Recipe: Rav3n_pl GAB v2.0.6

created by Rav3n_pl

Profile

• Name: Rav3n_pl GAB v2.0.6
• ID: 41091
• Shared with: Public
• Parent: None
• Children:
  • Rav3n_pl GABmutate
  • Rav3n_pl GAB mutate
  • Rav3n_pl GAB mutate
  • Rav3n_pl GAB Qmutate
  • Rav3n_pl GAB v2.0.5 (Energy Seeking)
  • Rav3n_pl GAB v2.0.5 LL
  • Rav3n_pl GAB maxLoss 20
  • Rav3n_pl GAB v2.0.5 no sheet/helix
  • Rav3n_pl GAB v2.0.5 1mill gen No loss limit
  • Rav3n_pl GAB v2.0.5 100mill
  • Rav GAB v2.0.5 no sheet/helix 100 mill
  • Rav3n_pl GAB v2.0.5 100mill
  • Rav3n_pl m GAB v2.0.5
  • Rav3n_pl GABm v2.0.5
  • Rav3n_pl GAB v2.0.5 - 1000
  • Rav3n_pl GAB v2.0.5 (Energy Seeking)
  • Rav3n_pl GAB v2.0.6 decompress
  • Rav3n_pl GAB v2.0.7
  • Rav3n_pl GAB v2.0.6 for filters
  • Rav3n_pl GAB v2.0.6 - edit
  • Rav3n_pl GAB v2.0.6
  • Rav3n_pl GAB v2.0.6 no fuze
  • Rav3n_pl GAB v2.0.6edited
  • Rav3n_pl GAB v2.0.6 edited
  • Rav3n_pl GAB v2.0.6 bett
  • Rav3n_pl GAB v2.0.6 for 739
  • Rav3n_pl GAB v2.0.6 746
  • Rav3n_pl GAB v2.0.6 Exploration
  • Rav GAB v2.0.6 Explore Gentle LowCI
  • Rav3n_pl GAB v2.0.5 filter
  • Rav3n_pl GAB v2.0.6
  • Rav3n_pl GAB v2.0.5adjCI
  • Rav3n_pl GAB v2.2 filter
  • Rav3n_pl GAB v2.0.7
  • Rav3n_pl GAB v2.0.7
  • Rav3n_pl GAB v2.0.6 ci0.2
  • Rav3n_pl GAB v2.0.6 (COPY)
• Created on: February 02, 2013 at 13:40 PM UTC
• Updated on: February 02, 2013 at 13:40 PM UTC
• Description:

  GAB in v2 LUA, now banding to 1st atom of sidechain.

Code

--[[
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

]]--

-- options:
energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
pullCI = 0.3 --Clash Impotrance during pull
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
useLigand = false --use ligand if true
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 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= 100, --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
minChng = 3, -- minimum change of band len accordig to current distance
maxUp = 6.1, -- maximum chnage up (push)
maxDn = 6.9, -- maximum change down (pull)
minSkip = 5, --minimum segment distance
minDist = 4, --minimum spatial distance
minLen = 2, --minimum lenght of created band
}

DoNotUse={--just comment lines below or add more areas to avoid
--{segCnt,segCnt}, --ligand cant be used
--{120,134},
--{1,50},
}
AlwaysUse={ --areas should be always used
--{segCnt,segCnt},--ligand need to be at one end
--{308,311}, --loopy
--{1,50}, --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
}
checkBoth=false --check both ends to above, if false only one end need to be true

--end of options

segCnt=structure.GetCount()
if useLigand==false then
    while structure.GetSecondaryStructure(segCnt)=="M" do segCnt=segCnt-1 end
end
p=print
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 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
p("Seed is: "..seed)
math.randomseed(seed)

function Wiggle(how, iters, minppi)
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end
    
    if iters>0 then
        iters=iters-1
        sp=Score()
        if how == "s" then 
                if mutateAlwas==true then structure.MutateSidechainsSelected(1) 
                                    else structure.ShakeSidechainsSelected(1) 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
end

function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        if g>0.01 then p("Gained another "..round(g).." pts.") end
        bestScore=Score()
        save.Quicksave(3)
    end
end
function SaveRB()
	local rb=0
	if energy==true then
        rb= recentbest.GetEnergyScore()
    else
        rb= recentbest.GetScore()
    end
	if rb>bestScore then
		save.Quicksave(4)
		recentbest.Restore()
		SaveBest()
		save.Quickload(4)
	end
end

function Qstab()
    selection.SelectAll()
    CI(0.1)
    if mutateOnce==true then
		CI(mutateOnceCI)
        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 n2==nil and n1==nil then
        return math.random() --float
    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
        local s2=random(segCnt)
        if s1>s2 then s1,s2=s2,s1 end --swap
        if #UseSegments>0 or CanBeUsed(s1,s2) then
            local str=random(bands.minStr,bands.maxStr)
            local len=0
            while true do --randomize corect distance
                len=random(-bands.maxDn,bands.maxUp)
                if len<-bands.minChng or len>bands.minChng then break end
            end
            b={s1,s2,str,len}
            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 CanBeUsed(sg1,sg2) --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
    function AreGood(s1,s2) --check that s1 and s2 can be used
        local ok=true
        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 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()
        local crt=critters[i] --critter
        local s=Score() --start score
        local bnds=crt.bands
        for b=1,#bnds do
            local bnd=bnds[b]
            local a1=5
            local a2=5
            if bnd[1]== structure.GetCount() then a1=6 end
            if bnd[2]== structure.GetCount() then a1=6 end
            if structure.GetAminoAcid(bnd[1])=='g' then a1=0 end
            if structure.GetAminoAcid(bnd[2])=='g' then a2=0 end
            band.AddBetweenSegments(bnd[1],bnd[2],a1,a2)
            local bc=band.GetCount()
if bc>0 then
            band.SetStrength(bc,bnd[3])
            local len=structure.GetDistance(bnd[1],bnd[2])+bnd[4]
            if len<bands.minLen then len=bands.minLen end
            band.SetGoalLength(bc,len)
end
        end
        selection.SelectAll()
        CI(pullCI)
        recentbest.Save()
        Wiggle("wb",1)
        band.DeleteAll()
        CI(1)
        if math.abs(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 solition (if any)
        band.DeleteAll()
        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 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()
    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
	if #AlwaysUse>0 then
		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
		end
		AlwaysUse={} --added to list, no need to check later
	end
    bestScore=Score()
    critterID=0
    gen=0
    ss=Score()
    save.Quicksave(3)
    recentbest.Save()
    p("Starting Rav3n_pl GAB Start score: "..round(ss))
    critters={}
    FillHerd()
    badGen=0
    while true do --this is (almost) endless script ;]
        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
    end
    p("Final score: "..round(Score()).." Total gain: "..round(Score()-ss))
end

-- main call
GAB()



--end of script

Comments

[Rav3n_pl]

• changed random seed to os.time
• fixed mutable detection
• added setting for CI on mutate once
• changed creation list of usable segments
• changed saving recent best

[Hanto_FZ140E_4G]

Recipe responds well until ' Error in line 405: Bad argument #1 to 'SetStrength' ( band index out of bounds ) ' Haven't got past this point, usually occurs so far in my experience on second generation.

[Hanto_FZ140E_4G]

No worries Rav, got it past the error. Thanks for all the GREAT!!!! recipes you produce.

[Rav3n_pl]

Please send me XML form script log when it will crash again. I need retrace it.

[AsDawnBreaks]

Wrokss well, and fast. I will be top on my list of recipes to use!

[doug.ehlert]

I changed it to use the return value from band.AddBetweenSegments() instead of band.GetCount() after seeing another thread on band.AddBetweenSegments() and that seemed to have fixed the problem.

[Jobriq]

Sometimes it will create a fresh new herd after 4 generations even if there was improvement in the score. I don't know if the previous issue mentioned could possibly cause this.

[Jobriq]

I think it may happens if there is no improvement specifically on the 4th generation rather than over all 4 generations.

[Jean-Bob]

nope that's always, because of an error on line 541

if genScore<=Score()

should in fact be the reverse, ie:

if genScore>=Score() 

[Rav3n_pl]

• changed min bands to 3
• bugfix preventing from script crash if band is not created