Recipe: Rav3n_pl GAB v2.2 filter

created by Rav3n_pl

Profile

• Name: Rav3n_pl GAB v2.2 filter
• ID: 100581
• Shared with: Public
• Parent: Rav3n_pl GAB v2.0.6
• Children:
  • Rav3n_pl GAB v2.3
  • Rav3n_pl GAB
• Created on: January 13, 2015 at 20:18 PM UTC
• Updated on: January 13, 2015 at 20:18 PM UTC
• Description:

  Genetic Algorithm on Bands. Using bands on 1st atom of sidechain. For filter puzzles

Code

--[[
GAB - Genetic Algorithm 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 assigning them to critters

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:
filters=true --if true filters are enabled only for scoring

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 CI used by script
CapCI=false --false=use maxci as multiplier, true=just cap it to maxci

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 mutate(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 generations w/o improvement
}
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. Bastards 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 according to current distance
maxUp = 6.1, -- maximum change up (push)
maxDn = 6.9, -- maximum 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
{
--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

function filtersOn()
    if filters then
        behavior.SetSlowFiltersDisabled(false)
    end
end
function filtersOff()
    if filters then
        behavior.SetSlowFiltersDisabled(true)
    end
end

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
        if CapCI==true then
            c=maxCI
        else
            c=c*maxCI
        end
    end
    behavior.SetClashImportance(c)
end
function round(x)--cut all after 3-rd place
    return x-x%0.001
end
function down(x)
    return x-x%1
end

function Score()--return score, exploration too
    filtersOn()
    local s=0
    if energy then
        s=current.GetEnergyScore()
    else
        s=current.GetScore()
    end
    filtersOff()
    return s
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
    filtersOn()
    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
    filtersOff()
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()
    filtersOn()
    recentbest.Save()
    filtersOff()
    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() --create 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 correct 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()
            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
        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 solution (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))
    filtersOff()
    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
    filtersOn()
    p("Final score: "..round(Score()).." Total gain: "..round(Score()-ss))
end

-- main call

GAB()

--end of script

Comments

[Rav3n_pl]

Added:

• disable slow filters (by default)
• maxCI manipulations

code: https://gist.github.com/Rav3nPL/a5836333e0b4f3d3b5e4