Recipe: Rav3n_pl GAB BiS 2.2.3F No Mutate

created by Bruno Kestemont

Profile

• Name: Rav3n_pl GAB BiS 2.2.3F No Mutate
• ID: 102336
• Shared with: Public
• Parent: Rav3n_pl GAB BiS Filter v2.2.4
• Children: None
• Created on: January 07, 2019 at 19:01 PM UTC
• Updated on: January 07, 2019 at 19:01 PM UTC
• Description:

  Bands! Bands in space! GAB BiS v2. Now it have options dialog! Never mutate (for contests)

Code

--[[
Bands! Bands in space!
GAB - Genetic Algorythm on Bands
by Rav3n_pl
based on CartoonVillan and Crashguard303 scripts
Lua V2

Definitions:
band: random band to space from random segment
critter: set of bands
herd: set of critters

1.
- randomize needed bands 
- randomly assigning 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

porky added the filter management
BK added more filters on recentbest and save

ver 2.02 Filter
--debugged line 239

ver 2.03
--debugged filter

ver 2.04
--debuggeg monomer

ver 2.05
-- just update the commands Get/SetFiltersDisabled

ver 2.06
-- debugged generic filter & second dialog

ver 2.1
-- second dialog with sliders (no text box). This reduces the range available
but it's also more convenient and it avoids user errors
ver 2.1.1 Generic filter only after dialog to save time at start
ver 2.1.2 Check conditions option on exploration puzzles
ver 2.1.3 debugged conditions
ver 2.2.0 added Jeff101's display on each loop, and archive in note by pauldunn
	keep user bands
	FILTERMANAGE activated (disable filter during wiggle)
ver 2.2.1 bug fixed in loop_count
ver 2.2.2 added quickshake
ver 2.2.3 undo.SetUndo
ver 2.2.3 No Mut Never mutate (for contests)
]]--

recipename= "Rav3n_pl GAB BIS 2.2.3 No Mut"
p=print
userbands=band.GetCount()
p("Starting "..recipename.. " on\n   puzzle "..(puzzle.GetName()))
p('   with puzzle ID '..(puzzle.GetPuzzleID())..' and '..userbands..' user-supplied bands.\n ')
ssstr="" -- jeff101
gen=0

--SLOTS:
--[[
3	 is best
4  used in recipe
5  used in recipe
50-100 used to record each big steps for movie at the end

]]--
SlotStepStart=50 -- New for SaveBigSteps()
SlotStep=SlotStepStart

undo.SetUndo(false)







--START Translate old filter functions in order to keep original recipe code Bruno Kestemont 7/1/2019
function behavior.GetFiltersDisabled()

	return not filter.AreAllEnabled()	--True if all filters are active

end

function behavior.SetFiltersDisabled(disabling)
	local disabling = disabling or true
	if disabling then 
		filter.DisableAll()	--Disables all filters
	else
		filter.EnableAll()	--Enables all filters
	end
end

function behavior.SetSlowFiltersDisabled(disabling)
	if disabling then 
		filter.DisableAll()	--Disables all filters
	else
		filter.EnableAll()	--Enables all filters
	end
end

--END --Translate old filter functions in order to keep original recipe code


OriginalFilterSetting = behavior.GetFiltersDisabled()
PROBABLEFILTER= false
GENERICFILTER=false
FILTERMANAGE= false
HASMUTABLE= false
IDEALCHECK= false
PROBABLESYM= false
SEPSIS= false
ELECTRON= false
CENTROID= false
HOTSPOT= false
EXPLORATION= false
conditions=false
sym=1


segCnt=structure.GetCount()
segCnt2=segCnt
while structure.GetSecondaryStructure(segCnt2)=="M" do segCnt2=segCnt2-1 end -- not used yet (ligand)


--START extraction of information from puzzle metadata	--Extrait des infos

function detectfilterandmut() -- Bruno Kestemont 10/10/2013; 13/2/2015; 5/1/2019
	local descrTxt=puzzle.GetDescription()
	local puzzletitle=puzzle.GetName()
	local function SymetryFinder() -- by Bruno Kestemont 7/2/2013, 25/8/2013
		local segMeanScore=(TopScore()-8000)/segCnt -- top score pour eviter les debuts de puzzle
		--p("Score moyen par segment= "..segMeanScore)
		if PROBABLESYM then
			 if       segMeanScore<33.39 then sym=1
				PROBABLESYM=false
				elseif segMeanScore<85  then sym=2 
				elseif segMeanScore<132 then sym=3 
				elseif segMeanScore<197 then sym=4
				else sym=5
			 end
		else sym=1
		end
		return
	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 SymetryFinder()
			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 SymetryFinder()
		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
	return
end
detectfilterandmut()

--END extraction of information from puzzle metadata	--Extrait des infos


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

-- Handy shorts module Original version by BitsPawn (WARNING: filter translator above is now necessary).


GENERICFILTER=false -- duplicate because it has to be in generic filter management

-- 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 behavior.GetFiltersDisabled() then

        behavior.SetFiltersDisabled(false)

    end

end

function FiltersOff()

    if behavior.GetFiltersDisabled()==false then

        behavior.SetFiltersDisabled(true)

    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)
function GenericFilterMngt()
	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
end
			
--STOP Generic Filter Management

--START SET NOTES BY PD
--[[ Set note with author, recipe and big steps -- By Pauldunn
This subroutine is used in much group recipe versions in various groups
originally in Go Science
It traces the various recipes and players that improved the current solution


Module to quick copy-paste it in existing recipes, by Bruno Kestemont
]]--


--HOW TO include in a recipe?


--1a) COPY from here ================

function InitNotes(recipename)
	local recipename=recipename or ""
	note_number=structure.GetCount()
	for seg=structure.GetCount(),1,-1 do
 	 if structure.GetNote(seg)~="" then break end
 	 note_number=seg
	end
	print(string.format("Recording "..recipename.." results in Note for segment %i",note_number))
	starting_score=current.GetScore()
--structure.SetNote(note_number,string.format("(%s) %.3f + %s(%i) %.3f",user.GetPlayerName(),starting_score,recipename,loop_count,current.GetScore()))
end


function SetNote(note_number, starting_score, recipename, loop_count)
	local recipename=recipename or ""
	local starting_score=starting_score or 0
	local loop_count=loop_count or 1
	
	--print(string.format("Recording "..recipename.." results in Note for segment %i",note_number))
	structure.SetNote(note_number,string.format("(%s) %.3f + %s(%i) %.3f",user.GetPlayerName(),starting_score,recipename,loop_count,current.GetScore()))
end

InitNotes(recipename) -- WARNING: and match "recipename" with the recipename of the recipe

--1b) COPY to here. ================

-- options:
energy=false --set true to seek energy in exploration puzzles; false works on all puzzles
pullCI=0.9 --Clash Impotrance during pull
shakeCI=0.21 --CI when shake on qstab or mutate once
maxCI=1 --maximum CI used by script
fastQstab=true -- only 1s1w after pull if true
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
onlyMutable=true --if true use ONLY all mutable aas, no matter of always use
mutateOnce=false --if true use mutate(1) instead of shake in qstab
mutateAlwas=false --if true use muatate(1) instead of all shakes

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
newRandom = 10, --adding new random ones each generation
maxGen= 1000, --maximum generations 
shuffle = true, --set true to run critters in random order
renew=4, --create totally fresh herd after that many gens w/o improvement
}
critter= --critter options
{
minBands=3, --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
maxUp = 12.1, -- maximum band lenght
minUp = 0.1 -- debugging case=0
}

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
--{238,238}--ligand need to be at one end
--{308,311}, --loopy
--{272,319}, --loopy
}
UseSegments= --use ONLY this segments
{
--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
}
--end of options

--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   = current.GetScore ()

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

local function New ( obj )
  return obj -- pass-new-obj-by-value
end

local _gses = New ( current.GetSegmentEnergySubscore )

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 = current.GetScore ()
      structure.ShakeSidechainsSelected ( iters )
      selection.DeselectAll () 
      if current.GetScore () > 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 CI(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 down(x)
    return x-x%1
end

function Score()--return score, exploration too
    if energy==true then
        return current.GetEnergyScore()
    else
        return current.GetScore()
    end
end

--local seed=recipe.GetRandomSeed() --NOT WORKING!!!
--calculate REALLY good seed
seed=os.time()/math.abs(Score())
seed=seed%0.001
seed=1/seed
while seed<10000000 do seed=seed*1000 end
seed=seed-seed%1
p("Seed is: "..seed)
math.randomseed(seed)
--REALLY good seed made by rav3n_pl :P

--[[ original Wiggle
function Wiggle(how, iters, minppi)
    if how==nil then how="wa" end
    if iters==nil then iters=3 end
    if minppi==nil then minppi=0.3 end
    
    if iters>0 then
        iters=iters-1
        sp=Score()
        if how == "s" then 
                if mutateAlwas==true then structure.MutateSidechainsSelected(1) 
                                    else structure.ShakeSidechainsSelected(1) end
            elseif how == "wb" then structure.WiggleAll(25, true,false)
            elseif how == "ws" then structure.WiggleAll(25, false,true)
            elseif how == "wa" then structure.WiggleAll(25, true,true)
        end
        ep = Score()
        ig=ep-sp
        if how~="s" then
            if ig > minppi then return Wiggle(how, iters, minppi) end --tail call
        end
    end
end
]]--

function Wiggle(how, iters, minppi) -- NEW one, with filter management, 17/4/2016
	if FILTERMANAGE then behavior.SetSlowFiltersDisabled(true) end-- new BK 8/4/2013, always disable filter here
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end
    
    if iters>0 then
        iters=iters-1
        sp=Score()
        if how == "s" then 
				if FILTERMANAGE then behavior.SetSlowFiltersDisabled(OriginalFilterSetting) end -- new BK 8/4/2013, always back to user settings
                if mutateAlwas==true then structure.MutateSidechainsSelected(1) 
                                    --else structure.ShakeSidechainsSelected(1) end
									else QuickShake() end
            elseif how == "wb" then structure.WiggleAll(2, true,false)
            elseif how == "ws" then structure.WiggleAll(2, false,true)
            elseif how == "wa" then structure.WiggleAll(2)
        end
        ep = Score()
        ig=ep-sp
        if how~="s" then
            if ig > minppi then return Wiggle(how, iters, minppi) end --tail call
        end
    end
	if FILTERMANAGE then behavior.SetSlowFiltersDisabled(OriginalFilterSetting) end -- new BK 10/10/2013, always back to user settings
end

function SaveBest()
    local g=Score()-bestScore
	if not (conditions and not current.AreConditionsMet) then
		if g>0 then
			if g>0.01 then p("Gained another "..round(g).." pts.") end
			bestScore=Score()
			save.Quicksave(3)
		end
	else
		print("Conditions not met. Returning to former solution") -- for DEBUG
	end
end
function SaveRB()
    if recentbest.GetScore()>bestScore or (recentbest.GetEnergyScore()>bestScore  and energy==true)then
		if not (conditions and not current.AreConditionsMet) then
			save.Quicksave(4)
			recentbest.Restore()
			SaveBest()
			save.Quickload(4)
		end
    end
end

function Qstab()
    selection.SelectAll()
    CI(shakeCI)
    if mutateOnce==true then
        structure.MutateSidechainsSelected(1)
    else
        Wiggle("s",1)
    end
    if fastQstab==false then 
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
    end
    CI(1)
    Wiggle()
end

function FuzeEnd()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    srb()
end
function Fuze1(ci1,ci2)
    CI(ci1)
    Wiggle("s",1)
    CI(ci2)
    Wiggle("wa",1)
end
function Fuze2(ci1,ci2)
    CI(ci1)
    Wiggle("wa",1)
    CI(1)
    Wiggle("wa",1)
    CI(ci2)
    Wiggle("wa",1)
end
function srb()
    recentbest.Restore()
    SaveBest()
end
function Fuze()
    p("Fuzing...")
    local scr=Score()
    selection.SelectAll()
    recentbest.Save()
    Fuze1(0.3,0.6) FuzeEnd()
    Fuze2(0.3,1) srb()
    Fuze1(0.05,1) srb()
    Fuze2(0.7,0.5) FuzeEnd()
    Fuze1(0.07,1)
    srb()
end

function random(n1,n2) --random function returns int or float depends on input vars
	if n1==nil then return math.random()
    else
        if n2==nil then
            if n1%1==0 then
                return math.random(n1) --integer
            else
                return math.random()*n1 --float
            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
            end
        end
    end
end

function FillHerd() --fill up herd
    local n=#critters
    if n>0 then --fill up
        n=herd.newRandom
    else --fresh herd
        n=herd.breedBest + herd.keepBest + herd.breedBastards 
    end
    p("Randomizing "..n.." new critters...")
    for i=1,n do
        AddCritter()
    end
end
function AddCritter() --vreate new random critter
    local c={}
    critterID=critterID+1
    c.no=critterID
    c.name=c.no..'-rnd'
    c.bands={}
    local r=random(critter.minBands, critter.maxBands)
    for i=1,r do
        c.bands[#c.bands+1]=AddBand()
    end
    critters[#critters+1]=c
    p(c.name.." bands: "..#c.bands)
end
function AddBand() --create one random band
    local cnt=0
    local b={}
    while true do --try till die
        cnt=cnt+1
        local s1=random(segCnt)
        if onlyMutable==true or #UseSegments>0 then
            s1=UseSegments[random(#UseSegments)]
        end
        if #UseSegments>0 or CanBeUsed(s1) then
            local str=random(bands.minStr,bands.maxStr)
            local length=random(bands.minUp,bands.maxUp) --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 = random(segCnt)
                segmentYAxis = random(segCnt)
                if segmentXAxis~=s1 and segmentYAxis~=s1 and segmentXAxis~=segmentYAxis then break end
            end
            --{segmentOrigin, segmentXAxis, segmentYAxis, rho, theta, phi}
            b={s1, segmentXAxis, segmentYAxis, length, theta, phi, str}
            break
        end
        
        if cnt>100 then
            p("Sorry! Cant create band! Breaking script!")
            BreakScript() --there is no such function, so it crashes script
        end
    end
    return b
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 CanBeUsed(sg1) --checking end of bands
    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] -- r={from,to}
            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 ScoreHerd() --score all critters from herd
    save.Quickload(3)
    p("Scoring "..#critters.." critters...")
    save.Quicksave(5)
    local herdScore=Score()
    for i=1,#critters do
        --band.DeleteAll()
		deletebands()
        local crt=critters[i] --critter
        local s=Score() --start score
        local bnds=crt.bands
        for b=1,#bnds do
            local bnd=bnds[b]
            local atom=5
            local sn=bnd[1]
            if sn==segCnt then atom=6 end --bug in last segment
            if structure.GetAminoAcid(sn)=='g' then atom=0 end --glycyne
            band.Add(sn,bnd[2],bnd[3],bnd[4],bnd[5],bnd[6],atom)
            local bc=band.GetCount()
            band.SetStrength(bc,bnd[7])
        end
        selection.SelectAll()
        CI(pullCI)
        recentbest.Save()
        Wiggle("wb",1)
        --band.DeleteAll()
		deletebands()
        CI(1)
        if s-Score() > qstabThresh then
            Qstab()
        else
            Wiggle()
        end
        if Score()-bestScore>fuzeThresh then 
            SaveRB()
            Fuze() 
        else
            SaveRB()
        end
        
        crt.score=Score()-s
        p("Critter "..crt.name.." : "..round(crt.score))
        
        if critter.maxLoss>0 then
            if Score()>herdScore-critter.maxLoss then
                save.Quicksave(5)
                herdScore=Score()
            else
                save.Quickload(5)
            end
        else
            save.Quickload(3)
        end
    end
    save.Quickload(3)
    if band.GetCount()>0 then --clean bands from best solution (if any)
        --band.DeleteAll()
		deletebands()
        save.Quicksave(3)
    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=random(mb,db)
    for i=1,bn,2 do
        kid.bands[#kid.bands+1]=mom.bands[random(#mom.bands)]
        kid.bands[#kid.bands+1]=dad.bands[random(#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 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()
    p("Breeding...")
    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=random(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=random(#critters)
            if r~=i then
                critters[i],critters[r]=critters[r],critters[i]
            end
        end
    end
end
function GAB()
    if onlyMutable==true then
        for i=1,segCnt do
        if structure.IsMutable(i) then
            UseSegments[#UseSegments+1]=i
        end
        end
    end
	
    critterID=0
    gen=0
    ss=Score()
    bestScore=ss
    save.Quicksave(3)
    recentbest.Save()
    p("Rav3n_pl Bands! Bands in space! GAB BiS")
    p("Start score: "..round(ss))
	if energy then
		energy=false
		ssNormal=Score()
		p("Normal score: "..round(ssNormal).. " Conditions= "..ss-ssNormal)
		energy=true
	end
    critters={}
    FillHerd()
    badGen=0
	ssstr=(ssstr..round(ss)) -- jeff101
    while true do --this is (almost) endless script ;]
		undo.SetUndo(false) -- reset each loop if gain will give a long list of interesting undos
        genScore=Score()
        gen=gen+1
        p()
        p("Generation: "..gen..", score: "..round(Score())..", gain: "..round(Score()-ss))
        ShuffleHerd()
        ScoreHerd()
        save.Quickload(3)
        if gen==herd.maxGen then break end --end of script
        
        if genScore<=Score() then badGen=badGen+1 else badGen=0 end
        if badGen>=herd.renew then 
            p("Creating fresh random herd...")
            critters={}
            FillHerd()
            badGen=0
        else
            BreedHerd()
        end
		
		-- START jeff101's display
        genEndScore=Score()
        genGain=genEndScore-genScore
        if gen>1 and (gen-1)==5*down((gen-1)/5) then -- New 18/1/2016 jeff101 log display
            ssstr=(ssstr..'\n  ') -- start new line every 5 generations
        end
        if genGain>=0 then
            ssstr=(ssstr..' + '..round(genGain))
			undo.SetUndo(true)
        else
            ssstr=(ssstr..' - '..(-round(genGain)))
        end
        p(ssstr..' = '..round(genEndScore))
		--END jeff101's display
--3a) COPY from here ---------------
		loop_count=gen
		SetNote(note_number, starting_score, recipename, loop_count) -- WARNING: and mach "recipename" and "loop_count" with the names of the recipe

--3b) COPY to here --------------	
		SaveBigSteps() -- for movie at the end
		
    end
    p("Final score: "..round(Score()).." Total gain: "..round(Score()-ss))
end

--START Movie store big steps
	StepScore= Score() -- New 4/11/2014
function StoreBigStep()
	StepScore= Score()
	save.Quicksave(SlotStep)
	SlotStep=SlotStep+1
end	

function SaveBigSteps() -- in order to be able to display big steps afterwards in undos
	local g=Score()-StepScore
	local s= Score()
	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(3)
	print("See remembering of big steps in undos")
end

--END Movie store big steps

function Cleanup(err) -- NEW BK 10/10/2013	
	start,stop,line,msg=err:find(":(%d+):%s()")
	err=err:sub(msg,#err)
	print('---')
	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
	print("Restoring CI, best result, filter and structures")
    CI(1)
	undo.SetUndo(true)
	if FILTERMANAGE then behavior.SetSlowFiltersDisabled(OriginalFilterSetting) end -- always back to user settings
    StoreBigStep()
	MovieSteps()
	save.Quickload(3)
--3a) COPY from here ---------------
		loop_count=gen
		SetNote(note_number, starting_score, recipename, loop_count) -- WARNING: and mach "recipename" and "loop_count" with the names of the recipe
--3b) COPY to here --------------
	deletebands() -- WARNING must be defined anywhere !!
    print(err)
end

function dialogOptions()
	local mut=false
	for i=1,segCnt do
		--if structure.IsMutable(i) then mut=true break end
	end
	if not mut then
		onlyMutable=false
		mutateOnce=false
	end
    opt = dialog.CreateDialog("Main Options")
    opt.lbl1 = dialog.AddLabel("GAB BiS main options:")
    opt.gen = dialog.AddTextbox("Generations:", herd.maxGen) 
    opt.pull= dialog.AddSlider("Pulling CI", pullCI, 0.05, 1, 2)--desctip, default, min, max, precision
    opt.shak= dialog.AddSlider("Shake CI", shakeCI, 0.01, 1, 2)
    opt.maxci= dialog.AddSlider("Maximum CI", maxCI, 0.05, 1, 2)
    opt.qstab=dialog.AddCheckbox("FastQstab", fastQstab)
    opt.energy=dialog.AddCheckbox("Seek energy", energy) -- will be better on on exploration puzzles
    opt.mutonly=dialog.AddCheckbox("Only mutable", onlyMutable)
    --opt.mutonce=dialog.AddCheckbox("Mutate once", mutateOnce)
    --opt.mutalways=dialog.AddCheckbox("Mutate always", mutateAlwas)
    opt.fuzeth=dialog.AddTextbox("Fuze threshold: ",fuzeThresh)
    opt.qsth=dialog.AddTextbox("Qstab threshold: ",qstabThresh)
	if EXPLORATION then
		opt.conditions=dialog.AddCheckbox("Check conditions", conditions)
	end
	if PROBABLEFILTER then
		opt.FILTERMANAGE=dialog.AddCheckbox("Fast filter during wiggle only: ",FILTERMANAGE)
		opt.GENERICFILTER=dialog.AddCheckbox("Fast filter unless for score: ",GENERICFILTER)
	end
    opt.run = dialog.AddButton("Start", 1)
    opt.more = dialog.AddButton("More", 2)
    opt.cancel = dialog.AddButton("Cancel (???)", 0)
    res=dialog.Show(opt)
    if  res>0 then
        energy=opt.energy.value
        pullCI=opt.pull.value
        shakeCI=opt.shak.value
        maxCI=opt.maxci.value
        fastQstab=opt.qstab.value
        fuzeThresh = tonumber(opt.fuzeth.value)
        qstabThresh= tonumber(opt.qsth.value)
        onlyMutable=opt.mutonly.value
        --mutateOnce=opt.mutonce.value
        --mutateAlwas=opt.mutalways.value
        herd.maxgen=tonumber(opt.gen.value)
		if PROBABLEFILTER then
			FILTERMANAGE=opt.FILTERMANAGE.value
			GENERICFILTER=opt.GENERICFILTER.value
		end
		if EXPLORATION then
			conditions=opt.conditions.value
		end
        if res==2 then
			opt = dialog.CreateDialog("More Options")
            opt.lbl1 = dialog.AddLabel("Herd:")
            opt.brbest=dialog.AddSlider("Breed best", herd.breedBest, 1, 20, 0)
            opt.kbest=dialog.AddSlider("Keep best", herd.keepBest, 1, 20, 0)
            opt.bas=dialog.AddSlider("Breed bastards", herd.breedBastards, 1, 20, 0)
            opt.rnd=dialog.AddSlider("New random", herd.newRandom, 1, 30, 0)
            opt.renew=dialog.AddSlider("Renew hers", herd.renew, 1, 10, 0)
            opt.shuff=dialog.AddCheckbox("Shuffle critters", herd.shuffle)
            opt.lbl2 = dialog.AddLabel("Critter:")
            opt.minb=dialog.AddSlider("Minimum bands:", critter.minBands, 1,4,0) 
            opt.maxb=dialog.AddSlider("Maximum bands:", critter.maxBands,4,50,0) 
            opt.keeps=dialog.AddSlider("Keep score:", critter.keepScore, -10, 10, 0) 
            opt.breeds=dialog.AddSlider("Breed score:", critter.breedScore, -40, 10,0) 
            opt.maxloss=dialog.AddSlider("Max loss:", critter.maxLoss, 0,50,0)
			opt.lbl4 = dialog.AddLabel("(0 to disable max loss)")
            opt.lbl3 = dialog.AddLabel("Bands:")
            opt.minst=dialog.AddSlider("Min str", bands.minStr, 0.1, 2, 1)
            opt.maxst=dialog.AddSlider("Max str", bands.maxStr, 0.2, 2, 1)
            opt.maxup=dialog.AddSlider("Max lenght", bands.maxUp, 1, 20, 0)
            opt.run = dialog.AddButton("Start", 1)
            dialog.Show(opt)
            
            herd.breedBest = opt.brbest.value
            herd.keepBest = opt.kbest.value
            herd.breedBastards = opt.bas.value
            herd.newRandom = opt.rnd.value
            herd.shuffle = opt.shuff.value
            herd.renew=opt.renew.value

            critter.minBands=tonumber(opt.minb.value)
            critter.maxBands=tonumber(opt.maxb.value)
            critter.keepScore = tonumber(opt.keeps.value)
            critter.breedScore=tonumber(opt.breeds.value)
            critter.maxLoss=tonumber(opt.maxloss.value)

            bands.minStr=opt.minst.value
            bands.maxStr=opt.maxst.value
            bands.maxUp = opt.maxup.value
        end
    else
        p("Exiting...")
        BreakScript()
    end    
    
end

-- main call

function MAIN()
	dialogOptions()
	GenericFilterMngt()
	GAB()
end

xpcall(MAIN,Cleanup)

--end of script

Comments

[Bruno Kestemont]

This "never mutate" version is safe for some Contests with user-defined sequences.

See here:
https://fold.it/portal/node/2003391

[Bruno Kestemont]

Adapted to new Lua all filters functions