SBScore
					print("Priority to filter. Filter score "..round3(LastFilter)..
						" Score: "..round3(PreferedScore).."/"..round3(bestScore))
					print("Total SCORE COST accepted: "..round3(bestScore-PreferedScore))
				end
				
			elseif improvedscore  then -- case filter cost for this gain
				if fg+LostFilterAllowed>0.1 then -- not at any filter cost ! (fg is negative)
					save.Quicksave(PreferredScoreSlot) -- be careful, we loose our best score here !!
					PreferedScore=SBScore
					if fg<-5 then
						print("Priority to score: "..round3(PreferedScore).."/"..round3(bestScore))
						print("FILTER COST accepted: "..round3(LastFilter-bestFScore).." Filter now: "..round3(LastFilter))
					end
				else
					TOOMUCHFILTERLOSS= true -- reinitialized and used in ScoreHerd
					if fg<-10 then print("Oops ! Filter change: "..round3(fg).." too high, REJECTING this solution")	end
					
					--here we do not save the solution
				end
				
			else -- now the simple default preferred gains, but with smaller thresholds
				
				if (improvedPscore and (improvedPfilter or samePfilter))
														or (pg>=0 and improvedPfilter) then
					print("Not bad ! Better than the preferred solution")
					if SBScore>BestItelligentScore then
						BestItelligentScore=SBScore
						save.Quicksave(BestItelligentSlot) -- archive for info only
						print("Updating intelligent score")
						--print("Intelligent filter cost accepted: "..round3(LastFilter-bestFScore))
					end
					save.Quicksave(PreferredScoreSlot) -- this case is evident !
					PreferedScore=SBScore
					preferredFScore=LastFilter
						
				elseif improvedPfilter and FiltersFirst then -- case improved P filter but lowest P score
					LostAllowed=pfg*LostpFgain/10 --new score smaller lost allowed for this P filter gain
					if pg-LostAllowed>0 then -- not at any cost !
						save.Quicksave(PreferredScoreSlot) -- be careful, we loose score here !!
						PreferedScore=SBScore
						preferredFScore=LastFilter
						print("Priority to filter score "..round3(LastFilter)..
							" Score: "..round3(PreferedScore).."/"..round3(bestScore))
						print("Rising SCORE COST accepted: "..round3(bestScore-PreferedScore))
					end
					
				elseif improvedPscore then -- case filter cost for this gain
					LostFilterAllowed=LostFpgain*pg/10 -- renewed threshold here with pg
					if pfg-LostFilterAllowed>0 then -- not at any filter cost !
						save.Quicksave(PreferredScoreSlot) -- be careful, we loose filter score here !!
						PreferedScore=SBScore
						preferredFScore=LastFilter
						print("Priority to score "..round3(LastFilter)..
							" Score: "..round3(PreferedScore).."/"..round3(bestScore))
						print("Total preferred filter cost accepted: "..round3(LastFilter-bestFScore))
					else
						TOOMUCHFILTERLOSS= true -- reinitialized and used in ScoreHerd
						if pfg<-10 then print("Oops ! preferred filter change: "..round3(pfg).." too high, rejecting this solution")	end
					end
				end
			
			end
		end
	  end
	  if TvdLFilteractive then FilterOn() end
	end
end -- by BK Including filter score optimization

bestFScore=FilterScore() -- with preferred options. FIRST Calculation gives also LastFilter, don't delete !
if bestFScore >10 or bestFScore <-10 then -- note that it will not see this at very begin, when no filter gains were achieved yet
	PROBABLEFILTER=true
	print("Start Filter or bonus Score ~= "..round3(bestFScore))
end

preferredFScore=bestFScore -- new BK 11/11/2014 -- best preferred filter score

--deleted generic filter re-initialization here. TO VERIFY

function SaveBestFilter()-- new BK 11/11/2014
	local SBfilterscore=FilterScore()
    fg=SBfilterscore-bestFScore -- global !!
    pfg=SBfilterscore-preferredFScore
    LostAllowed=fg*LostpFgain --score lost allowed for this filter gain
    improvedfilter = false
    samefilter=false
    improvedPfilter = false
    samePfilter=false
    if fg>0 then
    	bestFScore=SBfilterscore
        if fg>20 then print(" Found "..round3(fg).." filter pts. Best Filter= "..round3(bestFScore)) end
        save.Quicksave(BestFilterSlot)
        improvedfilter = true
    elseif fg==0 then
    	samefilter=true
    end
    if pfg>0 then
    	--preferredFScore=LastFilter -- later when selected only
        if pfg>20 then print(" Found "..round3(pfg).." preferred filter pts. Filter= "
        			..round3(preferredFScore).."/"..round3(bestFScore)) end
        improvedPfilter = true
    elseif pfg==0 then
    	samePfilter=true
    end
end -- by BK 15/12/2014

function SaveBest3() -- only trivial best filtered, unfiltered and filter bonus NOT USED

	if ScorePriority==0 then -- priority to score
		SaveBesttvdl()
	else -- priority to both score AND filter
		Score3() -- calculates the 2 types scores & official filter
		local fg3=FilterBonus3-BestFilterBonus3
		local gN3=ScoreNF3-BestScoreNF3
		local g3=Score3-bestScore3 -- same as global
		--filter module
		if fg3>0 then
			BestFilterBonus3=FilterBonus3
			if fg3>20 then print(" Found "..round3(fg3).." filter pts. Best Filter= "..round3(BestFilterBonus3)) end
			save.Quicksave(BestFilterBonus3Slot) -- global !?
			improvedfilter = true -- global !?
		elseif fg3>-0.1 then
			samefilter=true
		end
		if TvdLmaxbonus<BestFilterBonus3+0.2 then GotMaxFilter= true ScorePriority=0 end -- only score
		--filtered score module
		if g3>defminppi then -- classical absolute gain
			bestScore3=Score3
			if g3>0.01 then print(">>>Gained another "..round3(g3).." pts. Best score= "..round3(bestScore3)) end
			save.Quicksave(BestScoreSlot) -- global !?
			improvedscore = true  -- global !?
		end
		--unfiltered score module (filters disabled)
		if gN3>0 then -- gains on filters disabled NOT USED = to be deleted 
			BestScoreNF3=ScoreNF3
			if gN3>10 then print(">>>Found another "..round3(gN3).." uncredited pts. Best uncredited score= "..round3(BestScoreNF3)) end
			save.Quicksave(BestScoreNF3Slot) -- global !?
			improvedScoreNF3 = true  -- global
		end
		if (ScorePriority==1 and (improvedfilter or (samefilter and improvedscore))) 
					or (ScorePriority==2 and (improvedfilter or samefilter) and improvedscore) then 
				save.Quicksave(PreferredScoreSlot)
		end -- else nothing
	end

end

-- New WiggleFactor
WF=1
-- Wiggle function
-- Optimized due to Susumes ideas
-- Note the extra parameter to be used if only selected parts must be done
function Wiggle(how, iters, minppi,onlyselected, filtered, valit, mingps)
    --score conditioned recursive wiggle/shake
    --fixed a bug, absolute difference is the threshold now
    if how==nil then how="wa" end
    --if iters==nil then iters=3 end
    if minppi==nil then minppi=defminppi end
    if onlyselected==nil then onlyselected=false end
	if filtered==nil then filtered=true end
    local wf=1
    if maxCI then wf=WF end
	
    if iters==nil then iters=6 end

	if valit==nil then valit= 1 end
	if mingps==nil then mingps= 80 end
	if susume then valit= defiter*wf*iters end

    if iters>0 then
		startRecTime=os.clock ()
        iters=iters-1
        local sp=Score()
        if onlyselected then
            if how == "s" then
                -- Shake is not considered to do much in second or more rounds
                structure.ShakeSidechainsSelected((defiter+1)/3)
                return
            else
				if FILTERMANAGE and not filtered then FiltersOff() end-- new BK 8/5/2013, always disable filter here
				if how == "wb" then structure.WiggleSelected(valit,true,false)
				elseif how == "ws" then structure.WiggleSelected(valit,false,true)
				elseif how == "wa" then structure.WiggleSelected(valit,true,true)
				end
				if FILTERMANAGE and not filtered then return2GlobalOriginalFilterSetting()  FILTERON=not OriginalFilterSetting end -- new BK 8/5/2013, always back to user settings
			end
        else
            if how == "s" then
                -- Shake is not considered to do much in second or more rounds
                structure.ShakeSidechainsAll((defiter+1)/3)
                return
            else
				if FILTERMANAGE and not filtered then FiltersOff() end-- new BK 8/5/2013, always disable filter here
				if how == "wb" then structure.WiggleAll(valit,true,false)
				elseif how == "ws" then structure.WiggleAll(valit,false,true)
				elseif how == "wa" then structure.WiggleAll(valit,true,true)
				end
				if FILTERMANAGE and not filtered then return2GlobalOriginalFilterSetting() FILTERON=not OriginalFilterSetting end -- new BK 8/5/2013, always back to user settings
			end
        end
        ep = Score()
        ig=ep-sp
		timeperiteration =os.clock ()-startRecTime
		tppii=ig/timeperiteration
        if math.abs(Score()-sp) > minppi and tppii > mingps then return Wiggle(how, iters, minppi,onlyselected, filtered, valit, mingps) end
    end
end





-- end of handy shorts module

-- Segment set and list module
-- Notice that most functions assume that the sets are well formed
-- (=ordered and no overlaps)
-- 02-05-2012 TvdL Free to use for non commercial purposes

function SegmentListToSet(list)
    local result={}
    local f=0
    local l=-1
    table.sort(list)
    for i=1,#list do
        if list[i] ~= l+1 and list[i] ~= l then
            -- note: duplicates are removed
            if l>0 then result[#result+1]={f,l} end
            f=list[i]
        end
        l=list[i]
    end
    if l>0 then result[#result+1]={f,l} end
    --print("list to set")
    --SegmentPrintSet(result)
    return result
end

function SegmentSetToList(set)
    local result={}
    for i=1,#set do
        --print(set[i][1],set[i][2])
        for k=set[i][1],set[i][2] do
            result[#result+1]=k
        end
    end
    return result
end

function SegmentCleanSet(set)
-- Makes it well formed
    return SegmentListToSet(SegmentSetToList(set))
end

function SegmentInvertSet(set,maxseg)
-- Gives back all segments not in the set
-- maxseg is added for ligand
    local result={}
    if maxseg==nil then maxseg=segCnt end
    if #set==0 then return {{1,maxseg}} end
    if set[1][1] ~= 1 then result[1]={1,set[1][1]-1} end
    for i=2,#set do
        result[#result+1]={set[i-1][2]+1,set[i][1]-1}
    end
    if set[#set][2] ~= maxseg then result[#result+1]={set[#set][2]+1,maxseg} end
    return result
end

function SegmentInList(s,list)
    table.sort(list)
    for i=1,#list do
        if list[i]==s then return true
        elseif list[i]>s then return false
        end
    end
    return false
end

function SegmentInSet(set,s)
    for i=1,#set do
        if s>=set[i][1] and s<=set[i][2] then return true
        elseif s<set[i][1] then return false
        end
    end
    return false
end

function SegmentJoinList(list1,list2)
    local result=list1
    if result == nil then return list2 end
    for i=1,#list2 do result[#result+1]=list2[i] end
    table.sort(result)
    return result
end

function SegmentJoinSet(set1,set2)
    return SegmentListToSet(SegmentJoinList(SegmentSetToList(set1),SegmentSetToList(set2)))
end

function SegmentCommList(list1,list2)
    local result={}
    table.sort(list1)
    table.sort(list2)
    if #list2==0 then return result end
    local j=1
    for i=1,#list1 do
        while list2[j]<list1[i] do
            j=j+1
            if j>#list2 then return result end
        end
        if list1[i]==list2[j] then result[#result+1]=list1[i] end
    end
    return result
end

function SegmentCommSet(set1,set2)
    return SegmentListToSet(SegmentCommList(SegmentSetToList(set1),SegmentSetToList(set2)))
end

function SegmentSetMinus(set1,set2)
    return SegmentCommSet(set1,SegmentInvertSet(set2))
end

function SegmentPrintSet(set)
    print(SegmentSetToString(set))
end

function SegmentSetToString(set)
    local line = ""
    for i=1,#set do
        if i~=1 then line=line..", " end
        line=line..set[i][1].."-"..set[i][2]
    end
    return line
end

function SegmentSetInSet(set,sub)
    if sub==nil then return true end
    -- Checks if sub is a proper subset of set
    for i=1,#sub do
        if not SegmentRangeInSet(set,sub[i]) then return false end
    end
    return true
end

function SegmentRangeInSet(set,range)
    if range==nil or #range==0 then return true end
    local b=range[1]
    local e=range[2]
    for i=1,#set do
        if b>=set[i][1] and b<=set[i][2] then
            return (e<=set[i][2])
        elseif e<=set[i][1] then return false end
    end
    return false
end

function SegmentSetToBool(set)
    local result={}
    for i=1,segCnt do
        result[i]=SegmentInSet(set,i)
    end
    return result
end
--- End of Segment Set module

-- Module Find Segment Types
function FindMutablesList()
    local result={}
    for i=1,segCnt2 do if structure.IsMutable(i) then result[#result+1]=i end end
    return result
end
function FindMutables()
    return SegmentListToSet(FindMutablesList())
end

function FindFrozenList()
    local result={}
    for i=1,segCnt2 do if freeze.IsFrozen(i) then result[#result+1]=i end end
    return result
end
function FindFrozen()
    return SegmentListToSet(FindFrozenList())
end

function FindLockedList()
    local result={}
    for i=1,segCnt2 do if structure.IsLocked(i) then result[#result+1]=i end end
    return result
end
function FindLocked()
    return SegmentListToSet(FindLockedList())
end

function FindSelectedList()
    local result={}
    for i=1,segCnt do if selection.IsSelected(i) then result[#result+1]=i end end
    return result
end
function FindSelected()
    return SegmentListToSet(FindSelectedList())
end

function FindAAtypeList(aa)
    local result={}
    for i=1,segCnt2 do
        if structure.GetSecondaryStructure(i)== aa then result[#result+1]=i end
    end
    return result
end
function FindAAtype(aa)
    return SegmentListToSet(FindAAtypeList(aa))
end

function FindAminotype(at) --NOTE: only this one gives a list not a set
    local result={}
    for i=1,segCnt2 do
        if structure.GetAminoAcid(i) == at then result[#result+1]=i end
    end
    return result
end
-- end Module Find Segment Types

-- Module to compute subscores
-- TvdL, 14-12-2012
function GetSubscore(types,seg1,seg2,pose)
	if FILTERMANAGE then FiltersOff() end-- new BK 8/5/2013, always disable filter here
    local result=0
    if type(types) == "table" then
        for i=1,#types do result=result+GetSubscore(types[i],seg1,seg2,pose) end
    else
        if types==nil and seg1==nil and seg2==nil then return Score(pose) end
        if seg1==nil then seg1=1 end
        if seg2==nil then seg2=segCnt end --includes ligands!
        if seg1>seg2 then seg1,seg2=seg2,seg1 end
        if pose==nil then pose=current end
        if types==nil then
            for i=seg1,seg2 do result=result+pose.GetSegmentEnergyScore(i) end
        else
            for i=seg1,seg2 do result=result+pose.GetSegmentEnergySubscore(i,types) end
        end
    end
    if normal then return result else return result*pose.GetExplorationMultiplier() end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end 
end

function FindActiveSubscores(show)
	if FILTERMANAGE then FiltersOff() end-- new BK 8/5/2013, always disable filter here
    local result={}
    local Subs=puzzle.GetPuzzleSubscoreNames()
    local Showlist ="Computing Active Subscores"
    if show then print(Showlist) end
    for i=1,#Subs do
        local total=0
        for j=1,segCnt do
            total=total+math.abs(current.GetSegmentEnergySubscore(j,Subs[i]))
            if total>10 then
                result[#result+1]=Subs[i]
                break
            end
        end
    end
	if show then
		for i=1,#result do
			local totalpts=0
			for j=1,segCnt do
				totalpts=totalpts+current.GetSegmentEnergySubscore(j,result[i])
			end
			print("Active subscore "..result[i].." :"..down(totalpts))
		end
	end
	
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end-- new BK 8/5/2013, always disable filter here
    return result
end

function FindActiveFilter()-- BK 11/2/2015
	local result=true
 if bestFScore > -10 and  bestFScore < 10 then
	result= false
 else result=true
	PROBABLEFILTER=true -- if one time on the fly we have a filter score, then it's a filtered puzzle
 end
 return result
end
-- End module to compute subscores

-- Position stack module 1.0
-- uses slot 50 and higher
Stackmin=50
StackMarks={}
StackPos=50
function PushPosition()
    if StackPos==100 then
        print("Position stack overflow available slots, exiting")
        exit()
    end
    save.Quicksave(StackPos)
    StackPos=StackPos+1
end

function PopPosition()
    if StackPos==50 then
        print("Position stack underflow, exiting")
        exit()
    end
    StackPos=StackPos-1
    save.Quickload(StackPos)
end
function PushMarkPosition() -- not used
    StackMarks[#StackMarks+1]=StackPos
    PushPosition()
end
function PopMarkPosition() -- not used
    if #StackMarks == 0 then
        print("No marked position found, just popping")
    else
        StackPos=StackMarks[#StackMarks]+1
        StackMarks[#StackMarks]= nil
    end
    PopPosition()
end
function GetTopPosition()
    if StackPos==50 then
        print("No top position on the stack, exiting")
        exit()
    end
    save.Quickload(StackPos-1)
end
function ClrTopPosition()
    if StackPos > 50 then StackPos=StackPos-1 end
end
-- Start of module for bridgechecking
Cyslist={}
savebridges=false --default no bridgechecking
nrofbridges=0

function setCyslist()
    Cyslist=FindAminotype("c")
    nrofbridges=CountBridges()
end

function IsBridge(i)
    if structure.IsLocked(i) then return false end
	if FILTERMANAGE then FiltersOff() end
	local dsscore=current.GetSegmentEnergySubscore(i,'disulfides')
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
    return ''..dsscore ~= '-0'

end

function CountBridges()
    local count = 0
    for i = 1,#Cyslist do
        if IsBridge(Cyslist[i]) then count = count + 1 end
    end
    return count
end

function BridgesBroken()
    return savebridges == true and CountBridges() < nrofbridges
end

function Bridgesave()
    if savebridges then PushPosition() end
end

function Bridgerestore()
    if savebridges then
        if BridgesBroken() then PopPosition() else ClrTopPosition() end
    end
end

-- End module bridgechecking

-- Module find puzzle properties
-- Tvdl 14-12-2012
HASMUTABLE=false
HASDENSITY=false
HASLIGAND= (segCnt2<segCnt)
DENSITYWEIGHT=0
PROBABLESYM=false
FREEDESIGN=false
LAYERFILTER=false

function SetPuzzleProperties()
    print("Computing puzzle properties")
    -- Find out if the puzzle has mutables
    local MutList=FindMutablesList()
    HASMUTABLE= (#MutList>0)
    if HASMUTABLE then print("Mutables found") end
    FREEDESIGN= (segCnt2/2 < #MutList)
    if FREEDESIGN then print("Probable a free design puzzle") end

    -- Find out if the puzzle has possible bridges
    setCyslist()
    if #Cyslist > 1 then
        print("Puzzle has more than 1 cystine")
        if nrofbridges > 0 then
            print("Puzzle has bridges")
            savebridges=true
        end
    end
	if FILTERMANAGE  then FiltersOff() end
    -- Find out is the puzzle has Density scores and their weight if any
    local Densitytot=GetSubscore("density")
    local segtot=GetSubscore(nil,1,segCnt)
	if FILTERMANAGE  then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
    HASDENSITY= math.abs(Densitytot) > 0.0001
    if normal and HASDENSITY then
        print("Puzzle has Density scores")
        DENSITYWEIGHT=(Score()-segtot-8000)/Densitytot
        print("The Density component has an extra weight of "..round3(DENSITYWEIGHT))
    end

    -- Check if the puzzle is a probable symmetry one
    if normal and not HASDENSITY then
        PROBABLESYM=math.abs(Score()-segtot-8000) > 2
        if PROBABLESYM then print("Puzzle is probable a symmetry puzzle") end
    end

end

SetPuzzleProperties()
-- End of module find puzzle properties

-- Standard Fuze module
-- Picks up all gains by using recentbest

function GetRB(prefun,postfun)
    if RBScore()> Score() then
        if prefun ~= nil then prefun() end
        recentbest.Restore()
        if postfun ~= nil then postfun() end
    end
end

function FuzeEnd(prefun,postfun)
    if prefun ~= nil then prefun() end
    CI(1)
-- Wiggle("wa",1)
-- Wiggle("s",1)
    Wiggle(nil, nil, nil, false, false)
	--structure.WiggleAll(25) -- here a normal filtered wiggle ADDED if filtered elsewhere
    GetRB(prefun,postfun)
    if postfun ~= nil then postfun() end
    SaveBest()
end

function Fuze1(ci1,ci2,prefun,postfun)
    if prefun ~=nil then prefun() end
    CI(ci1)
    Wiggle("s",1)
    CI(ci2)
    Wiggle("wa",1)
    if postfun ~= nil then postfun() end
end

function Fuze2(ci1,ci2,prefun,postfun)
    if prefun ~= nil then prefun() end
    CI(ci1)
    Wiggle("wa",1)
    CI(1)
	Wiggle("wa",15)
    --structure.WiggleAll(15) -- here a normal filtered wiggle ADDED if filtered elsewhere
    CI(ci2)
    Wiggle("wa",1)
    if postfun ~= nil then postfun() end
end

function reFuze(scr,slot)
    local s=Score()
    if s<scr then
        save.Quickload(slot)
    else
        scr=s
        save.Quicksave(slot)
    end
    return scr
end

function Fuze(slot,prefun,postfun)
    local scr=Score()
    if slot == nil then
		slot=TotalSlot
		save.Quicksave(slot) -- Replaces TotalSlot ?? TO VERIFY !! (was like this slot 4 in original edrw)
	end

    recentbest.Save()
    Fuze1(0.3,0.6,prefun,postfun) FuzeEnd(prefun,postfun)
    scr=reFuze(scr,slot)
    Fuze2(0.3,1,prefun,postfun)
    GetRB(prefun,postfun)
    SaveBest()
    scr=reFuze(scr,slot)
    Fuze1(0.05,1,prefun,postfun)
    GetRB(prefun,postfun)
    SaveBest()
    scr=reFuze(scr,slot)
    Fuze2(0.7,0.5,prefun,postfun) FuzeEnd()
    scr=reFuze(scr,slot)
    Fuze1(0.07,1,prefun,postfun)
    GetRB(prefun,postfun)
    SaveBest()
    reFuze(scr,slot)
    GetRB(prefun,postfun)
    SaveBest()
end
-- end standard Fuze module


-- Module Random
-- Tvdl, 01-11-2012
Randomseed=os.time()%1000000
function Seedrandom()
    math.randomseed(Randomseed)
    math.random(100) -- Because the first is not random
end
Seedrandom()

-- Thanks too Rav4pl
function ShuffleTable(tab) --randomize order of elements
    local cnt=#tab
    for i=1,cnt do
        local r=math.random(cnt)
        tab[i],tab[r]=tab[r],tab[i]
    end
    return tab
end

function MutateSel(maxitter)
    if maxitter == nil then maxitter=2 end
    if LAYERFILTER then
    -- Needed because this filter restricts on the combination of restrictions
        local ss
        local Sellist=FindSelectedList()
        local itters=1
        repeat
            ss=Score()
            ShuffleTable(Sellist)
            for i=1,#Sellist do
                selection.DeselectAll()
                selection.Select(Sellist[i])
                structure.MutateSidechainsSelected(itters)
            end
            itters=itters+1
        until math.abs(ss-Score()) > 0.0001 or itters > maxitter
    else structure.MutateSidechainsSelected(maxitter) end
end

function MutateAll(maxitter)
    selection.SelectAll()
    MutateSel(maxitter)
end

-- Module setsegmentset
-- Tvdl, 11-05-2012 Free to use for noncommercial purposes
function SetSelection(set)
    selection.DeselectAll()
    if set ~= nil then for i=1,#set do
        selection.SelectRange(set[i][1],set[i][2])
    end end
end

function SelectAround(ss,se,radius,nodeselect)
    if nodeselect~=true then selection.DeselectAll() end
    for i=1, segCnt2 do
        for x=ss,se do
            if structure.GetDistance(x,i)<radius then selection.Select(i) break end
        end
    end
end

function SetAAtype(set,aa)
    local saveselected=FindSelected()
    SetSelection(set)
    structure.SetSecondaryStructureSelected(aa)
    SetSelection(saveselected)
end

SAVEDstructs=false
function AllLoop() --turning entire structure to loops
    local anychange=false
    for i=1,segCnt2 do
        if structure.GetSecondaryStructure(i)~="L" then
            anychange=true
            break
        end
    end
    if anychange then
        save.SaveSecondaryStructure()
        SAVEDstructs=true
        selection.SelectAll()
        structure.SetSecondaryStructureSelected("L")
    end
end

function qStab()
    -- Do not accept qstab losses
    local curscore=Score()
    PushPosition()
    CI(0.1)
    Wiggle("s",1,nil,true) --shake only selected part
    if InQstab then
        CI(1)
        doMutate()
    end
    if fastQstab==false then
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
		Wiggle(nil, nil, nil, false, false, nil, nil)
		--structure.WiggleAll(6) -- here a normal filtered wiggle ADDED if filtered elsewhere
    end
    CI(1)
	Wiggle("wa")
    --structure.WiggleAll(25) -- here a normal filtered wiggle ADDED if filtered elsewhere
    if Score() < curscore then PopPosition() else ClrTopPosition() end
end

function Sort(tab,items) --BACWARD bubble sorting - lowest on top, only needed items
    for x=1,items do --items do
        for y=x+1,#tab do
            if tab[x][1]>tab[y][1] then
                tab[x],tab[y]=tab[y],tab[x]
            end
        end
    end
    return tab
end

-- part to administrate what has been done
Donepart={} --To find fast if to be skipped
Blocked={} --A simple list so we can clear Donepart
Disj={} --To administrate which segments have be touched
disjunct=false
donotrevisit=true
clrdonelistgain=segCnt
curclrscore=StartEbolaScore

ProtectBest=0 -- nb best scoring to be freezed (depending on "worst subscores" parameters)
BestOnes={}
BestFrozen={}

function AddDone(first,last)
    if donotrevisit then
        Donepart[first+(last-first)*segCnt2]=true
        Blocked[#Blocked+1]=first+(last-first)*segCnt2
    end
    if disjunct then
        for i=first,last do Disj[i]=true end
    end
end

function CheckDone(first,last)
    if not donotrevisit then return false end
    local result=Donepart[first+(last-first)*segCnt2]
    if disjunct then
        for i=first,last do if Disj[i] then result=true end end
    end
    return result
end

function ChkDisjunctList(n)
    if not disjunct then return end
    local maxlen=0
    for i=1,segCnt2 do
        if Disj[i] then maxlen=0 else maxlen=maxlen+1 end
        if maxlen == n then return end
    end
    -- No part is big enough so clear Disjunctlist
    print("Clearing disjunct list")
    for i=1,segCnt2 do
        Disj[i]=false
    end
end

function ClearDoneList()
    --clear donelist
    for i=1,#Blocked do Donepart[Blocked[i]]=false end
    if disjunct then
        --clear disjunctlist also
        for i=1,segCnt2 do Disj[i]=false end
    end
    Blocked={}
    curclrscore=Score()
end

function ChkDoneList()
    if not donotrevisit and not disjunct then return end
    if Score() > curclrscore+clrdonelistgain then
        if donotrevisit then ClearDoneList() end
    end
end
--end of administration part

function FindWorst(firsttime)
	print("###########################################")
    print("Searching worst scoring parts of len "..lengthZ.." (it takes time ...)")
    ChkDisjunctList(lengthZ)
    wrst={}
    GetSegmentScores()
    local skiplist=""
    local nrskip=0
    for i=1,segCnt2-lengthZ+1 do
        if not CheckDone(i,i+lengthZ-1) and MustWorkon(i,i+lengthZ-1)
        then
            local s=getPartscore(i,i+lengthZ-1)
            wrst[#wrst+1]={s,i}
        else
            if CheckDone(i,i+lengthZ-1)
            then
                if nrskip==0 then print("Skipping") end
                nrskip=nrskip+1
                skiplist=skiplist..i.."-"..(i+lengthZ-1).." "
                if nrskip%7==0 then
                    print(skiplist)
                    skiplist=""
                end
            end
        end
    end
    if nrskip%7 ~= 0 then print(skiplist) end
    if nrskip > 0 then print("Number of skips: "..nrskip) end
    wrst=Sort(wrst,reBuild)
    areas={}
    local rb=reBuild
    if rb>#wrst then rb=#wrst end
    for i=1,rb do
        local w=wrst[i]
        local ss=w[2]
        areas[#areas+1]={ss,ss+lengthZ-1}
    end
    if firsttime and #wrst == 0 then
        print("No possibilities left so clearing Done list")
        ClearDoneList()
        FindWorst(false) -- not first time any more
    end
end

function FindBest (ScoreTable, items)
	local ScoreTable= ScoreTable
	local items= items
	BestOnes=Sort(ScoreTable,items) --BACWARD bubble sorting - lowest on top, only needed items
end

function ProtectBestSegs(ScoreTable, items)
	local ScoreTable= ScoreTable
	local items= items
	FindBest (ScoreTable, items)
	BestFrozen={}
	for i=1, #BestOnes do
		local seg=BestOnes[i][1]
		if not freeze.IsFrozen(seg) then
			freeze.Freeze(seg, true, true) --  backbone and sidechains
			BestFrozen[#BestFrozen+1]=seg
		end
	end
	print("Freezed"..#BestFrozen.." unfreezed best segments")
end

function UnProtectBestSegs()
	print("Unfreezing "..#BestFrozen.." best segments")
	for i= 1, #BestFrozen do
		freeze.Unfreeze(BestFrozen[i][1])
	end
end

-- Rebuild section
function localRebuild(maxiters)
    if maxiters==nil then maxiters=3 end
    local s=Score()
    local i=0
    if bandflip then band.DisableAll() end
    Bridgesave()
    repeat
        i=i+1
        if i>maxiters then break end
        structure.RebuildSelected(i)
    until Score()~=s and BridgesBroken() == false
    if bandflip and userbandenabled then band.EnableAll() end
    Bridgerestore()
    if Score()~=s then return true else return false end
end

function ReBuild(ss,se,tries)
	undo.SetUndo(false) -- it takes too much place in the Undo chart
	local tries = tries or 10

    ClearScores() --reset score tables
	displaySkipSlots="" -- reset list of skipped RB solutions
    if ss>se then ss,se=se,ss end --switch if needed
    local Foundone=false
	if tries == 0 then
	else
		for try=1,tries do -- perform loop for number of tries
			selection.DeselectAll()
			CI(rebuildCI)
			selection.SelectRange(ss,se)
			local extra_rebuilds = 1
			if savebridges then extra_rebuilds=3 end --extra if bridges keep breaking
			local done
			repeat
				done=localRebuild(nil)
				extra_rebuilds = extra_rebuilds -1
			until done or extra_rebuilds == 0
			SaveBest()
			if done==true then
				Foundone=true
				Bridgesave()
				if doSpecial==true then
					SelectAround(ss,se,9)
					CI(1)
					Wiggle("s",1,nil,true)
					Wiggle("ws",10,nil,true)
					selection.DeselectAll()
					selection.SelectRange(ss,se)
					Wiggle("wb",20,nil,true)
				elseif doShake==true then
					CI(shakeCI)
					Wiggle("s",1,nil,true)
				end
				Bridgerestore()
				if AfterRB then
					PushPosition() --save the current position for next round
					doMutate()
				end
				SaveScores(ss,se,try)
				if AfterRB then PopPosition() end
			end
			if (try > 3 or savebridges) and Foundone==false then
				print("No valid rebuild found on this section")
				print("After 9 or more rebuild attempts, giving up")
				break
			end
		end
	end
	if displaySkipSlots ~="" then
		print("Skipped RBns: "..displaySkipSlots.." user slots cost>"..SkipSlotThreshold)
	end
    CI(1)
	undo.SetUndo(defUndo)	
    return Foundone
end
-- end rebuild section

-- section to compute segmentscore(part)s
function getPartscore(ss,se,attr)
	if FILTERMANAGE then FiltersOn() end
    local s=0
    if attr=='total' then
        s=Score()
    elseif attr==nil then --is only called from findWorst
        for i=ss,se do
            s=s+SegmentScores[i]
        end
    elseif attr=='loctotal' then --total segment scores
        s=GetSubscore(nil,ss,se)
    elseif attr=='ligand' then --ligand score
        for i=segCnt2+1,segCnt do s=s+current.GetSegmentEnergyScore(i) end
	elseif attr=='filter' then -- new BK
		s=FilterScore()
    else
        s=GetSubscore(attr,ss,se)
    end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
    return s
end

WORKONbool={} -- list of segments with true if we may work on it and false if not
function InitWORKONbool()
    WORKONbool=SegmentSetToBool(WORKON)
end

function MustWorkon(i,j)
    for k=i,j do if not WORKONbool[k] then return false end end
    return true
end

SegmentScores={} --Optimalisation for fast worst search
lastSegScores=0 -- only to see if it has to be calculated again or not
function GetSegmentScores() -- total of all scrPart checked subscores for one segment
	if FILTERMANAGE then FiltersOn() end
    if lastSegScores~=Score() then
        lastSegScores=Score()
        for i=1,segCnt2 do
            if WORKONbool[i] then
                if #scrPart==0 then
                    -- if nothing specified by user default is
                    -- segmentenergy - reference + extra Density score
                    SegmentScores[i]=current.GetSegmentEnergyScore(i)
                    if not structure.IsMutable(i) then --ignore reference part but NOT for mutables)
                        SegmentScores[i]=SegmentScores[i]-current.GetSegmentEnergySubscore(i,'reference')
                    end
                    if math.abs(DENSITYWEIGHT) > 0 then --the Density component has extra weight
                        SegmentScores[i]=SegmentScores[i]+DENSITYWEIGHT*current.GetSegmentEnergySubscore(i,'density')
                    end
                else
                    SegmentScores[i]=GetSubscore(scrPart,i,i)
                end
            end
        end
    end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
end
-- end section segmentscore(part)s

-- Administration of the different slots and best scores
Scores={} --{SubscoreSlot_no,points,totscore,showlist,todo,rbnr}
--example: {14, 12.5, 9898.2, "print this", true, 15} ?
-- SubscoreSlot_no = ScoreParts[i][1]: 14= density = ScoreParts[14][2] I think

-- Compute which scoreparts to use
ActiveSub=FindActiveSubscores(true) -- false = save time on beginning (not displaying subscores)
FILTERS=FindActiveFilter()

if PROBABLEFILTER then -- gives TvdLmaxbonus
	--FilterBonus()
	TvdLFilterDialog()
	if ShadowFilter then print("Shadow filters seem present") end
	if TvdLFilteractive and ScorePriority==0 then FilterOff() end -- TO DO verify, may be duplicate, should come after choosing ScorePriority
end


ScoreParts={ --{SubscoreSlot_no,name,active} example {14, density, true}
    {4,'total',true},
    {5,'loctotal',true}
}
nextslot=6
if HASLIGAND then
    ScoreParts[#ScoreParts+1] = { nextslot,'ligand',true }
    nextslot=nextslot+1
    print("Ligand slot enabled")
end

for i=1,#ActiveSub do
    ScoreParts[#ScoreParts+1] = { nextslot,ActiveSub[i],true }
    nextslot=nextslot+1
end

if FILTERS then -- new BK
	ScoreParts[#ScoreParts+1] = { nextslot,'filter',true }
    nextslot=nextslot+1
    print("Filter slot enabled")
end

function ClearScores() -- renewed BK
    Scores={}
	SlotList={} -- new
    for i=1,#ScoreParts do -- including totals and filter which are not per segment
        if ScoreParts[i][3] then
            Scores[#Scores+1]={ScoreParts[i][1],-9999999,-9999999,'',false,-1}
			SlotList[#SlotList+1]={ScoreParts[i][1], ScoreParts[i][2]}
        end
    end
    slotScr={}
end

SkipSlotThresholdBase = 20000 -- set it huge if you want to keep all rebuilds like in original tvdl-edrwa
SkipSmallSlotThreshold = 0.5 -- if the rebuilds did not change anything, don't loose time with it (set to zero for default)
BestRBscore=-99999998 -- partial total rebuild score for this slots preferences
SkipSlotThreshold= Max(SkipSlotThresholdBase, SkipSlotThresholdBase + bestScore) -- global will be upgraded each rebuild round
displaySkipSlots=""

function SaveScores(ss,se,RBnr) -- total of treated zones for each subscore in latest ReBuild/remix (TO DO Filters?)
    local scr={} -- example {{1, 10.2},{14, -9.5}} 14 being ideality
	local RBscore=0 -- only to be able to skip it
	local CostOK=true
    for i=1,#ScoreParts do -- archiving all selected scoreparts for this rebuild nb
        if ScoreParts[i][3] then -- including totals and filter
			local ThisPartScore=getPartscore(ss,se,ScoreParts[i][2])
            scr[#scr+1]={ScoreParts[i][1],ThisPartScore}
			RBscore=RBscore+ThisPartScore -- NEW 10/2/2015
        end
    end
	if RBscore > BestRBscore then --NEW 10/2/2015
		BestRBscore=RBscore
		SkipSlotThreshold=Max(SkipSlotThresholdBase, SkipSlotThresholdBase + bestScore) -- it will skip worst RBs
	elseif RBscore + SkipSlotThreshold < BestRBscore or RBscore + SkipSmallSlotThreshold > BestRBscore then -- will keep any improvement, eliminate any worst from there
		--print("Skipping RBn "..RBnr.." , user slots cost>"..SkipSlotThreshold)
		CostOK=false --  eliminate this solution
		displaySkipSlots=displaySkipSlots..RBnr..", "
	end
	if CostOK then
		local totscore=Score()
		for i=1,#Scores do
			local s=scr[i][2] -- the subscore considered
			if s>Scores[i][2] then -- replacing the best subscore of this type for this zone now, except when total was too low
				local slot=scr[i][1] -- the slot number is always a subscore type e.g. 14= ideality
				save.Quicksave(slot) --print("Saved slot ",slot," pts" ,s) --debug
				Scores[i][2]=s -- the new best subscore for this zone
				Scores[i][3]=totscore -- the related total score
				Scores[i][6]=RBnr
			end
		end
	SaveBest()
	end
end

function ListSlots()
    --Give overview of slot occupation
    --And sets which slots to process
    local Donelist={}
    for i=1,#Scores do Donelist[i]=false end
    local Report=""
    for i=1,#Scores do
		if not Donelist[i] then
			local Curlist=" "..Scores[i][1]
			Scores[i][5]=true --This one we have to process
			-- Now find identical filled slots
			for j=i+1,#Scores do
				if Scores[j][3] == Scores[i][3] then -- total score of each slot
					Curlist=Curlist.."="..Scores[j][1]
					Donelist[j]=true
				end
			end
			Scores[i][4]=Curlist
			Report=Report.." "..Curlist
		end
	end
    print("Slotlist:"..Report)
end
-- end of administration of slots and scores

function PrintAreas()
    if #areas<19 then
        local a=""
        local x=0
        for i=1,#areas do
            x=x+1
            a=a..areas[i][1].."-"..areas[i][2].." "
            if x>6 then
                print(a)
                a=""
                x=0
            end
        end
        if x>0 then print(a) end
    else
        print("It is "..#areas.." places, not listing.")
    end
end

function AddLoop(sS)
    local ss=sS
    local ssStart=structure.GetSecondaryStructure(ss)
    local se=ss
    for i=ss+1,segCnt2 do
        if structure.GetSecondaryStructure(i)==ssStart then se=i
        else break end
    end
    if se-ss+2>minLen and loops==true then
        areas[#areas+1]={ss,se}
    end
    return se
end

function AddOther(sS)
    local ss=sS
    local ssStart=structure.GetSecondaryStructure(ss)

    local se=ss
    if ss>1 then
        for i=ss-1,1,-1 do --search bacward for start
            local sec=structure.GetSecondaryStructure(i)
            if sec=="L" then ss=i
            else break end
        end
    end
    if se<segCnt2-1 then --now forward to find end
        local change=false
        repeat
            se=se+1
            if se==segCnt2 then break end
            local sec=structure.GetSecondaryStructure(se)
            if change==false then
                if sec~=ssStart then change=true end
            end
        until change==true and sec~="L"
        if se<segCnt2 then se=se-1 end
    end
    if sheets==false and ssStart=="E" then return se end
    if helices==false and ssStart=="H" then return se end
    if se-ss+2>minLen then
        areas[#areas+1]={ss,se}
    end
    return se
end
function FindAreas()
    if loops then
        local done=false
        local ss=0
        repeat--loops
            ss=ss+1
            local ses=structure.GetSecondaryStructure(ss)
            if ses=="L" then
                ss=AddLoop(ss)
            end
            if ss==segCnt2 then done=true end
        until done~=false
    end
    if sheets or helices then
        local done=false
        local ss=0
        repeat--other
            ss=ss+1
            local ses=structure.GetSecondaryStructure(ss)
            if ses~="L" then
                ss=AddOther(ss)
            end
            if ss==segCnt2 then done=true end
        until done~=false
    end
end

firstRBseg=0
lastRBseg=0
number_of_remix=49	-- max number of remixes (depends on the slots available)

function doMutate() -- changed 23/12/2015 for FILTERPROTECT: little filter loss allowed here
    if not HASMUTABLE then return end
    -- Do not accept loss if mutating
    local curscore=Score()
	local curfilter=FilterScore()
    PushPosition()
    CI(MutateCI)
    Bridgesave()
    if MUTRB then
        selection.DeselectAll()
        selection.SelectRange(firstRBseg,lastRBseg)
        MutateSel()
    elseif MUTSur then
        SelectAround(firstRBseg,lastRBseg,MutSphere)
        MutateSel()
    else
        MutateAll()
    end
    Bridgerestore()
    if (Score() < curscore) or (FILTERPROTECT and FilterScore()<curfilter-LostFpgain) then PopPosition() else ClrTopPosition() end
end

function IdealAndMore(types,seg1,seg2) -- idealize (only, for the moment)
	if FILTERMANAGE then FiltersOn() end
	local types=types or "Ideality"
	local SpecialSubscore=GetSubscore(types,seg1,seg2) -- e.g. ideality
	local sz=seg2-seg1+1
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
	if SpecialSubscore<-5 then -- only on relatively bad idealities (absolute, not per segment)
	
	    if ( seg1 > 0 ) then
             structure.InsertCut ( seg1 )
        end

        if ( seg2 < segCnt2 ) then
            structure.InsertCut ( seg2)
        end

        --selection.DeselectAll ()
        --selection.SelectRange ( seg1,seg2 )

			print("Idealizing "..seg1.."-"..seg2)
			structure.IdealizeSelected ()

        if ( seg1 > 0 ) then
             structure.DeleteCut ( seg1 )
        end

        if ( seg2 < segCnt2 ) then
            structure.DeleteCut ( seg2 )
        end
		SelectAround(seg1,seg2,12) --local wiggle after
		structure.WiggleSelected ( 25 )
		SaveBest()
	end
end

IDEALCHECK=true -- 08/03/2014
CUTWORST=false -- 1/5/2015

function DeepRebuild()
    local ss=Score()
	local drg=0
    if struct==false then AllLoop() end
    save.Quicksave(PreferredScoreSlot) -- initialization at very begin of the recipe
    recentbest.Save()
    print("Ebola started at score: "..round3(ss))
    for i=1,#areas do
        local ss1=Score()
        local s=areas[i][1]
        local e=areas[i][2]
        local CurrentHigh=1 -- slot of current high
		local CurrentHigh2=1 -- slot of second best
        local CurrentAll="" -- to report where gains came from
        local CurrentHighScore= -99999998
		local CurrentHighScore2= -99999999
		local CurrentScore= -99999999 -- only for local checks
        firstRBseg=s
        lastRBseg=e
        Bridgesave()
		if Runnr > 0 then --Runnr 0 is to avoid bug when skippingworst zones
				ENOUGHFORGAB=false
				print("--")
				dr_string = "DR "..Runnr.."."..(e-s+1).."."..i
				print("DR "..Runnr.." len "..(e-s+1).." wrst "..i..": "..s.."-"..e.." "..
					  rebuilds.." times. Wait... Score: "..round3(Score()))
				if ReBuild(s,e,rebuilds) then -- false if skip

					-- Make sure we do not miss an improvement during rebuild
					if RBScore() > PreferedScore then
						Bridgesave()
						recentbest.Restore()
						Bridgerestore()
						if Score() > PreferedScore*1.1 and Score()> PreferedScore+ 10 then -- was 0.0001 only for huge miss (here we forget all our good intentions
							print(" Found a missed gain!!!")
							SaveScores(s,e,0) -- rebuild Nb 0
						end
						if Score() > bestScore+0.001 then
							print(" Archiving a missed gain!!!")
							bestScore=Score()
							save.Quicksave(BestScoreSlot)
						end
					end
					save.Quickload(PreferredScoreSlot) -- New 11/2/2015 to avoid starting too high This is slot n0 I think
					ListSlots() -- BUG here
					for r=1,#Scores do -- now we shake (or wiggle) on each slot depending on subscores preferences
						if Scores[r][5] then
							local slot=Scores[r][1]
							local subscoreName= SlotList[r][2]
							save.Quickload(slot)
							SelectAround(s,e,12) --local shake after rebuild
							Bridgesave()
							if not skipqstab then qStab()
							else
								CI(1)
								Wiggle("s",1,nil,true)
								Wiggle("ws",15,nil,true)
							end
							Bridgerestore()
							if AfterQstab then doMutate() end
							save.Quicksave(slot)
							if Score() > CurrentHighScore then
								 CurrentHigh2=CurrentHigh -- slot of second best
								 CurrentHigh=slot
								 CurrentAll=CurrentAll..Scores[r][4].."("..subscoreName.. ") "
								 CurrentHighScore2=CurrentHighScore
								 CurrentHighScore=Score()
							end
							SaveBest()
							--subscoreName= SlotList[r][2] --BUG
							print("Stabilized slot "..slot.." ("..subscoreName..") Score: "..round3(Score()).." (RBnr "..Scores[r][6]..")") --BUG

								--print("Stabilized slot "..slot.." Score: "..round3(Score()))
								--print("Stabilized slot "..slot.." Score: "..round3(Score()).." (rebuild nb "..Scores[r][6]..")")
						end
					end
					save.Quickload(CurrentHigh) -- taking the best rebuild in order to fuze it
					if not skipfuze and ss1-CurrentHighScore < maxlossbeforefuze*(e-s+1)/3 then -- start of the Fuze part
						print("Fuzing best position scoring "..round3(Score()))
						if not AfterQstab and BeFuze then doMutate() end
						tempFuzeSlot=TotalSlot
						tempFuzeSlot2=LocTotalSlot
						if CurrentHigh2==tempFuzeSlot then -- avoiding to use TotalSlot if it is the second best (we need it)
							tempFuzeSlot=LocTotalSlot
							tempFuzeSlot2=TotalSlot
						end
						save.Quicksave(tempFuzeSlot) -- archiving it in TotalSlot or LocTotalSlot because it's free now
						if savebridges then Fuze(tempFuzeSlot,Bridgesave,Bridgerestore) else Fuze(tempFuzeSlot) end
						if AfterFuze then doMutate() end
						CurrentHighFuzedScore=Score() -- New 11/2/2015
						CurrentHighFuzedScore2=CurrentHighFuzedScore-1 -- only for initializing in case there is no second best
						print("Done. Fuzed Score= "..round3(CurrentHighFuzedScore))

						SaveBest()
		--new    BK 4/2/2015

						if CurrentHighScore2*1.02> CurrentHighScore and CurrentHighScore2<CurrentHighScore 
								and FUZE2BEST and CurrentHigh2~= CurrentHigh then -- fuzing second best
							save.Quickload(CurrentHigh2) -- taking the second best in order to fuze it
							if not skipfuze and ss1-CurrentHighScore2 < maxlossbeforefuze*(e-s+1)/3 then
								print("Fuzing 2d best position scoring "..round3(CurrentHighScore2))
								--if not AfterQstab and BeFuze then doMutate() end
								save.Quicksave(tempFuzeSlot2)
								if savebridges then Fuze(tempFuzeSlot2,Bridgesave,Bridgerestore) else Fuze(tempFuzeSlot2) end
								--if AfterFuze then doMutate() end
								CurrentHighFuzedScore2=Score() -- New 11/2/2015
								print("Done. 2d best Fuzed Score= "..round3(CurrentHighFuzedScore2))
							end
							SaveBest()
						end

						--selecting the best of the 2 fuzes
						if CurrentHighFuzedScore> CurrentHighFuzedScore2-0.0001 then -- even if case there is no second best
							save.Quickload(tempFuzeSlot)
							CurrentHighScore=CurrentHighFuzedScore
						else
							save.Quickload(tempFuzeSlot2)
							CurrentHighScore=CurrentHighFuzedScore2
						end
						
					else -- not fuzed


					
					end -- end of the fuze part

				else
					save.Quickload(PreferredScoreSlot) -- if there was no rebuild, take the absolute best score
				end
				save.Quicksave(CurrentHigh) -- keeping it for GAB, 22/8/2017
				-- hopefully I have here the CurrentHighFuzedScore score (otherwise, check by adding a score computing)
				--NOW we have the best "after rebuild" (and Fuze) solution.
				
				-- save.Quickload(PreferredScoreSlot) -- sorry, mistake here before 22/8/2017
				
				--improvedscore is from lated saveBest, but we idealize from the latest rebuild
				if improvedscore or structure.GetSecondaryStructure(s)=="L" or NOREBUILDMODE then -- doing these options only if loop or score is high enough
					if IDEALCHECK then -- BK 08/03/2014, I think it can be interesting with big SS (like on an entire helix)
						IdealAndMore("Ideality",s,e) -- test with ideality
						CurrentScore= Score()
						if CurrentScore > CurrentHighScore then -- a local savebest
							CurrentHighScore=CurrentScore
							save.Quicksave(CurrentHigh)
							SaveBest() -- for archiving
						end
						save.Quickload(CurrentHigh) -- sinon on rebuild le suivant avec le score d'idealize !!
					end
					
					-- we are still on the temporal best "after rebuild and all" score.
					
					if IDEALCHECK then -- Remixing
						local sz=e-s+1
						if sz>3 and sz<12 then
							if ReMix(s,e,number_of_remix) then -- false if no remix found
								print("Remixing "..s.."-"..e) -- ToDo: check which type of score this is (other?) and adapt scores
								CurrentScore= Score()
								if CurrentScore > CurrentHighScore then -- a local savebest
									CurrentHighScore=CurrentScore
									save.Quicksave(CurrentHigh)
									SaveBest() -- for archiving
								end
								save.Quickload(CurrentHigh) -- sinon on rebuild le suivant avec le score de remix !!

								SelectAround(s,e,12) --local wiggle after (shake is already done inside)
								structure.WiggleSelected ( 25 )
								CurrentScore= Score()
								if CurrentScore > CurrentHighScore then -- a local savebest
									CurrentHighScore=CurrentScore
									save.Quicksave(CurrentHigh)
									SaveBest() -- for archiving
								end
								save.Quickload(CurrentHigh) -- sinon on rebuild le suivant avec le score de remix !!	
							end
						end
					end
					
					-- we are still on the temporal best "after rebuild and all" score.
					
					if CUTWORST and s+1 < e then -- new 1/5/2015, 14/1/2017 (don't cut len 2)
						cut(s+1)
						print("Cutting seg "..s+1)
						structure.WiggleAll ( 25 )
						uncut(s+1)
						recentbest.Save() -- NEW 23/11/2015 important to avoid recentbest in cut bug
						structure.WiggleAll ( 25 )
						recentbest.Restore()  -- IMPORTANT: recentbest must be saved after deleting cut
						CurrentScore= Score()
						if CurrentScore > CurrentHighScore then -- a local savebest
							CurrentHighScore=CurrentScore
							save.Quicksave(CurrentHigh)
							SaveBest() -- for archiving
						end
						save.Quickload(CurrentHigh) -- sinon on rebuild le suivant avec le score de remix !!
					end
				end
					-- we are still on the temporal best "after rebuild and all" score.
					
				--GAB section 19/10/2016

				if ss1-CurrentHighScore < GABfilter and CurrentHighScore-ss1< GABfilterHigh then -- 5/8/2015 no gab if big gain or loss
					ENOUGHFORGAB=true
					LaunchGab(s,e) -- will do it including bands to same worst areas, starting from this solution
					SaveBest()
				else
					print("Out of range => skipping GAB")
				end
				--SaveBest()
				save.Quickload(PreferredScoreSlot)
		end --skip section
        if savebridges then
            if BridgesBroken() then
                -- THIS SHOULD NOT HAPPEN
                print("Unexpected bridge broken, pls report\n")
                print("Restoring a good position, discarding wins\n")
                Bridgerestore()
                save.Quicksave(PreferredScoreSlot)
                PreferedScore=Score()
            else Bridgerestore()
            end
        else Bridgerestore() end
        if ss1+0.00001 < Score() then
            print("Finally gained from slots: ",CurrentAll)
        end
        AddDone(s,e)
        ChkDoneList()
		SaveBest() -- New 1/6/2015 not sure it's useful
		save.Quickload(PreferredScoreSlot) -- NEW 5/12/2014, sinon on rebuild le suivant avec le score avant gab?
		local currentscore= Score(current, true)
		drg= currentscore-StartEbolaScore  -- (preferred) deep rebuild gain
		local absoluteGain=bestScore-StartEbolaScore
		print("<<>>Total Ebola gain: "..round3(drg).." ("..round3(absoluteGain).."). Score from "..round3(StartEbolaScore).." to "..round3(currentscore).." ("..round3(bestScore)..")")
        drg4compare= currentscore-StartEbolaScoreLater
		if drg4compare > minGain then
			StartEbolaScoreLater= currentscore
		break end -- recalculate worst, force new round
    end
	ENOUGHFORGAB2=false
	if drg4compare > 70-GABfilter then ENOUGHFORGAB2=true end -- note that we reserve full GAB for occasions where there was big gain or small losses
	print("DeepRebuildGAB gain: "..round3(Score()-ss))
    if struct==false and SAVEDstructs then save.LoadSecondaryStructure() end
end -- This is the MAIN DRW

genEbola= 0
function DR_GAB()
	genEbola=genEbola+1
	PrintAreas()
	if ProtectBest>0 then ProtectBestSegs(SegmentScores, ProtectBest) end
	DeepRebuild() -- GAB is included on each loop here
	if ENOUGHFORGAB2 then LaunchGab() SaveBest() end-- overall GAB at each cycle with all worst areas I think
	if ProtectBest>0 then UnProtectBestSegs() end
	SaveBigSteps() -- for movie at the end
	StatusGen(genEbola) -- printing for jeff101
end

function DRcall(how)
	print("How: "..how)
    if how=="drw" then
		local stepsize=1
        if minLen>maxLen then stepsize= -1 end
        for i=minLen,maxLen,stepsize do --search from minl to maxl worst segments
            lengthZ=i
            --if longfirst then lengthZ=maxLen-i+minLen end
            FindWorst(true) --fill areas table. Comment it if you have set them by hand
			DR_GAB()
        end
    elseif how=="fj" then --DRW lengthZ cutted on pieces
        FindWorst(true) --add to areas table worst part
        areas2={}
        for a=1,#areas do
            local s=areas[a] --{ss,se}
            local ss=s[1] --start segment of worst area
            local se=s[2] --end segment of worst area
            for i=ss,se do
                for x=1,lengthZ do
                    if i+x<=se then
                        areas2[#areas2+1]={i,i+x}
                    end
                end
            end
        end
        areas=areas2
        DR_GAB()
    elseif how=="all" then
        areas={}
        for i=minLen,maxLen do
            for x=1,segCnt2 do
                if i+x-1<=segCnt2 then
                    areas[#areas+1]={x,x+i-1}
                end
            end
        end
        DR_GAB()
    elseif how=="simple" then
        FindWorst(true)
        DR_GAB()
    elseif how=="areas" then
        areas={}
        FindAreas()
        DR_GAB()
    end
end

function AskMoreOptions()
    local ask=dialog.CreateDialog("More DRW-Ebola options")
    ask.l1=dialog.AddLabel("Clear skip list if gain is more")
    ask.revlist=dialog.AddSlider("Cleargain:",clrdonelistgain,0,500,0)
    --ask.l2=dialog.AddLabel("Number of rebuilds each pass")
    ask.nrrebuilds=dialog.AddSlider("#Rebuilds:",rebuilds,0,100,0)
    --ask.l3=dialog.AddLabel("Number of full cycles")
    ask.nrcycles=dialog.AddSlider("#Cycles:",maxnrofRuns,1,1000,0)
	ask.l3a=dialog.AddLabel("Start Auto Pilot after:")
	ask.HoursResetOptions=dialog.AddSlider("#hours ",HoursResetOptions,1,240,0)
    ask.l4=dialog.AddLabel("Skip first worst parts (crash resume)")
    ask.nrskip=dialog.AddSlider("Skip parts:",nrskip,0,down(segCnt2/2),0)
    ask.reBuild=dialog.AddSlider("#wrst in 1st cycle:",reBuild,1,segCnt2,0)
    ask.reBuildm=dialog.AddSlider("#add each cycle:",reBuildmore,0,10,0)
	ask.IDEALCHECK=dialog.AddCheckbox("Idealize & remix",IDEALCHECK) -- 08/03/2014
	ask.CUTWORST=dialog.AddCheckbox("cut in worst",CUTWORST) -- 1/5/2015
    --ask.longfirst=dialog.AddCheckbox("Longest rebuild first",longfirst)
    ask.doSpecial=dialog.AddCheckbox("Local cleanup after rebuild SLOW",doSpecial)
    ask.doShake=dialog.AddCheckbox("Or Shake after rebuild",doShake)
    ask.shakeCI=dialog.AddSlider("Shake CI:",shakeCI,0,1,2)
    ask.bandflip=dialog.AddCheckbox("Disable bands during rebuild AND enable after",bandflip)
    ask.skipqstab=dialog.AddCheckbox("Local shake instead of Qstab",skipqstab)
    ask.skipfuze=dialog.AddCheckbox("Skip Fuze",skipfuze)
	ask.l5=dialog.AddLabel("------Launching GAB after rebuilds------")
	ask.GABfilter=dialog.AddSlider("GAB, loss filter", GABfilter, -10, 50, 0) -- New for ebola
	ask.GABfilterHigh=dialog.AddSlider("GAB, gain filter", GABfilterHigh, 0, 900, 0) -- New for ebola
	ask.SkipGAB=dialog.AddCheckbox("Do not launch GAB",SkipGAB)
    ask.OK = dialog.AddButton("OK",1)
	
    dialog.Show(ask)
	
	clrdonelistgain=ChangedOptions("clrdonelistgain",clrdonelistgain,ask.revlist.value)
    --clrdonelistgain=ask.revlist.value
	rebuilds=ChangedOptions("rebuilds",rebuilds,ask.nrrebuilds.value)
		if rebuilds == 0 then NOREBUILDMODE= true end -- onlyGAB= true	

	maxnrofRuns=ChangedOptions("maxnrofRuns",maxnrofRuns,ask.nrcycles.value)

	HoursResetOptions=ChangedOptions("HoursResetOptions",HoursResetOptions,ask.HoursResetOptions.value)
	
    nrskip=ChangedOptions("nrskip",nrskip,ask.nrskip.value)
    reBuild=ChangedOptions("reBuild",reBuild,ask.reBuild.value)

    reBuildmore=ChangedOptions("reBuildmore",reBuildmore,ask.reBuildm.value)
    IDEALCHECK=ChangedOptions("IDEALCHECK",IDEALCHECK,ask.IDEALCHECK.value)
    CUTWORST=ChangedOptions("CUTWORST",CUTWORST,ask.CUTWORST.value)
    --ChangedOptions("longfirst",longfirst,ask.longfirst.value)
    doShake=ChangedOptions("doShake",doShake,ask.doShake.value)
    doSpecial=ChangedOptions("doSpecial",doSpecial,ask.doSpecial.value)
    shakeCI=ChangedOptions("shakeCI",shakeCI,ask.shakeCI.value)
    bandflip=ChangedOptions("bandflip",bandflip,ask.bandflip.value)
    skipqstab=ChangedOptions("skipqstab",skipqstab,ask.skipqstab.value)
    skipfuze=ChangedOptions("skipfuze",skipfuze,ask.skipfuze.value)
    GABfilter=ChangedOptions("GABfilter",GABfilter,ask.GABfilter.value)
    GABfilterHigh=ChangedOptions("GABfilterHigh",GABfilterHigh,ask.GABfilterHigh.value)
    SkipGAB=ChangedOptions("SkipGAB",SkipGAB,ask.SkipGAB.value)
end

AfterRB=false
InQstab=false
AfterQstab=false
BeFuze=false
AfterFuze=false
MutateCI=0.9
MutSphere=8
MUTRB=false
MUTSur=false
FILTERPROTECT=false -- true=no filter loss allowed on mutate

if HASMUTABLE then -- note that the default is many mutates ! Slow !
    AfterQstab=true
    AfterFuze=true
    MUTSur=true
end

function AskMutateOptions()
    local ask = dialog.CreateDialog("Mutate Options")
    ask.AfterRB = dialog.AddCheckbox("Mutate after rebuild",AfterRB)
    ask.InQstab = dialog.AddCheckbox("Mutate during Qstab",InQstab)
    ask.AfterQstab = dialog.AddCheckbox("Mutate after Qstab",AfterQstab)
    ask.BeFuze = dialog.AddCheckbox("Mutate before Fuze",BeFuze)
    ask.AfterFuze = dialog.AddCheckbox("Mutate after Fuze",AfterFuze)
    ask.l1=dialog.AddLabel("-----What to rebuild or all")
    ask.OnlyRB=dialog.AddCheckbox("Mutate only rebuild part",MUTRB)
    ask.OnlySur=dialog.AddCheckbox("Mutate rebuild and surround",MUTSur)
    ask.l2=dialog.AddLabel("Sphere size to use with surround")
    ask.SurSize=dialog.AddSlider("Sphere:",MutSphere,3,15,0)
    ask.MutateCI=dialog.AddSlider("MutateCI:",MutateCI,0.1,1,2)
    ask.l3=dialog.AddLabel("Use workaround if Layer filter is active")
    ask.Layer=dialog.AddCheckbox("Mutate 1 by 1",LAYERFILTER)
	ask.FILTERPROTECT=dialog.AddCheckbox("Protect filter bonus",FILTERPROTECT) -- true=no filter loss allowed on mutate
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
		AfterRB=ChangedOptions("AfterRB",AfterRB,ask.AfterRB.value)
		InQstab=ChangedOptions("InQstab",InQstab,ask.InQstab.value)
		AfterQstab=ChangedOptions("AfterQstab",AfterQstab,ask.AfterQstab.value)
		BeFuze=ChangedOptions("BeFuze",BeFuze,ask.BeFuze.value)
		AfterFuze=ChangedOptions("AfterFuze",AfterFuze,ask.AfterFuze.value)
		MutateCI=ChangedOptions("MutateCI",MutateCI,ask.MutateCI.value)
		MutSphere=ChangedOptions("MutSphere",MutSphere,ask.SurSize.value)
		MUTRB=ChangedOptions("MUTRB",MUTRB,ask.OnlyRB.value)
		MUTSur=ChangedOptions("MUTSur",MUTSur,ask.OnlySur.value)
		LAYERFILTER=ChangedOptions("LAYERFILTER",LAYERFILTER,ask.Layer.value)
		FILTERPROTECT=ChangedOptions("FILTERPROTECT",FILTERPROTECT,ask.FILTERPROTECT.value)
    end
end

function printOptions(title)
    print(title)
    print("Based on rav4pl DRW 3.4")
    print("Length of rebuilds: "..minLen.." until "..maxLen)
    print("Rebuild area: "..SegmentSetToString(WORKON))
    if AfterRB then print("Mutates after each rebuild") end
    if InQstab then print("Mutates inside qStab") end
    if AfterQstab then print("Mutates after qStab") end
    if BeFuze then print("Mutates before Fuzing") end
    if AfterFuze then print("Mutates after Fuzing") end
    print("Nr of rebuilds each try: "..rebuilds)
    if not struct then print("Convert everything to loops") end
    if not donotrevisit then
        print("Will retry already tried rebuilds")
    else
        print("Clear retry blocks if gain raises above "..clrdonelistgain.." pts")
    end
    if doSpecial then print("Local cleanup after rebuild")
    elseif doShake then
        print("Initial shake after rebuild".."with CI="..shakeCI)
    end
    if skipqstab then print("Local shake instead of qStab") end
    if skipfuze then print("Skipping Fuzes") end
    print("Nr of full cycles: "..maxnrofRuns)
    if nrskip > 0 then print("SKIPPING "..nrskip.." worst zones") end
end

-- Module AskSelections
-- 02-05-2012 Timo van der Laan, Free to use for non commercial purposes

function AskForSelections(title,mode) -- to do: archive changed values
    local result={{1,segCnt}} -- All segments
    if mode == nil then mode={} end
    if mode.askloops==nil then mode.askloops=true end
    if mode.asksheets==nil then mode.asksheets=true end
    if mode.askhelixes==nil then mode.askhelixes=true end
    if mode.askligands==nil then mode.askligands=false end
    if mode.askselected==nil then mode.askselected=true end
    if mode.asknonselected==nil then mode.asknonselected=true end
    if mode.askmutateonly==nil then mode.askmutateonly=true end
    if mode.askignorelocks==nil then mode.askignorelocks=true end
    if mode.askignorefrozen==nil then mode.askignorefrozen=true end
    if mode.askranges==nil then mode.askranges=true end
    if mode.defloops==nil then mode.defloops=true end
    if mode.defsheets==nil then mode.defsheets=true end
    if mode.defhelixes==nil then mode.defhelixes=true end
    if mode.defligands==nil then mode.defligands=false end
    if mode.defselected==nil then mode.defselected=false end
    if mode.defnonselected==nil then mode.defnonselected=false end
    if mode.defmutateonly==nil then mode.defmutateonly=false end
    if mode.defignorelocks==nil then mode.defignorelocks=false end
    if mode.defignorefrozen==nil then mode.defignorefrozen=false end
    local Errfound=false
  repeat
    local ask = dialog.CreateDialog(title)
    if Errfound then
        ask.E1=dialog.AddLabel("Try again, ERRORS found, check output box")
        result={{1,segCnt}} --reset start
        Errfound=false
    end
    if mode.askloops then
        ask.loops = dialog.AddCheckbox("Work on loops",mode.defloops)
    elseif not mode.defloops then
        ask.noloops= dialog.AddLabel("Loops will be auto excluded")
    end
    if mode.askhelixes then
        ask.helixes = dialog.AddCheckbox("Work on helixes",mode.defhelixes)
    elseif not mode.defhelixes then
        ask.nohelixes= dialog.AddLabel("Helixes will be auto excluded")
    end
    if mode.asksheets then
        ask.sheets = dialog.AddCheckbox("Work on sheets",mode.defsheets)
    elseif not mode.defsheets then
        ask.nosheets= dialog.AddLabel("Sheets will be auto excluded")
    end
    if mode.askligands then
        ask.ligands = dialog.AddCheckbox("Work on ligands",mode.defligands)
    elseif not mode.defligands then
        ask.noligands= dialog.AddLabel("Ligands will be auto excluded")
    end
    if mode.askselected then ask.selected = dialog.AddCheckbox("Work only on selected",mode.defselected) end
    if mode.asknonselected then ask.nonselected = dialog.AddCheckbox("Work only on nonselected",mode.defnonselected) end
    if mode.askmutateonly then ask.mutateonly = dialog.AddCheckbox("Work only on mutateonly",mode.defmutateonly) end
    if mode.askignorelocks then
        ask.ignorelocks =dialog.AddCheckbox("Dont work on locked ones",true)
    elseif mode.defignorelocks then
        ask.nolocks=dialog.AddLabel("Locked ones will be auto excluded")
    end
    if mode.askignorefrozen then
        ask.ignorefrozen = dialog.AddCheckbox("Dont work on frozen",true)
    elseif mode.defignorefrozen then
        ask.nofrozen=dialog.AddLabel("Frozen ones will be auto excluded")
    end
    if mode.askranges then
        ask.R1=dialog.AddLabel("Or put in segmentranges. Above selections also count")
        ask.ranges=dialog.AddTextbox("Ranges","1-"..segCnt)
    end
	ask.designProtect=dialog.AddCheckbox("Freeze other backbones for design protection",designProtect)
	ask.ProtectBest=dialog.AddSlider("Don't work on best:",ProtectBest,0,segCnt,0)
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
        -- We start with all the segments including ligands
        if mode.askloops then mode.defloops=ask.loops.value end
        if not mode.defloops then
            result=SegmentSetMinus(result,FindAAtype("L"))
        end
        if mode.asksheets then mode.defsheets=ask.sheets.value end
        if not mode.defsheets then
            result=SegmentSetMinus(result,FindAAtype("E"))
        end
        if mode.askhelixes then mode.defhelixes=ask.helixes.value end
        if not mode.defhelixes then
            result=SegmentSetMinus(result,FindAAtype("H"))
        end
        if mode.askligands then mode.defligands=ask.ligands.value end
        if not mode.defligands then
            result=SegmentSetMinus(result,FindAAtype("M"))
        end
        if mode.askignorelocks then mode.defignorelocks=ask.ignorelocks.value end
        if mode.defignorelocks then
            result=SegmentSetMinus(result,FindLocked())
        end
        if mode.askignorefrozen then mode.defignorefrozen=ask.ignorefrozen.value end
        if mode.defignorefrozen then
            result=SegmentSetMinus(result,FindFrozen())
        end
        if mode.askselected then mode.defselected=ask.selected.value end
        if mode.defselected then
            result=SegmentCommSet(result,FindSelected())
        end
        if mode.asknonselected then mode.defnonselected=ask.nonselected.value end
        if mode.defnonselected then
            result=SegmentCommSet(result,SegmentInvertSet(FindSelected()))
        end
        if mode.askranges and ask.ranges.value ~= "" then
            local rangetext=ask.ranges.value
            local function Checknums(nums)
                -- Now checking
                if #nums%2 ~= 0 then
                    print("Not an even number of segments found")
                    return false
                end
                for i=1,#nums do
                    if nums[i]==0 or nums[i]>segCnt then
                        print("Number "..nums[i].." is not a segment")
                        return false
                    end
                end
                return true
            end

            local function ReadSegmentSet(data)
                local nums = {}
                local NoNegatives='%d+' -- - is not part of a number
                local result={}
                for v in string.gfind(data,NoNegatives) do
                    table.insert(nums, tonumber(v))
                end
                if Checknums(nums) then
                    for i=1,#nums/2 do
                        result[i]={nums[2*i-1],nums[2*i]}
                    end
                    result=SegmentCleanSet(result)
                else Errfound=true result={} end
                return result
            end
            local rangelist=ReadSegmentSet(rangetext)
            if not Errfound then
                result=SegmentCommSet(result,rangelist)
            end
        end
		designProtect=ask.designProtect.value -- new BK
		ProtectBest=ask.ProtectBest.value
    end
  until not Errfound
    return result
end
-- end of module AskSelections
WORKON={{1,segCnt2}}

--Start of module protect design
FREEZEPROTECT={}
designProtect=false -- true avoids macro destructuring

function ProtectDesign(NOTWORKON)
	if designProtect then
		print("Freezing unused backbones")
		for i= 1, #NOTWORKON do
			for seg=NOTWORKON[i][1], NOTWORKON[i][2] do
				if not freeze.IsFrozen(seg) then 
					freeze.Freeze(seg, true, false) -- only backbone
					FREEZEPROTECT[#FREEZEPROTECT+1]=seg -- a list
				end
			end
		end
	end
end

function UnProtectDesign(FREEZEPROTECT)
	if designProtect then
		print("Unfreezing unused backbones")
		for i= 1, #FREEZEPROTECT do
			freeze.Unfreeze(FREEZEPROTECT[i][1], true, false) -- only backbone
		end
	end
end
--End of module protect design


--ScoreFilterPart=false
function AskSubScores() -- slot selection after rebuild
    local ask = dialog.CreateDialog("Slot selection DRW "..DRWVersion)
    ask.l1=dialog.AddLabel("Specify which slots based on scorepart to use")
    for i=1,#ScoreParts do
        ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][1].." "..ScoreParts[i][2],ScoreParts[i][3])
    end
    if FILTERS and ScorePriority ==1 then  -- BK 2/6/2015
		--ask.ScoreFilterPart=dialog.AddCheckbox("Filters",FILTERS)
    	--ask.FiltersFirst=dialog.AddCheckbox("Priority to filters over score",FiltersFirst) -- duplicate
      	ask.l2=dialog.AddLabel("Filter priority grade")
      	ask.l2b=dialog.AddLabel("Lost points allowed per pt filter gain:")
    	ask.LostpFgain=dialog.AddSlider("Multiplier:",LostpFgain,0,100,0)
      	ask.l2c=dialog.AddLabel("Score priority grade")
      	ask.l2d=dialog.AddLabel("Lost filter allowed per 10 points gain:")
    	ask.LostFpgain=dialog.AddSlider("Multiplier:",LostFpgain,0,100,0)
    end
	if PROBABLEFILTER then
		ask.FILTERMANAGE = dialog.AddCheckbox ( "Disable filter during wiggle (fast)" , FILTERMANAGE )
		ask.GENERICFILTER = dialog.AddCheckbox ( "Always disable filter unless for score (turbo)" , GENERICFILTER )
	end
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
		for i=1,#ScoreParts do
			ScoreParts[i][3]=ChangedOptions(ScoreParts[i][2].." slot ",ScoreParts[i][3],ask[ScoreParts[i][2]].value)
		end
		if FILTERS and ScorePriority ==1  then -- BK 2/6/2015
			--ScoreFilterPart=ask.ScoreFilterPart.value
			--FiltersFirst=ask.FiltersFirst.value -- duplicate
			LostpFgain=ChangedOptions("LostpFgain",LostpFgain,ask.LostpFgain.value)
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
		end
		if PROBABLEFILTER then
			FILTERMANAGE=ChangedOptions("FILTERMANAGE",FILTERMANAGE,ask.FILTERMANAGE.value)
			GENERICFILTER=ChangedOptions("GENERICFILTER",GENERICFILTER,ask.GENERICFILTER.value)
		end
    end
end



-- NOT USED YET, it's implicit in above selection
function AskFilterScores() -- user defined filter selection NEW BK 10/2/2015
    local ask = dialog.CreateDialog("User filter selection ")
    ask.l1=dialog.AddLabel("Specify which own filters based on scorepart to use")
    for i=1,#ScoreParts do
        ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][1].." "..ScoreParts[i][2],ScoreParts[i][3])
    end
    if FILTERS then
		--ask.ScoreFilterPart=dialog.AddCheckbox("Filters",FILTERS)
    	--ask.FiltersFirst=dialog.AddCheckbox("Priority to filters over score",FiltersFirst) -- duplicate
      	ask.l2=dialog.AddLabel("Filter priority grade")
      	ask.l2b=dialog.AddLabel("Lost points allowed per pt filter gain:")
    	ask.LostpFgain=dialog.AddSlider("Multiplier:",LostpFgain,0,100,0)
      	ask.l2c=dialog.AddLabel("Score priority grade")
      	ask.l2d=dialog.AddLabel("Lost filter allowed per 10 points gain:")
    	ask.LostFpgain=dialog.AddSlider("Multiplier:",LostFpgain,0,100,0)
    end
	if PROBABLEFILTER then
		ask.FILTERMANAGE = dialog.AddCheckbox ( "Disable filter during wiggle (fast)" , FILTERMANAGE )
		ask.GENERICFILTER = dialog.AddCheckbox ( "Always disable filter unless for score (turbo)" , GENERICFILTER )
	end
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
      for i=1,#ScoreParts do ScoreParts[i][3]=ask[ScoreParts[i][2]].value end
		if FILTERS then -- new BK 11/11/2014
			--ScoreFilterPart=ask.ScoreFilterPart.value
			--FiltersFirst=ask.FiltersFirst.value -- duplicate
			LostpFgain=ask.LostpFgain.value
			FiltersFirst=LostpFgain>-2  -- always !!!(depends only on the cost we admit: -1 being default no cost)
		end
		if PROBABLEFILTER then
			FILTERMANAGE=ask.FILTERMANAGE.value
			GENERICFILTER=ask.GENERICFILTER.value
		end
    end
end

function AskSelScores() -- selecting worst subscores - Will be default all unless if we check something in this dialog
    local ask = dialog.CreateDialog("Set worst searching DRW "..DRWVersion)
    ask.l1=dialog.AddLabel("Specify which worst subscoretotal(s) to count")
	if FILTERS then
		for i=3,#ScoreParts-1 do -- impossible to select worst filter or total on segments !
			ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][2],false)
		end
	else
		for i=3,#ScoreParts do
			ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][2],false)
		end
	end
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    scrPart={}
    if dialog.Show(ask) > 0 then
		local limit=3
		if FILTERS then limit = #ScoreParts-1 else limit = #ScoreParts end
		for i=3,limit do
			if ask[ScoreParts[i][2]].value then scrPart[#scrPart+1]=ChangedOptions("subscore","Backbone",ScoreParts[i][2]) end
		end
    end
end

function AskDRWOptions()
    local askresult
    local askmutable=HASMUTABLE
    local ask = dialog.CreateDialog(recipename.." tvdl DRW options")
	--local velocity=3 -- normal options default
	local Duration=12
    if askmutable then
        print("Setting default mutate options")
        AfterQstab=true
        AfterFuze=true
        MutSur=true
    end
	repeat
		--ask.l7 = dialog.AddLabel("Time needed with current options: about".. Duration.." hours")
		--ask.l8 = dialog.AddLabel("Reset options wizard, from 1 fast to 5 slow:")
		--ask.reset=dialog.AddCheckbox("Reset options wizard, from 1 fast to 5 slow:",false)
		--ask.velocity = dialog.AddSlider("Reset options:",velocity,1,5,0)
		--ask.l9 = dialog.AddLabel("OR -------- Fine tuning of options:   --------")
		ask.l1 = dialog.AddLabel("Length to rebuild, From can be bigger than To")
		ask.minLen = dialog.AddSlider("From:",minLen,1,maxLenLimit,0)
		--ask.l2 = dialog.AddLabel("Maximum length to rebuild")
		ask.maxLen = dialog.AddSlider("To:",maxLen,1,maxLenLimit,0)
		ask.l3 = dialog.AddLabel("Force next round if gain is more than") -- recalculate worst
		ask.minGain = dialog.AddSlider("MinGain:",minGain,0,500,0)
		ask.fastQstab=dialog.AddCheckbox("Do a fast qStab",fastQstab)
		ask.l4 = dialog.AddLabel("Skip fuze if loss is more")
		ask.l5 = dialog.AddLabel("Threshold used is RBlength*threshold/3")
		ask.maxLoss = dialog.AddSlider("Skip fuze:",maxlossbeforefuze,-5,200,0)
		ask.donotrevisit = dialog.AddCheckbox("Do not things twice",donotrevisit)
		ask.SEL= dialog.AddCheckbox("(Re)select where to work on ",false)
		if HASMUTABLE then
			ask.MUTS = dialog.AddCheckbox("(Re)set Mutate Options",askmutable)
		end
		ask.selSP= dialog.AddCheckbox("(Re)select slots",false)
		ask.worst= dialog.AddCheckbox("(Re)set worst search params",false)
		if nrofbridges > 1 then ask.bridge = dialog.AddCheckbox("Keep sulfide bridges intact",savebridges) end
		ask.struct = dialog.AddCheckbox("Do not change all to loop",struct)
		ask.l6=dialog.AddLabel("Search only for disjunct from previous done")
		ask.disjunct=dialog.AddCheckbox("Disjunct",disjunct)
		ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
		ask.Options = dialog.AddButton("More",2)
		ask.GAB = dialog.AddButton("GAB",3)
		askresult=dialog.Show(ask)
		if askresult > 0 then
			minLen=ChangedOptions("minLen",minLen,ask.minLen.value)
			maxLen=ChangedOptions("maxLen",maxLen,ask.maxLen.value)
			minGain=ChangedOptions("minGain",minGain,ask.minGain.value)
			fastQstab=ChangedOptions("fastQstab",fastQstab,ask.fastQstab.value)
			maxlossbeforefuze=ChangedOptions("maxlossbeforefuze",maxlossbeforefuze,ask.maxLoss.value)
			donotrevisit=ChangedOptions("donotrevisit",donotrevisit,ask.donotrevisit.value)
			disjunct=ChangedOptions("disjunct",disjunct,ask.disjunct.value)
			struct=ChangedOptions("struct",struct,ask.struct.value)
	--[[
			if velocity~=ask.velocity.value then
				velocity=ask.velocity.value
				QuickOptions(velocity)
				Duration= velocity * 4
				if askresult==1 then askresult=4 end -- to force to return to the main menu in case of "OK"
			end --]]
			if nrofbridges > 1 then savebridges=ChangedOptions("savebridges",savebridges,ask.bridge.value) end
			if ask.SEL.value then
				local SelMode={}
				SelMode.askignorefrozen=false
				SelMode.defignorefrozen=true
				SelMode.askignorelocks=false
				SelMode.defignorelocks=true
				SelMode.askligands=false
				SelMode.defligands=false
				WORKON=AskForSelections("Tvdl enhanced DRW "..DRWVersion,SelMode)
				print("Selection is now, reselect if not oke:")
				print(SegmentSetToString(WORKON))
				if askresult==1 then askresult=4 end --to force return to main menu
			end
			if ask.selSP.value then
				AskSubScores()
				if askresult==1 then askresult=4 end
			end
			if ask.worst.value then
				AskSelScores()
				if askresult==1 then askresult=4 end
			end
			-- Do not try to rebuild frozen or locked parts or ligands
			WORKON=SegmentSetMinus(WORKON,FindFrozen())
			WORKON=SegmentSetMinus(WORKON,FindLocked())
			WORKON=SegmentSetMinus(WORKON,FindAAtype("M"))
			NOTWORKON=SegmentInvertSet(WORKON)
			
			if HASMUTABLE and ask.MUTS.value then
				AskMutateOptions()
				askmutable=false
				if askresult==1 then askresult=4 end --to force return to main menu
			end
			if askresult==2 then AskMoreOptions() end
			if askresult==3 then AskGABOptions() end
		end
	until askresult < 2
    return askresult > 0
end
-- Quick fix for failing first rebuild
for i=3,13 do save.Quicksave(i) end -- added 13 BK 11/11/2014


function Cleanup(err)
    print("Restoring CI, initial selection, best result and structures")
    CI(1)
    save.Quickload(PreferredScoreSlot)
    if SAVEDstructs then save.LoadSecondaryStructure() end
    selection.DeselectAll()
    if SAFEselection ~= nil then SetSelection(SAFEselection) end
	
	--CleanupGAB(err)
	print("Restoring CIGAB, best result, filter and structures")
    CIGAB(1)
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- new BK 8/4/2013, always back to user settings
    MovieSteps() -- New 4/11/2014
	save.Quickload(PreferredScoreSlot)
	MovieSteps()
	WhriteNote()  -- New 4/11/2014
	TOTALgain=Score(current, true)-DRWstartscore
	print(">>>>>TOTAL EBOLA GAIN (following preferences)= "..round3(TOTALgain))
	print("From "..round3(DRWstartscore).." to "..round3(Score(current, true)))
	print("Absolute best score = "..round3(bestScore))
	print("Total gain till credited score: "..round3(Score(current, true)-StartEbolaScore))
	print("Absolute best filter = "..round3(bestFScore))
	deletebands()
	
    print(err)
end

--[[
    USAGE
1. 'drw' - need 'minLen' and 'maxLen'; finding worst scores by lengthZ betwen that 2
2. 'fj' - need 'lengthZ'; searching lengthZ then cutting in pieces 2->lengthZ and rebuilds pieces
3. 'all' - need 'minLen' and 'maxLen'; rebuilding ENTIRE prorein (from min to max) like in WalkinRebuild script
4. 'simple' - need 'lengthZ'; find and rebuild worst scoring parts of that lenght
5. 'areas' - need secondary structure set and 'true' on at least one of structure
]]--
----------------- options below VVVV

areas={ --start segment, end segment. use for last line call
--{1,10},
--{20,30},
--{32,35},
}
scrPart={}

--options for (5)"areas" setting
loops=true --rebuild loops alone
sheets=false --rebuild sheets + surrounding loops
helices=true --false --rebuild helices + surrounding loops

doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
shakeCI=0.31 --clash importance while shaking

struct=false --set in all loop (if true work in structure mode)

fastQstab=true --false --if true faster stabilize

reBuild=4 --up to worst parts to look at
reBuildmore=1 --increased by every main cycle
rebuilds=10 --how many rebuilds to try, set at least 10! (because of slots)

rebuildCI=0 --clash importance while rebuild

lengthZ=6 --find worst segments part
minLen=3 --or specify minimum lengthZ
maxLen=5 --and maximim lengthZ

maxLenLimit=segCnt2 -- experimental 11/2/2015

-- New options
maxnrofRuns=1000 -- Set it very high if you want to run forever
Runnr=0
minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
if minGain < 40 then minGain=40 end
--longfirst=false --true -- Reverse the search, long ones first
skipqstab=false
skipfuze=false
ExistingBands=band.GetCount()
bandflip=ExistingBands > 0 -- true if user bands exist
userbandenabled= false

if bandflip and band.IsEnabled(1) then -- enabled bands will always be re-enabled on default !!
	--bandflip=false
	userbandenabled= true
end

maxlossbeforefuze=(segCnt2-segCnt2%4)/4 -- if loss is more no fuze is done
if maxlossbeforefuze < 30 then maxlossbeforefuze=30 end
nrskip=0

DRWVersion="2.5.1 beta BK"
--2.5.1. added cut worst

-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++
-- MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++ MAIN PROGRAM ++++

firstDRWcall=true
DRWstartscore=0
HoursResetOptions= 24 -- number of hours after which to reset options (out of context options)= Auto Pilot

function DRW()
	local scoreNow= Score()
	local formerScore=scoreNow
	local StarTime= os.time() -- initialized
	DRWstartscore=scoreNow
	gaingen=round3(DRWstartscore) -- list of gain each generation, for jeff101
	
    if firstDRWcall then
        printOptions("Tvdl enhanced DRW "..DRWVersion)
		print("###################################")
		print("OK you can go away ! No more dialog !")
        firstDRWcall=false
		if GENERICFILTER then
			print("Always disabling filter unless for scoring")	
			MutClass(structure, false)
			MutClass(band, true) -- for unideal loop bug
			MutClass(current, true)
			MutClass(recentbest, true) -- otherwise, it remembers cut solutions
			MutClass(save, true) -- better to save with full score
			FIRSTGENERICFILTER=true
		else
			print("No generic filter disabling")
			--MutClass(structure, true)
			--MutClass(band, true)
			--MutClass(current, true)
			--MutClass(recentbest, true) -- otherwise, it remembers cut solutions
			--MutClass(save, true) -- better to save with full score
		end
	else
		if GENERICFILTER then
			print("Always disabling filter unless for scoring")	
			MutClass(structure, false)
			MutClass(band, true)
			MutClass(current, true)
			MutClass(recentbest, true) -- otherwise, it remembers cut solutions
			MutClass(save, true) -- better to save with full score
			FIRSTGENERICFILTER=true
		elseif FIRSTGENERICFILTER then -- case disabling this on the fly (experimental, not tested)
			print("No generic filter disabling")
			MutClass(structure, true)
			MutClass(band, true)
			MutClass(current, true)
			MutClass(recentbest, true) -- otherwise, it remembers cut solutions
			MutClass(save, true) -- better to save with full score
		end
    end
    InitWORKONbool()
    if nrskip > 0 then -- if skipping since start, we do a first round with this rebuild number
        local sreBuild=reBuild
        reBuild=nrskip
        Runnr=0
         print("Ebola Init cycle")
        DRcall("drw")
        reBuild=sreBuild
    end

    for nrofRuns=1,maxnrofRuns do --uncomment method/s you want to use It STARTS HERE>>>>>>>>>>
		if not SKETCHBOOK then
			undo.SetUndo(false) -- reset after each loop
		end
         Runnr=nrofRuns -- global to be able to use it in log
		 
		 print("###########################")
         print("Main Ebola cycle nr ",nrofRuns) -- TO DO: change settings each round
		 if nrofRuns < 3 then DRcall("drw")
		 elseif nrofRuns < 5 then DRcall("areas")
		 elseif nrofRuns < 7 then DRcall("fj")
		 elseif nrofRuns < 8 then DRcall("simple")
		 elseif nrofRuns == 8 then DRcall("all")
		 elseif nrofRuns > 8 then DRcall("drw")
		 else DRcall("simple")
		 end

-- DRcall("areas")
    -- DRcall("drw")
-- DRcall("fj")
-- DRcall("all")
-- DRcall("simple")
		undo.SetUndo(defUndo)
		save.Quickload(PreferredScoreSlot)
        ChkDoneList()
        reBuild=reBuild+reBuildmore
		WhriteNote()  -- 
		FILTERS=FindActiveFilter() -- just in case we would discover a filter on the fly
		if HoursRun(StartTime) > HoursResetOptions then -- changing options every day for very long run
			StarTime= os.time() -- reinitialized
			ContextualOptions()
		end
    end
end

-- Change defaults if the startscore is negative
if StartEbolaScore < 4000 then
    local adjust=true
    if HASDENSITY then
		if FILTERMANAGE  then FiltersOff() end
        local oscore=GetSubscore("density")
        if StartEbolaScore-oscore*(DENSITYWEIGHT+1) > 4000 then
            adjust=false
            print("ED puzzle, score high enough not counting ED")
            print("so no auto blocking of qstab and fuze")
        end
		if FILTERMANAGE  then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
    end
    if adjust then
        print("Score < 4000, adjusting defaults")
        print("Now skipping Fuzes, replacing qStab")
        print("Can be changed in More options")
        skipfuze=true
        skipqstab=true
    end
end

SAFEselection=FindSelected()


--eDRW END ############################################################

--GABcut START ########################################################
--[[
GAB - Genetic Algorythm on Bands
by Rav3n_pl
based on CartoonVillan and Crashguard303 scripts
Lua V2

Definitions:
band: randomised: start segment, end segment, length, strength
critter: set of bands
herd: set of critters

1.
- randomize needed bands 
- randomly assignig them to criters

2.
- score each critter

3.
- keep critters scoring above score
- breed best critters
- breed bastards (best one + random one)
- forget about rest of critter
- randomize new critters to fill herd

VERSIONS:
2.0.5
2.0.5 Filter => Filter management added Bruno Kestemont 10/10/2013
16/04/2014: only added more score info in the log
3.0 : fuze using cuts 28/05/2014 Bruno Kestemont
3.1: cut bug fixed on deletecut 02/06/2014
3.2: using creditebest
3.3: creditbest bug fixed 02/06/2014 (do not use creditebest)
3.3.1: added Notes management and quicksaves for big gains (for archives when undo's) 4/11/2014
3.3.2: replaced shake by QuickShake  8/11/2014
]]--

recipename2="Rav3n_pl GAB 3.3.1 filter Cuts BK" -- + added use ligands and BIS

-- options:
energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
pullCI = 0.9 --Clash Importance during pull
maxCI = 1 --maximum CIGAB used by script
--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
fuzeThresh = 1 -- run fuze if we are close to best score (negative=new best score)
qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
if HASLIGAND then
	useLigand = true --use ligand if true
	AlwUseLigand= false -- GAB always band to ligand if true
else
	useLigand = false --use ligand if true
	AlwUseLigand= false
end
onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
mutateOnce = false --if true use mutate(1) instead of shake in qstab
mutateOnceCI = 0.21 --mutate on what clashing importance
mutateAlwas = false --if true use mutate(1) instead of all shakes
freqbis = 0.1 -- frequency of Band In Space
--cut=structure.InsertCut -- 28/05/2014
allowcut=false -- cuts in GAB and fuze using cuts
--uncut=structure.DeleteCut -- 28/05/2014
--SLOTS:
--[[
3	 is best
4  used in recipe
5  used in recipe
30-49 used to record each big steps for movie at the end

]]--
SlotStepStart=30 -- New 4/11/2014
SlotStepMax=49
SlotStep=SlotStepStart

herd= --herd options
{ 
breedBest = 5, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
keepBest = 3, --save up to 3 best scoring critters, rest are forgotten
breedBastards = 8, --number of best will have one random bastard
firstGen = 10, -- number of herds on first generation
newRandom = 4, --adding new random ones each generation
maxGen= 3, --maximum generations 
shuffle = true, --set true to run critters in random order
renew=2, --create totally fresh herd after that many gens w/o improvement
maxBadGen=2, -- Stop the script after X generations that dont increase the score
}
critter= --critter options
{
minBands=2, --minimum bands
maxBands=7, --maximum bands
keepScore = 0 , --survive to next gen only if score higher than
breedScore= -20, --will breed kids only if score higher. Basttards always breed
maxLoss=30, --maximum loss by critter. set 0 to disable
}

bands= --bands options
{
minStr=0.3, --minimum band str
maxStr=1.1, --maximum band str
minChng = 3, -- minimum change of band length, so the range will be [3;6.1] or [-6.9;-3]
maxUpBIS = 12.1, -- maximum band lenght
minUpBIS = 0.1, -- debugging case=0
maxUp = 6.1, -- maximum length change up (push)
maxDn = 6.9, -- maximum length change down (pull)
minSkip = 5, --minimum segment distance
minDist = 4, --minimum spatial distance
minLen = 2, --minimum length of created band
}

DoNotUse={--just comment lines below or add more areas to avoid
--{segCnt,segCnt}, --ligand cant be used
--{120,134},
--{1,10},
}
AlwaysUse={ --areas should be always used
--{segCnt,segCnt},--ligand need to be at one end
--{308,311}, --loopy
--{272,319}, --loopy
}
UseSegments= --use ONLY this segments for random select of bands
{
--2,3,4,5
}

-- bands by secondary structure
use=
{
Sheet=true, --set false to not band sheets
Helix=true, --set false to not band helices
Loop=true, --set false to not band loops
}
checkBoth=false --check both ends to above, if false only one end need to be true

--end of options

segCntGAB=segCnt  -- DUPLICATE DRW

	math.randomseed(os.clock()) -- 28/05/2014
	math.random() -- 28/05/2014
--[[
if useLigand==false then
    while structure.GetSecondaryStructure(segCntGAB)=="M" do segCntGAB=segCntGAB-1 end
end ]]--
--p=print



function cut(seg) -- 18/2/2016
	if (allowcut or CUTWORST) and not freeze.IsFrozen(seg) then
		if seg==segCnt then seg=segCnt-1 end
		structure.InsertCut(seg)
	end -- else nothing !
end

function uncut(seg) -- 18/2/2016
	if (allowcut or CUTWORST) and not freeze.IsFrozen(seg) then
		for i=1, segCnt do
			structure.DeleteCut(i)
		end
	end
end

function CIGAB(c)
if c>maxCI then c=maxCI end
behavior.SetClashImportance(c)
end
function round(x)--cut all afer 3-rd place
    return x-x%0.001
end

function ScoreGAB()--return score, exploration too
	if FILTERMANAGE then FiltersOn() end -- always disable before scoring
    if energy==true then
        return current.GetEnergyScore()
    else
        return current.GetScore()
    end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
end 
--local seed=recipe.GetRandomSeed() --NOT WORKING on windowz!!!
--calculate REALLY good seed from current score
seed=os.time()
seed=1/seed
while seed<10000000 do seed=seed*10 end
seed=seed-seed%1
--int("Seed is: "..seed)
math.randomseed(seed)
format=string.format

--START Archive in Notes, -- New 4/11/2014; 3/12/2015 added a flag for already used recipe, 24/4/216 added option archives

FlagRecipeUsed=false
function recipeUsed(lastnote) -- identifies if the recipe has already been used
	local lastnote=lastnote or "abcdefgh"
	if lastnote:find(recipename)~=nil then
		FlagRecipeUsed=true
		print(recipename .. " already used before")
	end
end

function SelectNote(recipename)
	store={}
	store.label=recipename or "" -- edit here the recipe name
	store.note_number=segCnt
	for seg=segCnt,1,-1 do
	  if structure.GetNote(seg)~="" then recipeUsed(structure.GetNote(seg)) break end -- New 3/12/2015
	  store.note_number=seg
	end
	dr_string = ""
	print(string.format("Recording results in Note for segment %i",store.note_number))
	print(string.format("Recording changed options in Note for segment %i",store.note_number+1))
	store.starting_score=StartEbolaScore
	--structure.SetNote(store.note_number,string.format("(%s) %.3f + FSP",user.GetPlayerName(),store.starting_score))
end

SelectNote(recipename)

function WhriteNote() -- all inits are in SelectNote function
	structure.SetNote(store.note_number,string.format("(%s) %.3f + %s(%s) %s %.3f",
		user.GetPlayerName(),store.starting_score,store.label,dr_string,ChangedOptionsTxt,Score()))
end

--END Archive in Notes

--START quick save algorithm

function QuickShake()
--[[------------------------------------------------------------------------------------------------
-- Algorithm for faster shake

REFERENCES
1. N/A

Copyright (C) 2014 Seagat2011 <http://fold.it/port/user/1992490>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

$Id$

------------------------------------------------------------------------------------------------]]--

--[[

v1
- Inception

1.2
- Loops until nogain 

]]--

local idx  = 1
local idx2 = structure.GetCount ()
local hash = {}
local cs   = Score ()

--print ( 'Quick Shake Algorithm v1.2 SG2011 - Current Score: '..cs )

local function New ( obj )
  return obj -- pass-new-obj-by-value
end
if FILTERMANAGE  then FiltersOn() end
local _gses = New ( current.GetSegmentEnergySubscore )
if FILTERMANAGE  then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end
local function SmartShake ( iters ) 
  local gain = true
  while (gain) do
    gain = false
    for i=idx,idx2 do
      local ci = _gses ( i,'clashing' ) 
      if ci <  _gses ( i,'hiding'   ) and
         ci <  _gses ( i,'packing'  ) and
         ci <  _gses ( i,'ideality' ) and
         ci <  _gses ( i,'sidechain') and
         ci <  _gses ( i,'bonding'  ) and
         ci <  _gses ( i,'other'    ) and
         ci <  _gses ( i,'reference') then
        selection.Select ( i )
      end -- test ci --
    end -- loop --
    if selection.GetCount () then
      local css = Score ()
      structure.ShakeSidechainsSelected ( iters )
      selection.DeselectAll () 
      if Score () > css then 
        gain = true 
      end -- test --
    end -- test --
  end -- loopf --
end

structure.SmartShake = SmartShake

structure.SmartShake ( 1 )

--print ( 'Done.' )
end

--END quick save algorithm

function WiggleGAB(how, iters, minppi)
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=defminppi end
    if FILTERMANAGE then FiltersOff() end
    if iters>0 then
        iters=iters-1
        sp=ScoreGAB() -- filter will be disabled then  returned to user settings here
        if how == "s" then 
				if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- new BK 8/4/2013, always back to user settings
                if mutateAlwas==true then structure.MutateSidechainsSelected(defiter/2) 
                                    --else structure.ShakeSidechainsSelected(1) end
									else QuickShake() end
            elseif how == "wb" then structure.WiggleAll(defiter, true,false)
            elseif how == "ws" then structure.WiggleAll(defiter, false,true)
            elseif how == "wa" then structure.WiggleAll(defiter)
        end
        local ep = ScoreGAB()
        local ig=ep-sp
        if how~="s" then
            if ig > minppi then return WiggleGAB(how, iters, minppi) end --tail call
        end
    end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- new BK 10/10/2013, always back to user settings
end

wiggleAllGAB=structure.WiggleAll -- 28/05/2014 No filter management

function SaveBestGAB()
	local sg=ScoreGAB()
    local g=sg-bestScoreGAB
	local m=PreferedScore-sg
	
	SaveBest() -- Test 12/2/2014, only to keep track of best scores and to be able to skip this generation
	
	if TOOMUCHFILTERLOSS then
		print("Rejecting this critter solution (filter cost too high)")
	else
		if g>0 then
			if g>0.01 then
				if m>= 0 then
					print(" Recovering "..round(g).." pts, (remaining "..round(m).." pts)")
				else
					m=-m
					print(" Recovering "..round(g).." pts, (total extra "..round(m).." pts). Score: "..round(sg).." pts)")
				end
			end
			bestScoreGAB=sg
			save.Quicksave(BestGABslot)
		end
	end
end

function SaveRBGAB()
	if ScoreGAB()>bestScoreGAB then
		save.Quicksave(GABrbSlot)
		recentbest.Restore() -- OK only if recentbest saved after deleting cuts
		SaveBestGAB()
		save.Quickload(GABrbSlot)
	end
end

function QstabGAB()
    selection.SelectAll()
    CIGAB(0.1)
    if mutateOnce==true then
		CIGAB(mutateOnceCI)
        structure.MutateSidechainsSelected((defiter+1)/3)
    else
        WiggleGAB("s",1)
    end
    if fastQstab==false then 
        CIGAB(0.4)
        WiggleGAB("wa",1)
        CIGAB(1)
        WiggleGAB("s",1)
    end
    CIGAB(1)
    WiggleGAB()
end

function FuzeCuts(ci1) -- 28/05/2014 by pauldunn NB: no filter management here . 02/06/2014 recentbest bug fixed
	  local seg=math.random(segCnt)
	  cut(seg)
	  CIGAB(1)
	  wiggleAllGAB(15,true,true)
	  CIGAB(ci1) --ci(0.01)
	  wiggleAllGAB(1,true,true)
	  CIGAB(1)
	  wiggleAllGAB(25,true,true)  
	  uncut(seg)
	  recentbest.Save() -- NEW 02/06/2014 important to avoid recentbest in cut bug
	  wiggleAllGAB(25,true,true)
	  CIGAB(ci1) --ci(0.01)
	  wiggleAllGAB(2,true,true)
	  CIGAB(1)
	  wiggleAllGAB(25,true,true)	  
end
function FuzeEndGAB()
    CIGAB(1)
    WiggleGAB("wa",1)
    WiggleGAB("s",1)
    WiggleGAB()
    srb()
end
function Fuse1GAB(ci1,ci2)
    CIGAB(ci1)
    WiggleGAB("s",1)
    CIGAB(ci2)
    WiggleGAB("wa",1)
end
function Fuse2GAB(ci1,ci2)
    CIGAB(ci1)
    WiggleGAB("wa",1)
    CIGAB(1)
    WiggleGAB("wa",1)
    CIGAB(ci2)
    WiggleGAB("wa",1)
end
function srb()
    recentbest.Restore()  -- IMPORTANT: recentbest must be saved after deleting cut
    SaveBestGAB()
end
function scb()
    recentbest.Restore() -- IMPORTANT: recentbest must be saved after deleting cut
    SaveBestGAB()
end

function FuzeWithCuts()
    print("Fuzing with cuts...")
    local scr=ScoreGAB()
    selection.SelectAll()
    recentbest.Save()
    Fuse1GAB(0.3,0.6) FuzeEndGAB()
	if SKETCHBOOK then return end -- the remaining part takes too much moves for a decreasing return
	FuzeCuts(0.01) scb() -- NEW 28/05/2014, 02/06/2014 -- HERE WITH CUTS
    Fuse2GAB(0.3,1) srb()
    Fuse1GAB(0.05,1) srb()
    Fuse2GAB(0.7,0.5) FuzeEndGAB()
	FuzeCuts(0.1) scb() -- NEW 28/05/2014, 02/06/2014 -- HERE WITH CUTS
    Fuse1GAB(0.07,1)
    srb()
end

function randomGAB(n1,n2) --random function returns int or float depends on input vars
    if n2==nil and n1==nil then
        return math.random() --float 0-1
    else
        if n2==nil then
            if n1%1==0 then
                return math.random(n1) --integer 1-n1
            else
                return math.random()*n1 --float 0-n1
            end
        else
            if n1%1==0 and n2%1==0 then
                return math.random(n1,n2) --integer between 
            else
                return math.random()*(n2-n1)+n1 --float between, including 0
				--return math.random(n1,n2) --float between BK 17/02/2015, this is also correct
            end
        end
    end
end

function FillHerd() --fill up herd (mixed BIS and BBS)
    local n=#critters
    if n>0 then --fill up
        n=herd.newRandom
    else --fresh herd
		if herd.maxGen~=1
			and herd.firstGen<herd.keepBest then
			n=herd.breedBest + herd.keepBest + herd.breedBastards
		else
			n=herd.firstGen
		end
        
    end
    print("Randomizing "..n.." new critters...")
    for i=1,n do
        AddCritter()
    end
end

function AddCritter() --create new random critter (NEW also for BIS), 15/2/2016
    local c={}
    critterID=critterID+1
    c.no=critterID
    c.name=c.no..'-rnd'
    c.bands={}
    local r=randomGAB(critter.minBands, critter.maxBands)
	local probabis= randomGAB(0.0, 1.0)
    for i=1,r do
		if probabis<= freqbis then
			c.bands[#c.bands+1]=AddBandIS()
		else
			c.bands[#c.bands+1]=AddBand()
		end
    end
    critters[#critters+1]=c
    --print(c.name.." bands: "..#c.bands)
end

function AddBand() --create one random band // ONLY Bands between segments here !
    local cnt=0
    local b={}
    while true do --try till die
        cnt=cnt+1
        local s1=randomGAB(segCntGAB) --integer 1-segCnt
        if onlyMutable==true or #UseSegments>0 then
            s1=UseSegments[randomGAB(#UseSegments)] --integer 1-UseSegments nb => s1= one of the use segments
        end
        local s2=randomGAB(segCntGAB) --integer 1-segCnt
		while s1==s2 do s2=randomGAB(segCntGAB) end -- to avoid band to itself New 22/12/2014
        if s1>s2 then s1,s2=s2,s1 end --swap
        if #UseSegments>0 or CanBeUsed(s1,s2) then
            local str=randomGAB(bands.minStr,bands.maxStr)
            local increment=-1 -- was 0 but I prefer to avoid 0 in case of bug bellow
            while true do --randomize correct distance
                increment=randomGAB(-bands.maxDn,bands.maxUp)
                if increment<-bands.minChng or increment>bands.minChng then break end -- we stop when it's good: never 0, never [-3;3] indeed
            end
            b={s1,s2,str,increment} -- increment is the increment (negative or positive) relative to the segment distance
            break
        end
        
        if cnt>100 then
            print("Sorry! Cant create band!")
            --BreakScript() --there is no such function, so it crashes script
			break
        end
    end
    return b
end

function CanBeUsed(sg1,sg2) --checking end of bands // only Bands between segments here !
    function ssCheck(ss)
        local good=false
            if use.Sheet and ss=="E" then good=true end
            if use.Helix and ss=="H" then good=true end
            if use.Loop and ss=="L"  then good=true end
        return good
    end
    function AreGood(s1,s2) --check that s1 and s2 can be used
        local ok=true
		if s2==s1 then ok=false end -- to avoid a possible bug
        if s2-s1<bands.minSkip then ok=false end
        if ok==true and structure.GetDistance(s1,s2)<bands.minDist then ok=false end
        return ok 
    end
    
    local ok=AreGood(sg1,sg2)
    if ok==true and #DoNotUse>0 then --none of 2 can be in that area
        for i=1, #DoNotUse do
            local r=DoNotUse[i]
            for x=r[1],r[2] do
                if x==sg1 or x==sg2 then
                    ok=false
                    break
                end
            end
            if ok==false then break end
        end
    end
    if ok==false then 
        return false --if false can`t be used
    else
        ok=false
        if #AlwaysUse>0 then --at least one have to be there
            for i=1, #AlwaysUse do
                local r=AlwaysUse[i]
                for x=r[1],r[2] do
                    if x==sg1 or x==sg2 then
                        ok=true
                        break
                    end
                end
                if ok==true then break end
            end
        else
            ok=true
        end
    end 
    
    if ok==true then --check structure
        ok=false
        local ss1=structure.GetSecondaryStructure(sg1)
        local ss2=structure.GetSecondaryStructure(sg2)
        if checkBoth then
            if ssCheck(ss1) and ssCheck(ss2) then ok=true end
        else
            if ssCheck(ss1) or ssCheck(ss2) then ok=true end
        end
    end
    return ok
end

function AddBandIS() --create one random band in space // ONLY Bands to center segment here !
    local cnt=0
    local b={}
    while true do --try till die
        cnt=cnt+1
        local s1=randomGAB(segCntGAB)
        if onlyMutable==true or #UseSegments>0 then
            s1=UseSegments[randomGAB(#UseSegments)]
        end
        if #UseSegments>0 or CanBeUsedBIS(s1) then -- adapted for ebola
            local str=randomGAB(bands.minStr,bands.maxStr)
            local length=randomGAB(bands.minUpBIS,bands.maxUpBIS) --debugged BK 15/2/2015, length cannot be 0
            local theta = math.acos(math.random())
            local phi = 2 * math.pi * math.random()
            local segmentXAxis=0
            local segmentYAxis=0
            while true do --all 3 must be different
                segmentXAxis = randomGAB(segCntGAB)
                segmentYAxis = randomGAB(segCntGAB)
                if segmentXAxis~=s1 and segmentYAxis~=s1 and segmentXAxis~=segmentYAxis then break end
            end
            --{segmentOrigin, segmentXAxis, segmentYAxis, rho, theta, phi, str}
            b={s1, segmentXAxis, segmentYAxis, length, theta, phi, str}
            break
        end
        
        if cnt>100 then
            p("Sorry! Cant create band in space")
            --BreakScript() --there is no such function, so it crashes script
			break
        end
    end
    return b
end

function CanBeUsedBIS(sg1) --checking end of band for BIS
    function ssCheck(ss)
        local good=false
            if use.Sheet and ss=="E" then good=true end
            if use.Helix and ss=="H" then good=true end
            if use.Loop and ss=="L"  then good=true end
        return good
    end
    local ok=true
    if #DoNotUse>0 then --none of 2 can be in that area
        for i=1, #DoNotUse do
            local r=DoNotUse[i]
            for x=r[1],r[2] do
                if x==sg1 then
                    ok=false
                    break
                end
            end
            if ok==false then break end
        end
    end
    if ok==false then 
        return false --if false can`t be used
    else
        ok=false
        if #AlwaysUse>0 then --at least one have to be there
            for i=1, #AlwaysUse do
                local r=AlwaysUse[i]
                for x=r[1],r[2] do
                    if x==sg1 then
                        ok=true
                        break
                    end
                end
                if ok==true then break end
            end
        else
            ok=true
        end
    end 
    
    if ok==true then --check structure
        ok=false
        if ssCheck(structure.GetSecondaryStructure(sg1)) then ok=true end
    end
    return ok
end

function deletebands() --leave user bands intact
    nbands=band.GetCount()
    if nbands>userbands then
        for i=nbands,userbands+1,-1 do -- count down from nbands to userbands+1
            band.Delete(i)
        end -- for i
    end -- if nbands
end -- function

function ScoreHerd() --score all critters from herd (make bands, act, delete bands)
    save.Quickload(BestGABslot)
    print("Scoring "..#critters.." critters...")
    save.Quicksave(GABherSlot)
    local herdScore=ScoreGAB()
    for i=1,#critters do
        deletebands()
        local crt=critters[i] --critter
        local s=ScoreGAB() --start score
        local bnds=crt.bands
		local crBIS= false -- false = critter of BBS; true = critter of BIS
        for b=1,#bnds do
			local DEBUG=false
            local bnd=bnds[b]
			if bnd[6] ~= nil then crBIS=true else crBIS=false end -- we have only BIS
			if DEBUG then if crBIS then print("BIS nb"..b.." / "..#bnds) else print("BBS nb"..b.." / "..#bnds) end end
			if bnd[1] ~= bnd[2] or crBIS then --  debugging, no band to itself
				local a1=5
				local a2=5
				if bnd[1]== segCnt then a1=6 end
				if bnd[2]== segCnt then a2=6 end -- changed a1 to a2 21/12/2014
				if structure.GetAminoAcid(bnd[1])=='g' then a1=0 end
				if structure.GetAminoAcid(bnd[2])=='g' then a2=0   end
				if crBIS then --b={segmentOrigin, segmentXAxis, segmentYAxis, rho=length, theta, phi, str}
					if DEBUG then print("BIS: seg="..bnd[1].." x= "..bnd[2].." y= "..bnd[3].." rho/length= "
													..bnd[4].." theta= "..bnd[5].." phi= "..bnd[6].." atom= "..a1.." Str= "..bnd[7]) end
					band.Add(bnd[1],bnd[2],bnd[3],bnd[4],bnd[5],bnd[6],a1) -- a1= atom, strength is not in list
					local bc=band.GetCount()
					band.SetStrength(bc,bnd[7])
				else --BBS: b={s1,s2,str,increment} -- increment is the increment (negative or positive) relative to the segment distance
					if not structure.IsHydrophobic(bnd[1]) and bnd[4]<0 then a1=0 end -- only hiding hydrophobics
					if not structure.IsHydrophobic(bnd[2]) and bnd[4]<0 then a2=0 end
					if structure.IsHydrophobic(bnd[1]) and bnd[4]>0 then a1=0 end -- don't push hydropobics to water
					if structure.IsHydrophobic(bnd[2]) and bnd[4]>0 then a2=0 end
					if DEBUG then print("Band: "..bnd[1].."-"..bnd[2].." a1: "..a1.." a2: "..a2) end
					if math.abs(bnd[1] - bnd[2]) < 2 then break end -- fixed band to adjascent segment gives a bug
					if DEBUG then print("Band: "..bnd[1].."-"..bnd[2].." a1: "..a1.." a2: "..a2) end
					band.AddBetweenSegments(bnd[1],bnd[2],a1,a2)
					local bc=band.GetCount()
					band.SetStrength(bc,bnd[3])
					local length=structure.GetDistance(bnd[1],bnd[2])+bnd[4]
					if length<bands.minLen then length=bands.minLen end
					band.SetGoalLength(bc,length)
					if DEBUG then print("Band: "..bnd[1].."-"..bnd[2].." a1: "..a1.." a2: "..a2.." str: "..round3(bnd[3]).." length= "..round3(length)) end
				end
			end
        end
		local bandDONE=" BBS"
		if crBIS then bandDONE= " BIS" end
		AddBand2UserBands() -- NEW 6/1/2016 adding bands to end userbands (for sym)
        selection.SelectAll()
        CIGAB(pullCI)
        recentbest.Save()
		local seg=math.random(segCnt) -- new 28/05/2014
		cut(seg) -- new 28/05/2014
        WiggleGAB("wb",1)
		uncut(seg)-- new 28/05/2014 PROBLEM here, recentbest includes cuts
		recentbest.Save() -- NEW 02/06/2014 to avoid recent best in cuts
		
        deletebands()
        CIGAB(1)
        if math.abs(s-ScoreGAB()) > qstabThresh then
            QstabGAB()
        else
            WiggleGAB()
        end
		--print("Critter "..crt.name)
		TOOMUCHFILTERLOSS=false -- reinitialized
        if ScoreGAB()-bestScoreGAB>fuzeThresh and not skipfuze then -- this will also check TOOMUCHFILTERLOSS
            SaveRBGAB()
            FuzeWithCuts() -- new 02/06/2014
        else
            SaveRBGAB()
        end
        
        crt.score=ScoreGAB()-s
        --print("Critter "..crt.name.." : "..round(crt.score))
        if critter.maxLoss>0 and not TOOMUCHFILTERLOSS then -- on critter level
            if ScoreGAB()>herdScore-critter.maxLoss then -- we accept to loose a bit more on each herd
                save.Quicksave(GABherSlot)
                herdScore=ScoreGAB()
            else
                save.Quickload(GABherSlot) -- we start again from best herd score
            end
        else
            save.Quickload(BestGABslot) -- we start again from best critter score
        end
    end
    save.Quickload(BestGABslot)
    if band.GetCount()>0 then --clean bands from best solution (if any)
        deletebands()
        save.Quicksave(BestGABslot)
    end
end
function BreedCritters(mom,dad,t) --breed 2 critters. bands are taken randomly
    local kid={}
    critterID=critterID+1
    kid.no=critterID
    kid.name=kid.no.."-"..t..mom.no..'/'..dad.no
    kid.bands={}
    local mb=#mom.bands
    local db=#dad.bands
    if mb>db then mb,db=db,mb end --kid have bands count between mom and dad bands
    local bn=randomGAB(mb,db)
    for i=1,bn,2 do
        kid.bands[#kid.bands+1]=mom.bands[randomGAB(#mom.bands)]
        kid.bands[#kid.bands+1]=dad.bands[randomGAB(#dad.bands)]
    end
    --p(kid.name.." bands: "..#kid.bands)
    return kid
end
function KeepGood() --copy best scoring critters form last gen if score above
    local newHerd={}
    for i=1,herd.keepBest do
        if critters[i].score>critter.keepScore and (math.abs(critters[i].score)>0.1 or critters[i].score>0) then
            newHerd[#newHerd+1]=critters[i]
        end
    end
    return newHerd
end
function SortCritters() --bubble sort
    for i=1,#critters do
        for j=i+1,#critters do
            if critters[i].score<critters[j].score then
                critters[i],critters[j]=critters[j],critters[i] --love lua :)
            end
        end
    end
end
function BreedHerd()
    print("Breeding "..herd.breedBest.." kids and "..herd.breedBastards.." bastards")
    SortCritters()
    newHerd=KeepGood()
    for i=1, herd.breedBest do
        local mom=critters[i]
        if mom.score>critter.breedScore or i<2 then --breed only good ones, 1st is always breed anyway
            for j=i+1, herd.breedBest do
                local dad=critters[j]
                newHerd[#newHerd+1]=BreedCritters(mom,dad,"kid-")
                newHerd[#newHerd+1]=BreedCritters(dad,mom,"kid-")
            end
        end
    end

    for i=1, herd.breedBastards do --they will always appear ;]
        local mom=critters[i]
        local j=randomGAB(herd.breedBastards+1,#critters)
        local dad=critters[j]
        newHerd[#newHerd+1]=BreedCritters(mom,dad,"bas-")
        newHerd[#newHerd+1]=BreedCritters(dad,mom,"bas-")
    end
    critters=newHerd
    FillHerd()
end
function ShuffleHerd()
    if herd.shuffle==true then 
        for i=1,#critters do
            local r=randomGAB(#critters)
            if r~=i then
                critters[i],critters[r]=critters[r],critters[i]
            end
        end
    end
end

-- ReMix section
function ReMix(ss,se,nrresults)
    ClearScores() --reset score tables
    local Foundone=false
    if ss>se then ss,se=se,ss end --switch if needed
    selection.DeselectAll()
    selection.SelectRange(ss,se)
    local nfound=structure.RemixSelected(StartRemixSlot,nrresults)
    print("Nr of remix found "..nfound)
    for i=0,nfound-1 do
        save.Quickload(StartRemixSlot+i)
        if not BridgesBroken()
        then
			--print("Remix "..i)
            Foundone=true
            Bridgesave()
            if doSpecial==true then
                SelectAround(ss,se,9)
                Wiggle("s",1,nil,true)
                Wiggle("ws",2,nil,true)
                selection.DeselectAll()
                selection.SelectRange(ss,se)
                Wiggle("wb",4,nil,true)
                SelectAround(ss,se,9)
            elseif doShake==true then
                CI(shakeCI)
                Wiggle("s",1,nil,true)
                CI(1)
            end
            Bridgerestore()
            if AfterRB then
                doMutate()
            end
            SaveScores(ss,se,i) -- if any slotted subscore had improved, save it, including savebest
        end
    end
    if Foundone==false then
        print("No valid Remix found on this section")
    end
    CI(1)
    return Foundone
end
-- end remix section

function GAB()
	print()
	print(recipename2)
	print("Starting GAB at "..round(ScoreGAB()).." Goal= "..round(PreferedScore).." Abs. best= "..round(bestScore))
	UseSegments={} -- new to be reinitialized here in ebola each round !! 17/2/2015
    if onlyMutable==true then
        for i=1,segCntGAB do
			if structure.IsMutable(i) then
				UseSegments[#UseSegments+1]=i
			end
		end
    end
	if #AlwaysUse>0 then
		listused=""
		for i=1,#AlwaysUse do
			local ss=AlwaysUse[i][1]
			local se=AlwaysUse[i][2]
			if ss>se then ss,se=se,ss end
			for j=ss,se do
				UseSegments[#UseSegments+1]=j
			end
			listused=listused..ss.."-"..se.." "
		end
		print("Always use:")
		if ENOUGHFORGAB2 then
			PrintAreas()
		elseif ENOUGHFORGAB then
			print(listused)
		end
		AlwaysUse={} --added to list, no need to check later
	else
		print("Full random bands")
	end
    bestScoreGAB=ScoreGAB() -- renamed for ebola
    critterID=0
    gen=0
    ss=ScoreGAB()
    save.Quicksave(BestGABslot)
    --recentbest.Save()  -- WARNING !! TO BE DELETED ?
    
    critters={}
    FillHerd()
    badGen=0
    while true do --this is (almost) endless script ;]
        genScore=ScoreGAB()
		gen=gen+1 -- will stop when max gen or max bad gen is achieved
        --p()
        print("Generation: "..gen)
		if badGen>=herd.renew then  -- will not occur the first generation
            print("Creating fresh random herd...")
            critters={}
            FillHerd()
            badGen=0
        elseif gen>1 then -- will not occur the first generation
            BreedHerd()
        end

        ShuffleHerd()
        ScoreHerd()
        save.Quickload(BestGABslot)
        if gen==herd.maxGen then break end --end of loop
        local genScore2=ScoreGAB()
		if genScore+0.001>=genScore2 then
			badGen=badGen+1
			if badGen==herd.maxBadGen then break end
		else
			badGen=0 -- will continue indefinitely when gains
		end
		print("Generation ".. gen.." found "..round3(genScore2-genScore).." pts. Score "..round3(genScore2))
    end
    print("Final GAB score: "..round(ScoreGAB()).." GAB improvement: "..round(ScoreGAB()-ss))
	if ScoreGAB()<=PreferedScore+0.001 then
		print ("It's not enough :( Loading preferred solution scoring ".. round(PreferedScore))
	else
		print("OK ! Evaluating GAB gains:")
	end
end

preciseBands=true
function LaunchGab(alwaysFrom,alwaysTo)
	if not SkipGAB then
		if struct==false and SAVEDstructs then save.LoadSecondaryStructure() end
		recentbest.Save() -- just for security because there are restores in GAB // but TO DO verify cuts
		local alwaysFrom=alwaysFrom or 0
		local alwaysTo=alwaysTo or 0
		if preciseBands then
			if ENOUGHFORGAB and (alwaysFrom*alwaysTo >0) then
				--print("Score is sufficient for starting precise GAB")
				AlwaysUse={}
				table.insert(AlwaysUse, {alwaysFrom, alwaysTo})
			end
			if HASLIGAND then
				if AlwUseLigand then
					table.insert(AlwaysUse, {segCnt, segCnt}) -- segCnt is the ligand if ligands
				end
			end					
			if ENOUGHFORGAB2 then
				--print("Score is sufficient for starting whole GAB")
				AlwaysUse=areas
			end
		end
		GAB()
		recentbest.Restore() -- TO DO :  This is dangerous with cuts
	end
end

function onlyGABoptions()
		GABfilter=20
		LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
		LostFpgain= 9 -- default filter lost allowed per 10 pt score gain
		disjunct=false
		donotrevisit=true
		IDEALCHECK=false
		if HASMUTABLE then
			AfterRB=false -- default no mutate used
			InQstab=false
			AfterQstab=true
			BeFuze=false
			AfterFuze=false
			MutateCI=0.9
			MutSphere=8
			MUTRB=false
			MUTSur=true
			FILTERPROTECT=true
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=false
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=false --rebuild sheets + surrounding loops
		helices=true --false --rebuild helices + surrounding loops

		doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=false --set in all loop (if true work in structure mode)

		fastQstab=true --false --if true faster stabilize, but longer

		reBuild=1 --up to worst parts to look at
		reBuildmore=0 --increased by every main cycle
		rebuilds=1 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=4 --find worst segments part
		minLen=4 --or specify minimum lengthZ
		maxLen=4 --and maximim lengthZ

		-- New options
		maxnrofRuns=50 -- Set it very high if you want to run forever
		minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
		if minGain < 40 then minGain=40 end
		--longfirst=false --true -- Reverse the search, long ones first
		skipqstab=false
		skipfuze=false
		--bandflip=false
		maxlossbeforefuze=(segCnt2-segCnt2%4)/4 -- if loss is more no fuze is done
		if maxlossbeforefuze < 30 then maxlossbeforefuze=30 end
		nrskip=0
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = 1 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = true --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
		mutateOnce = false --if true use mutate(1) instead of shake in qstab
		mutateOnceCI = 0.21 --mutate on what clashing importance
		mutateAlwas = false --if true use mutate(1) instead of all shakes
		preciseBands=false
		allowcut=false
		herd= --herd options
			{ 
			breedBest = 3, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 3, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 2, --number of best will have one random bastard
			firstGen = 10, -- number of herds on first generation
			newRandom = 4, --adding new random ones each generation
			maxGen= 20, --maximum generations
			shuffle = true, --set true to run critters in random order
			renew=5, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=10, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=2, --minimum bands
			maxBands=7, --maximum bands
			keepScore = 0 , --survive to next gen only if score higher than
			breedScore= -20, --will breed kids only if score higher. Basttards always breed
			maxLoss=0, --maximum loss by critter. set 0 to disable
			}
	

end

function AskGABOptions()
local ask=dialog.CreateDialog("GAB options")

	ask.L1=dialog.AddLabel("Generations:")
	ask.maxGen=dialog.AddSlider("Max generations", herd.maxGen, 1, 20, 0) -- New for ebola
	ask.L2=dialog.AddLabel("Max generations without gain for:")
	ask.renew=dialog.AddSlider("Start full random", herd.renew, 1, 10, 0)
	ask.maxBadGen=dialog.AddSlider("Stop", herd.maxBadGen, 1, 10, 0)
	
	ask.L3=dialog.AddLabel("Critters:")
	ask.firstGen=dialog.AddSlider("Nb herds 1st gen.", herd.firstGen, 1, 20, 0)
	ask.maxLoss=dialog.AddSlider("Max loss/critter", critter.maxLoss, 0, 50, 0)
	
	ask.L4=dialog.AddLabel("Other:")
	ask.fuzeThresh=dialog.AddSlider("Fuze filter", fuzeThresh, -10, 50, 0)
	ask.qstabThresh=dialog.AddSlider("qstab filter", qstabThresh, -10, 50, 0)
	if HASLIGAND then
		ask.useLigand=dialog.AddCheckbox("Use ligand",useLigand)
		ask.AlwUseLigand=dialog.AddCheckbox("Always band to ligand",AlwUseLigand)
	end
	if HASMUTABLE then
		ask.onlyMutable=dialog.AddCheckbox("Use only mutable segments",onlyMutable)
	end
    ask.preciseBands=dialog.AddCheckbox("Precise bands to worst part",preciseBands)
	ask.freqbis=dialog.AddSlider("Freq. BIS", freqbis, 0.0, 1.0, 2)
	
	ask.allowcut=dialog.AddCheckbox("Use cuts",allowcut)
	
    ask.OK = dialog.AddButton("OK",1)
	
    dialog.Show(ask)
	herd.maxGen=ChangedOptions("herd.maxGen",herd.maxGen,ask.maxGen.value)
	herd.renew=ChangedOptions("herd.renew",herd.renew,ask.renew.value)
	maxBadGen=ChangedOptions("herd.maxBadGen",herd.maxBadGen,ask.maxBadGen.value)
	herd.firstGen=ChangedOptions("herd.firstGen",herd.firstGen,ask.firstGen.value)
	critter.maxLoss=ChangedOptions("critter.maxLoss",critter.maxLoss,ask.maxLoss.value)
	fuzeThresh=ChangedOptions("fuzeThresh",fuzeThresh,ask.fuzeThresh.value)
	qstabThresh=ChangedOptions("qstabThresh",qstabThresh,ask.qstabThresh.value)
	if HASLIGAND then
		useLigand=ChangedOptions("useLigand",useLigand,ask.useLigand.value)
		AlwUseLigand=ChangedOptions("AlwUseLigand",AlwUseLigand,ask.AlwUseLigand.value)
	end
	if useLigand==false then
		while structure.GetSecondaryStructure(segCntGAB)=="M" do segCntGAB=segCntGAB-1 end
	end
	if HASMUTABE then
		onlyMutable=ChangedOptions("onlyMutable",onlyMutable,ask.onlyMutable.value)
	end
	preciseBands=ChangedOptions("preciseBands",preciseBands,ask.preciseBands.value)
	freqbis=ChangedOptions("freqbis",freqbis,ask.freqbis.value)
	allowcut=ChangedOptions("allowcut",allowcut,ask.allowcut.value)
end

--START Bands to end existing bands (for symmetrics)
distancesb={} -- a list of distances between segments and end bands
distScore=Score()
probBands2Userbands=0.8 -- on each critter !!! (keep it small !!)

if bandflip and PROBABLESYM then BAND2USERBANDS=true -- if existing bands, we'll band to their end (for symmetrics)
else
	BAND2USERBANDS=false
end

function Band2Userbands(s,b) -- from seg to band
	local iBand= 0
	local Goallength=randomGAB(2.0,4.9) -- small but not too small
	local Strength=randomGAB(0.2,1.5)
	iBand = band.AddToBandEndpoint(s, b)
	band.SetStrength(iBand,Strength)
	band.SetGoalLength(iBand,Goallength)
end

function AddBand2UserBands() -- NEW 6/1/2016 , not too many bands
	local seg=1
	local b=0
	local Nbband2Ubands=1
	if BAND2USERBANDS then
		if probBands2Userbands>randomGAB(0.00,0.99) then
			Nbband2Ubands=randomGAB(1,ExistingBands)
			if Nbband2Ubands> 3 then Nbband2Ubands=3 end
			for i=1, Nbband2Ubands do
				seg=randomGAB(segCnt2)
				b=randomGAB(1,ExistingBands)
				Band2Userbands(seg,b)
			end
		end
	end
end	

--STOP Bands to end existing bands (for symmetrics)

function ContextualOptions() -- to propose options adapted to pc and puzzle (at start only, then every day)
	--options linked to type of puzzle
	LoopOptions=LoopOptions+1
	timeLeft=os.difftime(puzzle.GetExpirationTime(),startRecTimeSec)/86400 -- in days, reinitialized
	if LoopOptions==1 then
		print(down(timeLeft/24).." hours left. Proposing contextual options")
	else
		print(down(timeLeft/24).." hours left. Resetting contextual options")
	end
	if timeLeft>2 and LoopOptions < 2 and WorstGroups=="All" then -- intial "All", thus it will give "Backbone" on early game
		WorstGroups="Backbone"
	elseif timeLeft>2 and LoopOptions < 3 and WorstGroups=="Backbone" then
		WorstGroups="Sidechains"
	elseif timeLeft>2 and LoopOptions < 4 and WorstGroups=="Sidechains" then
		WorstGroups="Others"
	else
		WorstGroups="All" -- most of the cases
	end
	
	print("Select Worst "..WorstGroups)
	
	if WorstGroups=="Backbone" then--{"clashing", "packing", "backbone", "ideality"}, -- 2:Backbone 07/02/2014
		scrPart={"clashing", "packing", "backbone"} -- start with worst backbone scores, like in Ebola Rebuild
		for i=1,#ScoreParts do -- slots
			if ScoreParts[i][2]=="backbone" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="clashing" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="packing" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="ideality" then ScoreParts[i][3]=true -- not in worst because it's not always present
			elseif ScoreParts[i][2]=="total" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="loctotal" then ScoreParts[i][3]=true
			else ScoreParts[i][3]=false
			end
		end
	elseif WorstGroups=="Sidechains" then--{"hiding", "bonding", "sidechain"}
		scrPart={"hiding", "bonding"} -- sidechain is not always present
		for i=1,#ScoreParts do -- slots
			if ScoreParts[i][2]=="sidechain" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="hiding" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="bonding" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="total" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="loctotal" then ScoreParts[i][3]=true
			else ScoreParts[i][3]=false
			end
		end
	elseif WorstGroups=="Others" then--{"density", "reference", "other"}
		scrPart={} -- all because not sure they are present
		for i=1,#ScoreParts do -- slots
			if ScoreParts[i][2]=="density" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="reference" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="other" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="total" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="loctotal" then ScoreParts[i][3]=true
			else ScoreParts[i][3]=false
			end
		end
	else
		scrPart={} -- worst default = all of them
		for i=1,#ScoreParts do -- slots
			ScoreParts[i][3]=true -- all slots the latest days
		end
	end
	if ELECTRON or HASDENSITY then -- score others= density + reference
		if timeLeft>2 then
			scrPart={'density'} -- Test. Note that worst default is also perfect for density
			for i=1,#ScoreParts do -- slots
				if ScoreParts[i][2]=="density" then ScoreParts[i][3]=true
				elseif ScoreParts[i][2]=="reference" then ScoreParts[i][3]=true
				elseif ScoreParts[i][2]=="other" then ScoreParts[i][3]=true
				elseif ScoreParts[i][2]=="total" then ScoreParts[i][3]=true
				elseif ScoreParts[i][2]=="loctotal" then ScoreParts[i][3]=true
				else ScoreParts[i][3]=false
				end
			end
		else
			scrPart={} -- worst default is perfect for density
			for i=1,#ScoreParts do -- slots
				ScoreParts[i][3]=true -- all slots the latest days
			end
		end
	end
	if DISULFIDEBONUS then-- scoreothers --experimental NOT USED
		for i=1,#ScoreParts do -- slots
			if ScoreParts[i][2]=="density" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="reference" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="other" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="total" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="loctotal" then ScoreParts[i][3]=true
			elseif ScoreParts[i][2]=="filter" then ScoreParts[i][3]=true -- added the filters
			else ScoreParts[i][3]=false
			end
		end
	end
	if CENTROID then -- nothing yet TO DO
		--to be experimented in CI() and in Wiggle(): CI=1, no shake, no sidechain
	end
	if SEPSIS or HOTSPOT then -- ebola does not work good with zones on sepsis
		herd.maxGen=10 -- max generations GAB au total
		herd.renew=5 -- gab aleatoire apres 5 echecs
		herd.maxBadGen=6-- max echecs successifs
		reBuild=1 --up to worst parts to look at reduce zone to minimum to avoid bug
		reBuildmore=0 --increased by every main cycle
		lengthZ=3 --find worst segments part
		minLen=1 --or specify minimum lengthZ
		maxLen=3 --and maximim lengthZ
		freqbis=0.3 -- I think it's better bands in space in case of sepsis and related puzzle types
	end
	if PROBABLESYM then
		freqbis=0.9 -- for sym, it's much better BIS (unless on the mono at start)
	end
	if LoopOptions==2 then -- reinitialize several thinks TO DO
		 nrskip=nrskip+1 -- skipping one worst more (bug resume)
	end
	if LoopOptions==3 then -- reinitialize several thinks TO DO
		nrskip=nrskip+1 -- skipping one worst more (bug resume)
		freqbis = 0.3 -- frequency of Band In Space
	end
	if Score()<7000 then --only drw? or only GAB?
		-- TO DO
	end
	if Score()<4000 then-- no fuze
		-- already done in DRW
	end
	if onlyGAB then -- set long GAB options -- new BK 25/10/2013
		onlyGABoptions()
	end
	if NOREBUILDMODE then
		rebuilds= 0
		IDEALCHECK=true
	end
	wholeProt= false -- not used because it's inplicit when asking for maximum worst parts
	if wholeProt then --adapted to current pc power TO DO
		reBuild=segCnt2 -- all worst parts
	end

	
	if RecTime>200 then -- very slow pc or big protein
		velocity=1
	elseif RecTime>100 then -- slow pc or big protein
		velocity=2
	elseif RecTime>10 then
		velocity=3
	elseif  RecTime>5 then
		velocity=3
	elseif   RecTime>0.5 then
		velocity=4
	else -- very quick pc or very small protein
		velocity=5
	end

	if timeLeft<2 and RecTime<50 then -- last day I think we can propose the ultimate force
		velocity=4 -- TO DO: evaluate and refine (copy paste here) for "on the fly"
		nrskip=nrskip+2 -- skipping  worst because we certainly have already used a lot of eDRW recipes
		reBuild=reBuild +2 -- more worst ones to try after this skips
		disjunct=true
		donotrevisit=true
	end
	if timeLeft<1 and RecTime<150 then -- last day I think we can propose the ultimate force
		velocity=5
		nrskip=nrskip+4 -- skipping  worst because we certainly have already used a lot of eDRW recipes
		reBuild=reBuild + 10 -- near to all protein last day
		disjunct=true
		donotrevisit=true
		IDEALCHECK=false -- always
	end
	
	if SKETCHBOOK then
		print("Sketchbook puzzle, reducing action number")
		defUndo= true
		undo.SetUndo(defUndo)
		velocity=5
		defminppi= 20
		defiter= 8 -- ((defiter+1)/3)=3 for shakes and mutate
	end
	print("Velocity= "..velocity)
	print("Default skipping= "..nrskip.." worst parts")
	print("Default try = "..reBuild.." worst parts")
end

function QuickOptions(choice) -- to quick set default options based on velocity (after first dialog only)
local choice=choice or 3 -- default, choice is the velocity
 if FlagRecipeUsed then nrskip=2 end -- not repeating all the same worst as before
 
	if choice==1 then -- super quick or start game (rough, about 1 hour)
		GABfilter= -1 -- only on gain
		GABfilterHigh=5
		if NEGATIVEFILTER then
			LostpFgain= 100 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 1 -- default filter lost allowed per 10 pt score gain		
		else
			LostpFgain= -1 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 100 -- default filter lost allowed per 10 pt score gain
		end
		disjunct=true
		donotrevisit=true
		IDEALCHECK=false
		if HASMUTABLE then
			AfterRB=false
			InQstab=false
			AfterQstab=false
			BeFuze=false
			AfterFuze=false
			MutateCI=0.9
			MutSphere=4
			MUTRB=false
			MUTSur=false
			FILTERPROTECT=false -- true=no filter loss allowed on mutate
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=true
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=false --rebuild sheets + surrounding loops
		helices=false --false --rebuild helices + surrounding loops

		doShake=false --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=false --set in all loop (if true work in structure mode)

		fastQstab=true --false --if true faster stabilize, but longer if false

		reBuild=1 --up to worst parts to look at
		reBuildmore=1 --increased by every main cycle
		rebuilds=5 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=4 --find worst segments part
		minLen=3 --or specify minimum lengthZ
		maxLen=4 --and maximum lengthZ

		-- New options
		maxnrofRuns=400 -- Set it very high if you want to run forever
		minGain=(segCnt2-segCnt2%4)/2 -- If less gain then try the next one, else recompute
		if minGain < 80 then minGain=80 end
		--longfirst=false --true -- Reverse the search, long ones first
		skipqstab=true
		--skipfuze=false (Initiated on start)
		if timeLeft>4 and HANDFOLD then -- keep the structure !
			skipfuze=true
		end
		--bandflip=true
		maxlossbeforefuze=(segCnt2-segCnt2%4)/40 -- if loss is more no fuze is done
		if maxlossbeforefuze < 1 then maxlossbeforefuze=1 end
		nrskip=nrskip+2 -- 2 or 4 if recipe already used before
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = -1 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 10 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = false --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		if HASMUTABLE then
			onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
			mutateOnce = false --if true use mutate(1) instead of shake in qstab
			mutateOnceCI = 0.21 --mutate on what clashing importance
			mutateAlwas = false --if true use mutate(1) instead of all shakes
		end
		preciseBands=true
		allowcut=false
		herd= --herd options
			{ 
			breedBest = 2, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 3, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 2, --number of best will have one random bastard
			firstGen = 4, -- number of herds on first generation
			newRandom = 1, --adding new random ones each generation
			maxGen= 2, --maximum generations 
			shuffle = true, --set true to run critters in random order
			renew=1, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=1, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=2, --minimum bands
			maxBands=5, --maximum bands
			keepScore = 1 , --survive to next gen only if score higher than
			breedScore= -2, --will breed kids only if score higher. Bastards always breed
			maxLoss=0, --maximum loss by critter. set 0 to disable
			}

	elseif choice==2 then -- quick (about 4 hours)
		GABfilter=1
		if NOREBUILDMODE then GABfilter=-1 end
		GABfilterHigh=10
		if NEGATIVEFILTER then
			LostpFgain= 50 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 1 -- default filter lost allowed per 10 pt score gain		
		else
			LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 20 -- default filter lost allowed per 10 pt score gain
		end
		disjunct=true
		donotrevisit=true
		IDEALCHECK=false
		if HASMUTABLE then
			AfterRB=false
			InQstab=false
			AfterQstab=false
			BeFuze=false
			AfterFuze=false
			MutateCI=0.9
			MutSphere=6
			MUTRB=true
			MUTSur=false
			FILTERPROTECT=true -- true=no filter loss allowed on mutate
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=false
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=false --rebuild sheets + surrounding loops
		helices=true --false --rebuild helices + surrounding loops

		doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=false --set in all loop (if true work in structure mode)

		fastQstab=true --false --if true faster stabilize, but longer ?

		reBuild=2 --up to worst parts to look at
		reBuildmore=1 --increased by every main cycle
		rebuilds=8 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=4 --find worst segments part
		minLen=2 --or specify minimum lengthZ
		maxLen=4 --and maximum lengthZ

		-- New options
		maxnrofRuns=1000 -- Set it very high if you want to run forever
		minGain=(segCnt2-segCnt2%4)/3 -- If less gain then try the next one, else recompute
		if minGain < 60 then minGain=60 end
		--longfirst=false --true -- Reverse the search, long ones first
		--skipqstab=false (initiated on start)
		--skipfuze=false (Initiated on start)
		if timeLeft>4 and HANDFOLD then -- keep the structure !
			skipfuze=true
		end
		--bandflip=false
		maxlossbeforefuze=(segCnt2-segCnt2%4)/20 -- if loss is more no fuze is done
		if maxlossbeforefuze < 15 then maxlossbeforefuze=15 end
		nrskip=nrskip+ 1 -- 1 or 3 if recipe already used before
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = 0 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 2 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = false --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		if HASMUTABLE then
			onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
			mutateOnce = false --if true use mutate(1) instead of shake in qstab
			mutateOnceCI = 0.21 --mutate on what clashing importance
			mutateAlwas = false --if true use mutate(1) instead of all shakes
		end
		preciseBands=true
		allowcut=false
		herd= --herd options
			{ 
			breedBest = 3, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 4, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 2, --number of best will have one random bastard
			firstGen = 6, -- number of herds on first generation
			newRandom = 2, --adding new random ones each generation
			maxGen= 3, --maximum generations 
			shuffle = true, --set true to run critters in random order
			renew=1, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=1, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=2, --minimum bands
			maxBands=6, --maximum bands
			keepScore = 0 , --survive to next gen only if score higher than
			breedScore= -10, --will breed kids only if score higher. Basttards always breed
			maxLoss=2, --maximum loss by critter. set 0 to disable
			}

	elseif choice==3 then -- default (about 8 hours)
		GABfilter=5
		if NOREBUILDMODE then GABfilter=-1 end
		GABfilterHigh=20
		if NEGATIVEFILTER then
			LostpFgain= 20 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 2 -- default filter lost allowed per 10 pt score gain		
		else
			LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 9 -- default filter lost allowed per 10 pt score gain
		end
		--disjunct=disjunct
		--donotrevisit=donotrevisit
		--IDEALCHECK=true
		if HASMUTABLE then
			AfterRB=false -- default no mutate used
			InQstab=false
			AfterQstab=true
			BeFuze=false
			AfterFuze=false
			MutateCI=0.9
			MutSphere=8
			MUTRB=false
			MUTSur=true
			FILTERPROTECT=true -- true=no filter loss allowed on mutate
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=false
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=false --rebuild sheets + surrounding loops
		helices=true --false --rebuild helices + surrounding loops

		doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=false --set in all loop (if true work in structure mode)

		fastQstab=true --false --if true faster stabilize, but longer

		reBuild=3 --up to worst parts to look at
		reBuildmore=2 --increased by every main cycle
		rebuilds=10 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=6 --find worst segments part
		minLen=2 --or specify minimum lengthZ
		maxLen=4 --and maximim lengthZ

		-- New options
		maxnrofRuns=1000 -- Set it very high if you want to run forever
		minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
		if minGain < 40 then minGain=40 end
		--longfirst=false --true -- Reverse the search, long ones first
		-- skipqstab=false (initiated on start)
		--skipfuze=false (Initiated on start)
		if timeLeft>4 and HANDFOLD then -- keep the structure !
			skipfuze=true
		end
		--bandflip=false
		maxlossbeforefuze=(segCnt2-segCnt2%4)/4 -- if loss is more no fuze is done
		if maxlossbeforefuze < 30 then maxlossbeforefuze=30 end
		nrskip=nrskip -- 0 or 2 if recipe already used before
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = 1 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = true --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		if HASMUTABLE then
			onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
			mutateOnce = false --if true use mutate(1) instead of shake in qstab
			mutateOnceCI = 0.21 --mutate on what clashing importance
			mutateAlwas = false --if true use mutate(1) instead of all shakes
		end
		preciseBands=true
		allowcut=false
		herd= --herd options
			{ 
			breedBest = 3, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 3, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 2, --number of best will have one random bastard
			firstGen = 10, -- number of herds on first generation
			newRandom = 3, --adding new random ones each generation
			maxGen= 3, --maximum generations 
			shuffle = true, --set true to run critters in random order
			renew=1, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=2, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=2, --minimum bands
			maxBands=7, --maximum bands
			keepScore = 0 , --survive to next gen only if score higher than
			breedScore= -20, --will breed kids only if score higher. Basttards always breed
			maxLoss=20, --maximum loss by critter. set 0 to disable
			}
			
	elseif choice==4 then -- slow (about 1 day)
		GABfilter=10
		if NOREBUILDMODE then GABfilter=-1 end
		GABfilterHigh=40
		if NEGATIVEFILTER then
			LostpFgain= 10 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 2 -- default filter lost allowed per 10 pt score gain		
		else
			LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 5 -- default filter lost allowed per 10 pt score gain
		end
		--disjunct=false
		--donotrevisit=true
		--IDEALCHECK=true
		if HASMUTABLE then
			AfterRB=false
			InQstab=false
			AfterQstab=true
			BeFuze=false
			AfterFuze=true
			MutateCI=0.9
			MutSphere=8
			MUTRB=false
			MUTSur=true
			FILTERPROTECT=true -- true=no filter loss allowed on mutate
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=false
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=false --rebuild sheets + surrounding loops
		helices=true --false --rebuild helices + surrounding loops

		doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=false --set in all loop (if true work in structure mode)

		fastQstab=false --false --if true faster stabilize, but longer

		reBuild=4 --up to worst parts to look at
		reBuildmore=3 --increased by every main cycle
		rebuilds=15 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=6 --find worst segments part
		minLen=5 --or specify minimum lengthZ REVERSED in mode 4
		maxLen=2 --and maximum lengthZ

		-- New options
		maxnrofRuns=1000 -- Set it very high if you want to run forever
		minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
		if minGain < 30 then minGain=30 end
		--longfirst=true --true -- Reverse the search, long ones first
		-- skipqstab=false (initiated on start)
		--skipfuze=false (Initiated on start)
		if timeLeft>4 and HANDFOLD then -- keep the structure !
			skipfuze=true
		end
		--bandflip=false
		maxlossbeforefuze=(segCnt2-segCnt2%4)/3 -- if loss is more no fuze is done
		if maxlossbeforefuze < 35 then maxlossbeforefuze=35 end
		nrskip=nrskip -- 0 or 2 if recipe already used before
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = 5 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = true --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		if HASMUTABLE then
			onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
			mutateOnce = true --if true use mutate(1) instead of shake in qstab
			mutateOnceCI = 0.21 --mutate on what clashing importance
			mutateAlwas = false --if true use mutate(1) instead of all shakes
		end
		preciseBands=true
		allowcut=false
		herd= --herd options
			{ 
			breedBest = 4, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 5, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 3, --number of best will have one random bastard
			firstGen = 10, -- number of herds on first generation
			newRandom = 3, --adding new random ones each generation
			maxGen= 4, --maximum generations 
			shuffle = true, --set true to run critters in random order
			renew=2, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=2, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=3, --minimum bands
			maxBands=8, --maximum bands
			keepScore = 0 , --survive to next gen only if score higher than
			breedScore= -25, --will breed kids only if score higher. Basttards always breed
			maxLoss=30, --maximum loss by critter. set 0 to disable
			}
			
	elseif choice==5 then -- days or end game
	
		GABfilter=20
		if NOREBUILDMODE then GABfilter=-1 end
		GABfilterHigh=100
		if NEGATIVEFILTER then
			LostpFgain= 10 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 1 -- default filter lost allowed per 10 pt score gain		
		else
			LostpFgain= 0 -- default score lost allowed for each pt of preferred filter gain
			LostFpgain= 1 -- default filter lost allowed per 10 pt score gain
		end
		if timeLeft>2 then -- else take the default ones for end game (true, true)
			disjunct=false
			donotrevisit=false
		end
		if HASMUTABLE then
			AfterRB=true
			InQstab=false
			AfterQstab=true
			BeFuze=false
			AfterFuze=true
			MutateCI=0.9
			MutSphere=8
			MUTRB=false
			MUTSur=true
			FILTERPROTECT=true -- true=no filter loss allowed on mutate
		end
		if PROBABLEFILTER then
			FiltersFirst=LostpFgain>-2  -- always true!!!(depends only on the cost we admit: -1 being default no cost)
			FILTERMANAGE=true -- note that it will be true on all puzzles where filters are observed
			GENERICFILTER=false
		end
		--DRW options
		--options for (5)"areas" setting
		loops=true --rebuild loops alone
		sheets=true --rebuild sheets + surrounding loops
		helices=true --false --rebuild helices + surrounding loops

		doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
		doSpecial=true -- local shake, wiggle sidec, wiggle backbone, even slower
		shakeCI=0.31 --clash imortance while shaking

		struct=true --set in all loop (if true work in structure mode)

		fastQstab=false --false --if true faster stabilize, but longer

		reBuild=5 --up to worst parts to look at
		reBuildmore=5 --increased by every main cycle
		rebuilds=20 --how many rebuilds to try, set at least 10!

		rebuildCI=0 --clash importance while rebuild

		lengthZ=6 --find worst segments part
		minLen=7 --or specify minimum lengthZ REVERSED in mode 5
		maxLen=2 --and maximim lengthZ

		-- New options
		maxnrofRuns=1000 -- Set it very high if you want to run forever NOT more than 1000 !
		minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
		if minGain < 30 then minGain=30 end
		--longfirst=true --true -- Reverse the search, long ones first
		-- skipqstab=false (initiated on start)
		--skipfuze=false (Initiated on start)
		if timeLeft>5 and HANDFOLD then -- keep the structure !
			skipfuze=true
		end
		--bandflip=false
		maxlossbeforefuze=(segCnt2-segCnt2%4)/2 -- if loss is more no fuze is done
		if maxlossbeforefuze < 40 then maxlossbeforefuze=40 end
		nrskip=nrskip -- 0 or 2 if recipe already used before
		
		--GAB options
		energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
		pullCI = 0.9 --Clash Importance during pull
		maxCI = 1 --maximum CIGAB used by script
		--fastQstab = true -- only 1s1w after pull if true DUPLICATE DRW
		fuzeThresh = 10 -- run fuze if we are close to best score (negative=new best score)
		qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
		if HASLIGAND then
			useLigand = true --use ligand if true
			AlwUseLigand= false  -- always band to ligand if true
		end
		if HASMUTABLE then
			onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
			mutateOnce = true --if true use mutate(1) instead of shake in qstab
			mutateOnceCI = 0.21 --mutate on what clashing importance
			mutateAlwas = false --if true use mutate(1) instead of all shakes
		end
		preciseBands=true
		allowcut=true
		herd= --herd options
			{ 
			breedBest = 5, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
			keepBest = 5, --save up to 3 best scoring critters, rest are forgotten
			breedBastards = 3, --number of best will have one random bastard
			firstGen = 10, -- number of herds on first generation
			newRandom = 3, --adding new random ones each generation
			maxGen= 4, --maximum generations 
			shuffle = true, --set true to run critters in random order
			renew=2, --create totally fresh herd after that many gens w/o improvement
			maxBadGen=4, -- Stop the script after X generations that dont increase the score
			}
		critter= --critter options
			{
			minBands=4, --minimum bands
			maxBands=12, --maximum bands
			keepScore = 0 , --survive to next gen only if score higher than
			breedScore= -30, --will breed kids only if score higher. Basttards always breed
			maxLoss=0, --maximum loss by critter. set 0 to disable
			}
	end

	-- now some generic inits
	if NOREBUILDMODE then
		rebuilds= 0
		IDEALCHECK=true
	end
	
	if SKETCHBOOK then
		print("Sketchbook puzzle, reducing action number")
		defUndo= true
		undo.SetUndo(defUndo)
		velocity=5
		defminppi= 20
		defiter= 8 -- ((defiter+1)/3)=3 for shakes and mutate
		skipqstab=true
		skipfuze=true
		rebuilds=25 -- actually, it depends on the remaining moves (this number of moves is needed)
		maxlossbeforefuze= -5 -- only on gain
		fuzeThresh=-10
		qstabThresh=-10
		allowcut=false -- because a cut is a move
		GABfilter= -10 -- only on big gain
		doSpecial= false
	end

end

--START Movie store big steps
	StepScore= ScoreGAB() -- New 4/11/2014
function StoreBigStep()
	StepScore= ScoreGAB()
	save.Quicksave(SlotStep)
	if SlotStep==SlotStepMax then -- we erase the first ones, only keeping the latest steps
		SlotStep=SlotStepStart
	else
		SlotStep=SlotStep+1
	end
end	

function SaveBigSteps() -- in order to be able to display big steps afterwards in undos
	local s= ScoreGAB()
	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)
	for i= SlotStepStart, SlotStep do
		save.Quickload(SlotStep)
	end
	--save.Quickload(PreferredScoreSlot)
	print("See remembering of big steps in undos")
end

--END Movie store big steps

--jeff101 status per generation by Bruno Kestemont
-- round3 & down must been defined

function StatusGen(loop)
	local loop = loop or 0
	if loop==0 then -- init
		scoreNow=current.GetScore()
		StatusStartScore= scoreNow
		formerScore=scoreNow
		gaingen=round3(scoreNow)
	elseif loop >0 then
		formerScore=scoreNow
		scoreNow=current.GetScore()
		TOTALgain=scoreNow-StatusStartScore
		GainThisGen=scoreNow-formerScore
		print("Score: "..round3(scoreNow))
		print(">>Gain loop "..loop..": "..round3(GainThisGen))
		print(">>>Total gain till now: "..round3(TOTALgain))
        if loop>1 and (loop-1)==5*down((loop-1)/5) then
            gaingen=(gaingen..'\n  ') -- start new line every 5 generations
        end
		gaingen=gaingen.." + " ..round3(GainThisGen)
		gaingen2print=gaingen.." = " ..round3(scoreNow)
		print(gaingen2print)
		print("Loop: ".. loop..", score: "..round3(scoreNow)..", gain: "..round3(TOTALgain).." ("..os.date()..")")
	end
end
StatusGen(0) -- init

--end jeff101 status

velocity=3
function AskEbolaOptions()
    local askresult
    local askmutable=HASMUTABLE
	local suspectnorebuild= SUSPECTNOREBUILD
    local ask = dialog.CreateDialog(recipename)
	local Duration=12
    if askmutable then
        print("Setting default mutate options")
        AfterQstab=true
        AfterFuze=true
        MutSur=true
    end

--repeat
	ask.l7 = dialog.AddLabel("Time needed with current options: about ".. Duration.." hours")
	ask.l8 = dialog.AddLabel("Reset options wizard, from 1 fast to 5 slow:")
	--ask.reset=dialog.AddCheckbox("Reset options wizard, from 1 fast to 5 slow:",false)
	ask.velocity = dialog.AddSlider("Reset options:",velocity,1,5,0)
	if SKETCHBOOK then
		ask.defminppi=dialog.AddSlider("minppi in wiggle", defminppi, 0, 100, 1)
	end
	if SUSPECTNOREBUILD then
		ask.SUSPECTNOREBUILD=dialog.AddCheckbox("Don't rebuild",suspectnorebuild)
	end

	ask.l9 = dialog.AddLabel("Go! = go with wizard options!")
	ask.l10 = dialog.AddLabel("Options = tune options")
	--ask.l11 = dialog.AddLabel("More = tune more Ebola and GAB options")
	--ask.l12 = dialog.AddLabel("GAB = tune GAB options")

    ask.OK = dialog.AddButton("Go!",1) ask.Cancel = dialog.AddButton("Cancel",0)
    ask.DRW = dialog.AddButton("Options",2)
	--ask.More = dialog.AddButton("More",3)
	--ask.GAB = dialog.AddButton("GAB",4)
    askresult=dialog.Show(ask)
    if askresult > 0 then
		if SUSPECTNOREBUILD then
			SUSPECTNOREBUILD=ChangedOptions("SUSPECTNOREBUILD",SUSPECTNOREBUILD,ask.SUSPECTNOREBUILD.value)
		end
		if SUSPECTNOREBUILD then
			NOREBUILDMODE= true
		end

		velocity=ChangedOptions("velocity",velocity,ask.velocity.value)
			QuickOptions(velocity) -- reset all options just before to start or add more dialog
			Duration= velocity * 5
		if SKETCHBOOK then
			defminppi=ChangedOptions("defminppi",defminppi,ask.defminppi.value)
		end
	    WORKON=SegmentSetMinus(WORKON,FindFrozen())
        WORKON=SegmentSetMinus(WORKON,FindLocked())
        WORKON=SegmentSetMinus(WORKON,FindAAtype("M"))
        if askresult==2 then
			AskDRWOptions()
			ProtectDesign(NOTWORKON) -- optional in AskForSelections
		end
		--if askresult==3 then AskMoreOptions() end
		--if askresult==4 then AskMoreOptions() end -- To Do: GAB dialog
--until askresult < 2
	print("Options based on velocity= "..velocity)
	print("Approximative duration per cycle: about ".. Duration.." hours")
    return askresult > 0
	end
end



--Not used (copied in Cleanup)
function CleanupGAB(err) -- NEW BK 10/10/2013
    print("Restoring CIGAB, best result, filter and structures")
    CIGAB(1)
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- new BK 8/4/2013, always back to user settings
    MovieSteps() -- New 4/11/2014
	save.Quickload(PreferredScoreSlot)
	MovieSteps()
	WhriteNote()  -- New 4/11/2014
	TOTALgain=Score()-DRWstartscore
	print(">>>>>TOTAL EBOLA GAIN (following preferences)= "..round3(TOTALgain))
	print("From "..round3(DRWstartscore).." to "..round3(Score()))
	print("Absolute best score = "..round3(bestScore))
	print("Total gain till credited score: "..round3(Score(current, true)-StartEbolaScore))
	print("Absolute best filter = "..round3(bestFScore))
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- always back to user settings
	deletebands()
    print(err)
	LastWish()
end



--GABcut END###########################################################

function LastWish()
	--recentbest.Restore()
	undo.SetUndo(true)
	CI(1)
	return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting
	band.DisableAll()
	print("Keeping different best solutions in 5 undos")
	save.Quicksave(PreferredScoreSlot)
		save.Quickload(BestScoreSlot)
		save.Quickload(BestFilterSlot)
		--save.Quickload(bwslot)
		save.Quickload(BestItelligentSlot)
	save.Quickload(PreferredScoreSlot)
	if Priority==0 then save.Quickload(BestScoreSlot) print("Ending with best score")
	elseif Priority==1 then save.Quickload(BestFilterSlot) print("Ending with best filter")
	elseif Priority==2 then save.Quickload(BestItelligentSlot) print("Ending with optimal filter&score solution")
	else save.Quickload(PreferredScoreSlot) print("Ending with preferred solution")
	end
	UnProtectDesign(FREEZEPROTECT)
end

function DumpErr(err)
	start,stop,line,msg=err:find(":(%d+):%s()")
	err=err:sub(msg,#err)
	p(true, '---')
	if err:find('Cancelled')~=nil then
		print("User stop.")
	else
		print("unexpected error detected.")
		--p("Error line: %i.")
		--p("Error : %s.")
		p("Error line: ", line)
		p("Error: ", err)
	end
	--Cleanup()
	undo.SetUndo(true)
	print("Restoring CI, initial selection, best result and structures")
    CI(1)
    save.Quickload(PreferredScoreSlot)
    if SAVEDstructs then save.LoadSecondaryStructure() end
    selection.DeselectAll()
    if SAFEselection ~= nil then SetSelection(SAFEselection) end
	
	    print("Restoring CIGAB, best result, filter and structures")
    CIGAB(1)
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() FILTERON= not OriginalFilterSetting end -- new BK 8/4/2013, always back to user settings
    MovieSteps() -- New 4/11/2014
	save.Quickload(PreferredScoreSlot)
    if SAVEDstructs then save.LoadSecondaryStructure() end
	MovieSteps()
	WhriteNote()  -- New 4/11/2014
	TOTALgain=Score()-DRWstartscore
	print(">>>>>TOTAL EBOLA GAIN (following preferences)= "..round3(TOTALgain))
	print("From "..round3(DRWstartscore).." to "..round3(Score()))
	print("Absolute best score = "..round3(bestScore))
	print("Total gain till credited score: "..round3(Score(current, true)-StartEbolaScore))
	print("Absolute best filter = "..round3(bestFScore))
	deletebands()
    print(err)
	LastWish()
end
	
				
function MAIN()
	print("Based on ".."Tvdl enhanced DRW "..DRWVersion.." and "..recipename2)

	ContextualOptions()


	if AskEbolaOptions() then
		print(ChangedOptionsTxt)
	    DRW()
	end
	LastWish()
end


xpcall(MAIN,DumpErr)

Comments

[Bruno Kestemont]

Basically, it's a Deep Rebuild and Band Worst (DRBW) recipe

For the worst scoring zones of several segments:
-rebuild and shake several times
-fuze selected for best rebuild_shake results only
-if it's a good solution, add bands from and to this zone, wiggle selected, fuze if gain, wiggle all
-go to next worst zone

[Bruno Kestemont]

It's a complete reset of Ebola Rebuild.

The strategy is exactly the same as Ebola Rebuild, but with modern eDRW and GAB, and a better user interface.

It takes the advantages of latest tvdl enhanced DRW which constitutes the core of the recipe, including managing puzzle types (less contextual bugs) and optionally selecting where to work on.

In the between of each DRW, it starts an enhanced version of GAB including cuts and banding to ends of user bands (this is usefull to band to symmetrics or to space in the wanted direction).

[Bruno Kestemont]

Its a very long lasting recipe for Middle-End game on Low wiggle power.

I typically use it only:

-on small puzzles
-when eDRW and GAB recipes do not gain anymore, and I don't know what to do and several days are remaining and I don't want to switch to High wiggle power
-when I'll be absent from keyboard for a long time (I need a long lasting patient recipe): > 8 hours

Interesting options:

-Priority to filter: for filtered puzzles, you may give the priority to filter over points;
-Band to Symmetrics: put band to symmetric or to space and disable before to run, GAB will band to the symmetric or wanted space too;
-Band to worst segments;
-Cuts in GAB and in Fuse;
-Idealize and remix
-Auto-proposes the best options considering your computer power and the puzzle state and characteristics
-Quick start: simply click on "ok" if you trust the options "out of context"

[Bruno Kestemont]

(only in case of CI not 1) Like in tvtleDRW, but it resets CI to 1 by default

[Bruno Kestemont]

Shadow filter is a bonus which is not related to segments, like in Electron Density puzzles.

Filter bonus is explicitly given on the top of your screen. Typical in Design and Contact puzzles. I recommend to select "2" "filter bonus" on start game, and "1" while you did not get the highest possible bonus. "0" should be used the latest 2 days in order to gain points.

Default "0" is fast and corresponds to a classical recipe behaviour.

Note that selecting "1" or "2" reduces the probability of fast score gain: the recipe does not always build on the highest score (but this can be recovered when clicking on "Best credited score" at the end). Read the log in order to follow the recipe's strategy.

[Bruno Kestemont]

(after the eventual preludes above)

The default will depends on the context (puzzle size, computer power, deadline). Just type "Go" and it will be ok.

If you want another set of default options, just change the slide from 1 ("fast") to 5 ("slow") and type "Go !"

After selecting the slide "Reset options", you might want to refine the proposed ones by clicking on "Options". Other dialogs bellow are only accessible by clicking on "Options" here: for advanced or curious players only !

[Bruno Kestemont]

This is a typical eDRW dialog.
Most options are the same as in eDRW.
Some subdialogs might be different depending on context (like Reselect Slots will also give the filter options on filtered puzzles).
"More" and "GAB" are new to Ebola.

[Bruno Kestemont]

More
New to eDRW: Idealize & remix, cut in worst and GAB launch criteria.

After each rebuild & shake, a GAB will occur on the best rebuild ONLY if it's resulting score is:
-not lower than "last preferred score - loss filter" (negative loss = GAB only after gain)
-not higher than "last preferred score + gain filter"

"Do not launch GAB" results in a simple DRW recipe ! (it might be proposed as default on start game).

[Bruno Kestemont]

This is almost the same as in Ebola Rebuild.

"Full random" means that it will not band to worst parts anymore (a normal random GAB)
More herds = more time needed, less points
Fuze & qstab filters are the loss allowed before to do this (negative = fuze only on gain).
Use cuts in GAB gives a good result on end game.

It's possible to limit Ebola to only GAB by changing the DRW options to minimum rebuild numbers, "launch GAB" almost always, setting a high max generations, never stop here and no precise bands. (But then why not using a normal GAB recipe? for the cuts?).

[Bruno Kestemont]

(Re)select slots
This is an example of the (Re)select slots Dialog in the case of a puzzle with Filters (this dialog will change with puzzle context).

The first part is the same as in original eDRW. The slots are the Deep rebuild solutions that would be further fuzed and/or used for GAB.

The aim is to favor what you like depending on the game status. Most of the time, we simply select the best total score (and/or segments local total). But in Electron Density puzzles, we might want to also select the rebuild which gives the best Density subscore (this option would be present on the dialog for this type of puzzle).

The second part is specific to filtered puzzles. Check the filter subscore to favor this. Then specify how many points you are ready to loose for each Filter Bonus gain, or the filter lost you are ready to pay for any total score gain.

Finally, decide to disable filter during wiggle (to save a lot of time, on the cost of possible filter gains), or even almost always (turbo but reduced chances to rise bonus).