Recipe: Tvdl VoidCrushers 4.1.5

created by Bruno Kestemont

Profile

• Name: Tvdl VoidCrushers 4.1.5
• ID: 101510
• Shared with: Public
• Parent: Tvdl VoidCrushers 3.1.2
• Children:
  • Tvdl VoidCrushers 4.2.2
• Created on: April 18, 2019 at 21:43 PM UTC
• Updated on: April 18, 2019 at 21:43 PM UTC
• Description:

  Wiggle Factor added, NC adapted, hiding hydrophobes, voids to user end bands (band to symmetrics)

Code

--[[
Voids Killer by rav3n_pl
script is searching for possible banding across voids.
Because we not have any voids detection in Lua, I do some math to find them
Not always perfect, but mostly works :)

Tvdl: 09-01-2012
Added extra option to pull all the bands in one go,
pulls harder, if wanted, on hydro's
Works also as a stabilizer (like Hydrophobic script)
Compacts the protein
Warning: when used all at once will accept a loss
If so the previous score is in slot 3

Tvdl: 12-07-2012
- Made totally V2

MDC: 2-19-2014
Added Wiggle Factor 

BK: 2-22-*-2014
restore recursive wiggle

BK: 3.03 infinite run

BK: 3.04 change options on each loop

BK: 3.05 added set notes

BK: 3.1.0 atoms on hydrophobic pull & more hydrophobics

BK: 3.1.1 fixed main loop

BK: 3.1.2 fixed delete bands

BK: 4.0.0 added bands to existing bands (for symmetric): if the user previously add bands to symmetrics,
the recipe will be able to add bands to symmetrics and detect voids between the 2 monomers

BK: 4.1.0 optional band to existing bands (TO DO:  recognizes sym puzzles)
	WARNING: end point is only in one direction. If you want the 2 end points, you have to add a reverse band
	(this is only possible for bands to main monomer)
BK: 4.1.1 added a log to recall scores on each steps (jeff101's display)
BK: 4.1.2 SemiRandomStr added (slightly randomizes band strength on pull all)
BK: 4.1.3 added CI function, deleted abs in wiggle, for debugging
BK: 4.1.4 smaller band length when banded to end of sidechains
BK: 4.1.5 fixed a bug on end band line 550

]]--

Version="4.1.5"
recipename="Void Crusher  "..Version


-- Handy shorts module
normal= (current.GetExplorationMultiplier() == 0)
--CI=behavior.SetClashImportance
segCnt=structure.GetCount()
segCnt2=segCnt
while structure.GetSecondaryStructure(segCnt2)=="M" do segCnt2=segCnt2-1 end
DIST2USERBANDS= false

ExistingBands=band.GetCount()
if ExistingBands >0 then DIST2USERBANDS = true end
print("Starting "..recipename.. " on\n   puzzle "..(puzzle.GetName()))
print('   with puzzle ID '..(puzzle.GetPuzzleID())..' and '..ExistingBands..' user-supplied bands.\n ')

CIfactor=1

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

-- Score functions
function Score()
    if normal==nil or normal==true then
        -- FIX for big negatives
        local total= current.GetEnergyScore()

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

        return total
    else
        return current.GetScore()
    end
end

function SegScore()
    local total=8000
    for i=1,segCnt2 do
        total=total+current.GetSegmentEnergyScore(i)
    end
    return total
end

function RBScore()
    if normal then
        return recentbest.GetEnergyScore()
    else
        return recentbest.GetScore()
    end
end

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


--START SET NOTES BY PD
--[[ Set note with author, recipe and big steps -- By Pauldunn
module to paste it in existing recipe, by BK
]]-- 


--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 mach "recipename" with the recipename of the recipe

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

--2) PASTE somewhere to the beginning of your recipe.

--3a) COPY from here ---------------

--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 --------------

--4) PASTE at the end of the main loop function of your recipe, at the end of the cleanup function, at the end of the recipe
--better loop_count a global variable

--END SET NOTES BY PD

bestScore=Score()
function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        if g>0.01 then print("Gained another "..round3(g).." pts.") end
        bestScore=Score()
        SetNote(note_number, starting_score, recipename, loop_count)
        save.Quicksave(3)
    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) -- 22/02/2014 reset recursive wiggle
    --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=0.1 end
    if onlyselected==nil then onlyselected=false end
    local wf=1
    if maxCI then wf=WF end

--print("Wiggle FactorA= ",WF)

    if iters>0 then
        --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(1)
                return
            elseif how == "wb" then structure.WiggleSelected(2*wf*iters,true,false)
            elseif how == "ws" then structure.WiggleSelected(2*wf*iters,false,true)
            elseif how == "wa" then structure.WiggleSelected(2*wf*iters,true,true)
            end
        else
            if how == "s" then
                -- Shake is not considered to do much in second or more rounds
                structure.ShakeSidechainsAll(1)
                return
            elseif how == "wb" then structure.WiggleAll(2*wf*iters,true,false)
            elseif how == "ws" then structure.WiggleAll(2*wf*iters,false,true)
            elseif how == "wa" then structure.WiggleAll(2*wf*iters,true,true)
            end
        end
        if Score()-sp > minppi then return Wiggle(how, iters, minppi,onlyselected) end
		iters=iters-1 -- 22/02/2014
    end
end

-- end of handy shorts module

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

function FuzeEnd()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    if RBScore()> Score() then recentbest.Restore() end
    SaveBest()
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 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)
    local scr=Score()

    recentbest.Save()
    Fuze1(0.3,0.6) FuzeEnd()
    scr=reFuze(scr,slot)
    Fuze2(0.3,1)
    if RBScore()>Score() then recentbest.Restore() end
    SaveBest()
    scr=reFuze(scr,slot)
    Fuze1(0.05,1)
    if RBScore()>Score() then recentbest.Restore() end
    SaveBest()
    scr=reFuze(scr,slot)
    Fuze2(0.7,0.5) FuzeEnd()
    scr=reFuze(scr,slot)
    Fuze1(0.07,1)
    if RBScore()>Score() then recentbest.Restore() end
    SaveBest()
    reFuze(scr,slot)
    if RBScore()>Score() then recentbest.Restore() end
    SaveBest()
end
-- end standard Fuze module

-- Distance lib
--
distances={} -- a list of distances between segments only
distancesb={} -- a list of distances between segments and end bands
distScore=Score()
function getDist() -- 1 dim for speed
    if #distances<1 or distScore ~= Score() then
        distScore=Score()
        distances[1]=0
        print("Calculating distances...")
        for i=1,segCnt do --filling table
            for j=i+1,segCnt do --not counting from beginning - no need :)
                distances[i*segCnt+j]=structure.GetDistance(i,j)
            end
        end
        print("Done")
    end
end

function dist(a,b)
    if a==b then return 0 end
    if a>b then a,b=b,a end
    return distances[a*segCnt+b]
end

function getDist2Band() -- 1 dim for speed
    if #distancesb<1 or distScore ~= Score() then
        distScore=Score()
        distancesb[1]=0
        print("Calculating distances to end bands...")
        for i=1,segCnt do --filling table
			if DIST2USERBANDS then -- New 15/12/2015
				for j=1,ExistingBands do
					distancesb[i*segCnt+j]=dist2band(i,j)
				end
			end
        end
        print("Done")
    end
end

function distSeg2band(a,b)
    if b==0 then return 0 end
    return distancesb[a*segCnt+b]
end

function dist2band(s,b) -- distance between a segment and a band end point VERY SLOW !!
	local iBand= 0
	iBand = band.AddToBandEndpoint(s, b)
	local distance=band.GetLength(iBand)
	band.Delete(iBand)
	return distance
end

-- Safe band module
--ExistingBands=band.GetCount()
--if ExistingBands >0 then DIST2USERBANDS = true end


function disableExistingBands()
    for i=1,ExistingBands do band.Disable(i) end
end

function enableExistingBands()
    for i=1,ExistingBands do band.Enable(i) end
end

function bandDisableAll()
    for i=ExistingBands+1,band.GetCount() do band.Disable(i) end
end

function bandEnableAll()
    for i=ExistingBands+1,band.GetCount() do band.Enable(i) end
end

function bandDeleteAll()
    for i=ExistingBands+1,band.GetCount() do band.Delete(ExistingBands+1) end
end

function bandSetStrengthAll(str) -- randomized
	if SemiRandomStr then
		local minBS2, maxBS2=minBS, maxBS
		if str-minBS > maxBS-str then minBS2= 2*str - maxBS else maxBS2= 2* str - minBS end
		local strbase=str
		for i=ExistingBands+1,band.GetCount() do
			strbase= random2numbers(minBS2,maxBS2)
			band.SetStrength(i,strbase)
		end
	else
		for i=ExistingBands+1,band.GetCount() do band.SetStrength(i,str) end
	end
end

function bandGetCount()
    return band.GetCount()-ExistingBands
end
-- end safe band module
function down(x)
    return x-x%1
end

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

function qStab()
    CI(0.1)
    Wiggle("s",1)
    if fastQstab==false then
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
    end
    CI(1)
    Wiggle()
end

math.randomseed(Score())
math.random(100) -- Because first random is not random

function random2numbers(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 Sort(tab,items)
    for x=1,items do
        for y=x+1,#tab do
            if tab[x][2]>tab[y][2] then
                tab[x],tab[y]=tab[y],tab[x]
            end
        end
    end
    return tab
end

function BuildTargetList(first) -- to segments or end points of user bands
	targetList={} -- reset list of segments and endpoints
    for first = 1,segCnt do
        targetList[#targetList + 1] = {"s",i}
    end
	if DIST2USERBANDS then -- New 15/12/2015
		for i = 1,ExistingBands do
			targetList[#targetList + 1] = {"b",i}
		end
	end
end

function mkBand(a) --make band if found void in area of that segment
    print("Banding segment "..a)
    getDist() -- distances between all segments
	getDist2Band() -- distances between all end band and all segs
    local t={}--there we store possible segments
	local ts={}--there we store possible voids between symmetrics
    local first=1
    if allatonce then first=a+2 end
    if first > segCnt then return false end
	--BuildTargetList(first)-- to segments or end points of user bands
    for b=first,segCnt do --test all segments
      if useRegionBool[a] or useRegionBool[b] then -- case of segments to segments
        local ab=dist(a,b) --distance between segments
		voids=false -- voids between segments
        if ab>minLength and ab < maxLength and math.abs(a-b) >= minDist then --no void if less
            --print(a," ",b," ",ab)
            local void=true
            for c=1,segCnt do --searching that is any segment between them
                local ac=dist(a,c)
                local bc=dist(b,c)
                if ac~=0 and bc~=0 and ac<ab and bc<ab and ac>4 and bc>4 then
                    if ac+bc<ab+1.5
                        then void=false break --no void there for sure
                    end
                end
            end
            if void==true and (not allatonce or a<b) then
                    t[#t+1]={a,b}
					voids=true
            end
        end
      end
	end
	if DIST2USERBANDS then -- New 15/12/2015
		for b= 1, ExistingBands do
		  if useRegionBool[a] and b>0 then -- case of symmetric, bands to end user bands
			local ab=distSeg2band(a,b)
			voidss=false -- voids between segs and bands (monomers in symmetric)
			if ab>minLength and ab < maxLength then
			local voidb=true
				for c=1,segCnt do --searching that is any segment between them
					local ac=dist(a,c)
					local bc=distSeg2band(c,b)
					if ac~=0 and bc~=0 and ac<ab and bc<ab and ac>4 and bc>4 then
						if ac+bc<ab+1.5
							then voidb=false break --no void there for sure
						end
					end
				end
				if voidb then
					ts[#ts+1]={a,b}
					voidss=true
				end
			end
		  end
    end
	end
	
	if voids or voidss then
		local tt= #t + #ts
		print("Found "..tt.." possible bands across voids")
	else
		print("No voids found")
	end

    if voids then
        --print("Found "..#t.." possible bands across voids (seg to seg)")
        for i=1,#t do
            local s=t[i][1]
            local e=t[i][2]
			local atoms=0
			local atome=0

			if OrangeInside or OrangeSidechain then
				if structure.IsHydrophobic(s) and structure.GetAtomCount(s)>0 then
					atoms=1
					if OrangeSidechain then atoms=structure.GetAtomCount(s) end
				end
				if structure.IsHydrophobic(e) and structure.GetAtomCount(e)>0 then
					atome=1
					if OrangeSidechain then atome=structure.GetAtomCount(e) end
				end
			end
			band.AddBetweenSegments(s,e,atoms,atome)
            local d=dist(s,e)
            d=d-compFrac - (atome+ atoms -2)-- compFrac= 3, distance between atoms of sidechains is more or less 1
            if d<2 then d=2 end -- was 3 but for sidechains, bonds are <3
            if d>20 then d=20 end
            local bnr=band.GetCount()
            band.SetGoalLength(bnr,d)
            if allatonce then
                if structure.IsHydrophobic(s) or structure.IsHydrophobic(e) then band.SetStrength(bnr,pullextrahydro*allBS)
                 else band.SetStrength(bnr,allBS) end
            end
        end
	end
	
	if voidss then -- voids between segs and bands (monomers in symmetric)
		--print("Found "..#ts.." possible bands across voids (seg to end band)")
        for i=1,#ts do
            local s=ts[i][1]
            local b=ts[i][2]
			local atoms=0
			if OrangeInside or OrangeSidechain then -- WARNING: here I favour hydrophillic to end points
			-- because end points (on symmetric) are supposed to be outside of the protein !!! Good for H-Bonds
				if not structure.IsHydrophobic(s) and structure.GetAtomCount(s)>0 then -- not hydrophobic !
					atoms=1
					if OrangeSidechain then atoms=structure.GetAtomCount(s) end
				end
			end
			band.AddToBandEndpoint(s, b, atoms)
            local d=distSeg2band(s,b)
            d=d-compFrac - (atoms -2)-- compFrac= 3, distance between atoms of sidechains is more or less 1, here only one sidechain (end band is on atom 0)
            if d<2 then d=2 end -- was 3 but for sidechains, bonds are <3
            if d>20 then d=20 end
            local bnr=band.GetCount()
            band.SetGoalLength(bnr,d)
            if allatonce then
                if structure.IsHydrophobic(s) then band.SetStrength(bnr,pullextrahydro*allBS)
                 else band.SetStrength(bnr,allBS) end
            end
        end
    end
end

function SaveRB()
    if RBScore() > Score() then
        save.Quicksave(9)
        recentbest.Restore()
        SaveBest()
        save.Quickload(9)
    end
end

function Pull(List) -- List is a list of segments
    disableExistingBands()
    if List==nil then for i=1,segCnt do mkBand(i) end
    else for i=1,#List do mkBand(List[i]) end
    end
    if bandGetCount() >0 then -- it counts new bands only
        CI(pullingCI)
        -- Make an estimation of the required strength
        if lastAllBS > 0 then lastBS=lastAllBS/bandGetCount() end
        if lastBS < minBS then lastBS=minBS end
        if lastBS > maxBS then lastBS=maxBS end
        recentbest.Save()
        local loss=math.abs(down(Score()*maxLoss/100))
        for str=lastBS,maxBS,0.11 do --search enough band strenght to move
            recentbest.Restore()
            ss=Score()
            if not allatonce then bandSetStrengthAll(str) end
            Wiggle("wb",1)
            if ss-Score()>loss then
                lastAllBS=(str-0.1)*bandGetCount()
                break
            end
        end
        bandDeleteAll()
        SaveRB() --because sometimes it missing fractions
        print("Stabilizing...")
        CI(1)
        recentbest.Save() --after pulling
        qStab()
        if bestScore-Score()<doFuze or allatonce then
            SaveBest()
            print("Fuzing....")
            Fuze(4)
            SaveBest()
        end
        if not allatonce then save.Quickload(3) --load best state
		end
        print("Current score: "..round3(Score()).." VC gain: "..round3(Score()-StartScore))
    end
end
loop_count=0
function KillVoids() -- main loops are here
	loop_count=loop_count+1 -- for setnotes
    if allatonce then lastBS=allBS minBS=allBS maxBS=allBS end
    lastBS=minBS
    local s={}

    getDist() --calculate distances now
	getDist2Band() -- calculate distances of all segs with ends of all existing bands

    if #Speclist > 0 then
        for i=1,#Speclist do s[#s+1]={Speclist[i], current.GetSegmentEnergyScore(Speclist[i])} end
    else
        for i=1,segCnt do
            s[#s+1]={i, current.GetSegmentEnergyScore(i)}
        end
    end
    if Vworst==true then
        Sort(s,#s)
    end
    if Vrandom==true then -- not really random, it's always the same !!
        for i=1,#s do
            local r=math.random(#s)
            s[i],s[r]=s[r],s[i]
        end
    end
    if allatonce then Pull()
    else
        local Speclist2={} --Clear list
        for i=1,#s/Combinum do
            print("Loop "..loop..". Kill "..i.." of "..(#s-#s%Combinum)/Combinum.." started.")
            for j=1,Combinum do Speclist2[j]=s[Combinum*i-Combinum+j][1] end
            Pull(Speclist2)
        end
    end

end

-- 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=structure.GetCount() 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,structure.GetCount() do
        result[i]=SegmentInSet(set,i)
    end
    return result
end
--- End of Segment Set module

-- Module Find Segment Types
function FindMutables()
    local result={}
    for i=1,structure.GetCount() do if structure.IsMutable(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindFrozen()
    local result={}
    for i=1,structure.GetCount() do if freeze.IsFrozen(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindLocked()
    local result={}
    for i=1,structure.GetCount() do if structure.IsLocked(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindSelected()
    local result={}
    for i=1,structure.GetCount() do if selection.IsSelected(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindAAtype(aa)
    local result={}
    for i=1,structure.GetCount() do
        if structure.GetSecondaryStructure(i)== aa then result[#result+1]=i end
    end
    return SegmentListToSet(result)
end
function FindAminotype(at)
    -- This one returns a list not a set
    local result={}
    for i=1,structure.GetCount() do
        if structure.GetAminoAcid(i) == at then result[#result+1]=i end
    end
    return result
end

-- end Module Find Segment Types
-- Module AskSelections
-- 02-05-2012 Timo van der Laan, Free to use for non commercial purposes
function AskForSelections(title,mode)
    local result={{1,structure.GetCount()}} -- 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,structure.GetCount()}} --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","")
    end
    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]>structure.GetCount() 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
    end
  until not Errfound
    return result
end
-- end of module AskSelections

--MAIN is in askMode here
function askMode()
    local ask = dialog.CreateDialog("Voidcrusher "..Version.." Runmode")
    ask.l1=dialog.AddLabel("Run specified number of kills at a time")
    ask.Combi = dialog.AddSlider("Nr of segments: ",Combinum,1,10,0)
    ask.allatonce=dialog.AddCheckbox("Or pull all in one go",allatonce)
    ask.l3=dialog.AddLabel("Or do multiple runs on 1 to 6 segments")
    ask.multi=dialog.AddSlider("Repeat multi",multi,0,20,0)
    ask.l2 = dialog.AddLabel("The choices above also apply if selections are made")
    ask.selected=dialog.AddCheckbox("Set selection where to pull from",false)
    ask.selection=dialog.AddCheckbox("Select segments where 1 bandend must be",false)
	ask.OrangeInside=dialog.AddCheckbox("Hide hydrophobic chains",OrangeInside)
	ask.OrangeSidechain=dialog.AddCheckbox("Band end of sidechains",OrangeSidechain)
	if DIST2USERBANDS then
		ask.DIST2USERBANDS=dialog.AddCheckbox("Band to end of user bands",DIST2USERBANDS)
	end
    ask.l4 = dialog.AddLabel("Modify fine tuning options, depended on mode")
    
ask.WF = dialog.AddSlider("WiggleFactor:",WF,1,5,0)
--print("Wiggle FactorB= ",ask.WF.value)

    ask.modOptions=dialog.AddCheckbox("Modify options",false)
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)


    if dialog.Show(ask) > 0 then
        Combinum=ask.Combi.value
        allatonce=ask.allatonce.value
        multi=ask.multi.value
		OrangeInside=ask.OrangeInside.value
		OrangeSidechain=ask.OrangeSidechain.value
		if DIST2USERBANDS then -- possibility to disable in case of non symmetric but wanted keeping bands
			DIST2USERBANDS=ask.DIST2USERBANDS.value
		end
  WF=ask.WF.value
  -- print("Wiggle FactorC= ",ask.WF.value)

        if ask.selected.value then
            local SelMode={}
            SelMode.askligands=true --override the defaults
            SelMode.defligands=true
            SelMode.defignorelocks=false
            SelMode.defignorefrozen=false
            local PullFrom=AskForSelections("Set where to pull from",SelMode)
            for i=1,segCnt do
                if SegmentInSet(PullFrom,i) then Speclist[#Speclist+1]=i end
            end
        end
        if ask.selection.value then
            local SelMode={}
            SelMode.askligands=true --override the defaults
            SelMode.defligands=true
            SelMode.askignorelocks=false
            SelMode.defignorelocks=true
            SelMode.defignorefrozen=false
            useRegion=AskForSelections("At least one bandend must be",SelMode)
        else
            useRegion={{1,segCnt}}
            useRegion=SegmentSetMinus(useRegion,FindLocked())
        end
        useRegionBool=SegmentSetToBool(useRegion)
        if ask.modOptions.value then
            AskOptions()
        end
        
		MAIN()
    end
end

function ChangeOptions()
	print("Changing all options:")
	if minDist==1 then minDist=15 else minDist= minDist-1 end--minimum segment distance
	if minLength==2 then minLength= 10 else minLength=minLength-1 end --minimum spatial distance
	maxLength=50 --maximum spatial distance
	fastQstab = not fastQstab --1s1w then true, double if false
	if compFrac==1 then compFrac= 3 else compFrac=compFrac-1 end --how much shorter band should be

-- Defaults here VVV
	Vworst=not Vworst --start form worst scoring one
	Vrandom=not Vrandom --true --go it in random order
-- if both are false then it will band form 1st to last

	if multi==0 then multi=1 else multi=0 end-- Multirun overrides all other options
	if Combinum==10 then Combinum=1 else Combinum=1+1 end-- Nr of segments to be treated in 1 go
	if doFuze==-5 then doFuze=5 else doFuze= doFuze-1 end --run fuzes when close to saved best (negative - run if gain after qstab)
	if pullingCI<=0.1 then pullingCI=0.90 else pullingCI=pullingCI-0.1 end--clash importance during pull
	Speclist={}
	minBS=0.12 --absolute minimum band strength
	if maxBS==5 then maxBS=1 else maxBS=maxBS+1 end--absolute maximum band strength
	if maxLoss==5 then maxLoss=1 else maxLoss=maxLoss+1 end --pull till perc loss (ie 1 on 10`000 ptsy = pull till 100 pt loss after pull)

-- New options
	allatonce=not allatonce --false -- set to true if all at once
	pullextrahydro=1.1 --multiplier for extra pull on hydro segments
	allBS=0.12 -- strength if all
	lastAllBS=0
	lastBS=minBS
	OrangeInside= not OrangeInside
	OrangeSidechain= not OrangeSidechain
	SemiRandomStr = not SemiRandomStr

	PrintOptions()
end

function AskOptions() -- fine tuning
    local ask = dialog.CreateDialog("Finetune options Voidcrusher "..Version)
    if not allatonce or #Speclist > 0 then
        ask.l1=dialog.AddLabel("Band strength during pull")
        ask.BandsAbsMin=dialog.AddSlider("Minimum",minBS,0.1,1,2)
        ask.BandsAbsMax=dialog.AddSlider("Maximum",maxBS,0.1,2,2)
		ask.SemiRandomStr=dialog.AddCheckbox("and semi-random",SemiRandomStr)
    end
    if not allatonce then
        ask.l2=dialog.AddLabel("Order of treatement")
        ask.random=dialog.AddCheckbox("Random",Vrandom)
        ask.worst=dialog.AddCheckbox("Worst first",Vworst)
        ask.l3=dialog.AddLabel("Pull harder if loss is less")
        ask.maxLoss=dialog.AddSlider("Percentage",maxLoss,0,2,1)
        ask.l4 = dialog.AddLabel("Run fuze if qstab is close to recent best")
        ask.doFuze = dialog.AddSlider("Neg, only after gain",doFuze,-10,20,1)
    else
        ask.l11=dialog.AddLabel("Band strength to pull with")
        ask.allBS = dialog.AddSlider("Band strength",allBS,0.1,1,2)
        ask.l21 = dialog.AddLabel("Multiplier to pull hydrophobics more")
        ask.hydro = dialog.AddSlider("Phobic factor: ",pullextrahydro,0.5,3,1)
    end
    ask.lx1= dialog.AddLabel("Maximum band length")
    ask.maxLength=dialog.AddSlider("maxLength",maxLength,15,100,1)
    ask.l5 = dialog.AddLabel("Clash importance while pulling")
    ask.CI = dialog.AddSlider("Clash importance",pullingCI,0.3,1,2)
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
        if not allatonce or #Speclist > 0 then
            minBS=ask.BandsAbsMin.value
            maxBS=ask.BandsAbsMax.value
			SemiRandomStr=ask.SemiRandomStr.value
        end
        if not allatonce then
            maxLoss=ask.maxLoss.value
            Vrandom=ask.random.value
            Vworst=ask.worst.value
            doFuze=ask.doFuze.value
        else
            allBS=ask.allBS.value
            pullextrahydro=ask.hydro.value
        end
        maxLength=ask.maxLength.value
        pullingCI=ask.CI.value
    end
end

function PrintOptions()
	print("Options: ")
	print("minimum segment distance: "..minDist) --minimum segment distance
	print("minimum spatial distance: "..minLength) --minimum spatial distance
	print("maximum spatial distance: "..maxLength) --maximum spatial distance
	if fastQstab then print("fastQstab") end --1s1w then true, double if false
	print("Band should be "..compFrac.." Amstr. shorter") --how much shorter band should be

-- Defaults here VVV
	if Vworst then print("start from worst scoring one") end
	if Vrandom then print("go it in random order") end
-- if both are false then it will band form 1st to last
	if not Vworst and not Vrandom then print("band form 1st to last") end

	if multi==0 then print("Multirun (overrides all other options)") end
	print("Nr of segments to be treated in 1 go: "..Combinum)-- Nr of segments to be treated in 1 go
	print("Fuze when distance to Best < "..doFuze) -- (negative - run if gain after qstab)
	print("Pulling CI= "..pullingCI) --clash importance during pull

	print("Min band strength= "..minBS) --absolute minimum band strength
	print("Maximum band strength ="..maxBS) --absolute maximum band strength
	if SemiRandomStr then print ("Semi-random strength") end
	print("pull till loss < max "..maxLoss.." %") --pull till perc loss (ie 1 on 10`000 ptsy = pull till 100 pt loss after pull)

-- New options
	if allatonce then print("all at once") end--false -- set to true if all at once
	print("multiplier for extra pull on hydro segments: "..pullextrahydro)
	if OrangeInside then print ("Hide hydrophobic chains") end
	if OrangeSidechain then print ("Band end of sidechains") end
end

loop=0
	
function MAIN() -- called by askMode() just above
					--thus dialog with user is already done just before
	StartScore=Score()
    save.Quicksave(3)
	print("Starting Void Crusher "..Version.." by BK, Tvdl and rav3n_pl")
    print("Start score: "..round3(StartScore))
    
    PrintOptions()
	ssstr=(round(Score()))
	
	for step=1, 10000 do
		loop= loop+1
		local sls= Score()
		local les=sls
		print("##########################")
		print("MAIN LOOP "..loop.."/10000")
        genScore=les
        gen= step
        print("")
		print("Generation: "..gen..", score: "..round(Score())..", gain: "..round(Score()-StartScore).." ("..(os.date())..")")		
			if multi > 0 then
				allatonce=false
				for i=1,multi do
					for j=1,6 do
						Combinum=j
						KillVoids()
					end
				end
			else KillVoids()
			end
		les=Score()
		print("Loop "..loop.." gained "..round3(les-sls))
        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))
        else
            ssstr=(ssstr..' - '..(-round(genGain)))
        end
        print(ssstr..' = '..round(genEndScore))
		print("Total VC gain= "..round3(les-StartScore).." from "..round3(StartScore).." to "..round3(Score()))
		ChangeOptions()
	end
end
		
--- OPTIONS THERE! vvv

useRegion={}
useRegionBool={}
minDist=15 --minimum segment distance
minLength=10 --minimum spatial distance
maxLength=50 --maximum spatial distance
fastQstab = true --1s1w then true, double if false
compFrac=3 --how much shorter band should be (in Amstroms)

-- Defaults here VVV
Vworst=false --start form worst scoring one
Vrandom=true --true --go it in random order
-- if both are false then it will band form 1st to last

multi=0 -- Multirun overrides all other options
Combinum=1 -- Nr of segments to be treated in 1 go
doFuze=5 --run fuzes when close to saved best (negative - run if gain after qstab)
pullingCI=0.90 --clash importance during pull
Speclist={}
minBS=0.12 --absolute minimum band strength
maxBS=1 --absolute maximum band strength
maxLoss=1 --pull till perc loss (ie 1 on 10`000 ptsy = pull till 100 pt loss after pull)

-- New options
allatonce=false --false -- set to true if all at once
pullextrahydro=1.3 --multiplier strength extra pull on hydrophobic segments
allBS=0.12 -- strength if all
lastAllBS=0
lastBS=minBS

SemiRandomStr= false
OrangeInside= true -- band to hydrophobic sidechains to pull (could help to turn)
OrangeSidechain=false

targetList={} -- list of segments and endpoints, to be built later

--END OF OPTIONS ^^^

function Cleanup(err)
    print("Resetting CI and best score, removing extra bands")
    save.Quickload(3)
    CI(1)
	if bandGetCount() >0 then
		bandDeleteAll()
	end
    SetNote(note_number, starting_score, recipename, loop_count)
    print(err)
end

xpcall(askMode,Cleanup)

Comments

[Bruno Kestemont]

Tvdl: 12-07-2012 - Made totally V2

MDC: 2-19-2014 Added Wiggle Factor

BK: 2-22-*-2014 restore recursive wiggle

BK: 3.03 infinite run

BK: 3.04 change options on each loop

BK: 3.05 added set notes

BK: 3.1.0 atoms on hydrophobic pull & more hydrophobics

BK: 3.1.1 fixed main loop

BK: 3.1.2 fixed delete bands

BK: 4.0.0 added bands to existing bands (for symmetric): if the user previously add bands to symmetrics,
the recipe will be able to add bands to symmetrics and detect voids between the 2 monomers

BK: 4.1.0 optional band to existing bands
WARNING: end point is only in one direction. If you want the 2 end points, you have to add a reverse band
(this is only possible for bands to main monomer)

BK: 4.1.1 added a log to recall scores on each steps (jeff101's display)

[Bruno Kestemont]

Added semi-ransom option for band strength

[heyubob]

I don't understand how you made this recipe, and I would not understand if you told me. However, it is AWESOME. 5 stars to you. BTW:I gave you a five and page reports a 4!

[Bruno Kestemont]

oops, fixed a problem in fuze (CI was lacking)

[Bruno Kestemont]

Smaller bands to end of sidechains.

[Bruno Kestemont]

Bug line 500 fixed

[malphis]

Hi Bruno, thanks for all the helpful scripts!

I noticed that parts of this script run much more quickly when objectives are disabled. Is it possible that toggling objectives at key points in the script might improve the overall speed without losing effectiveness? If so, it would really help on larger proteins with objectives.

[malphis]

Oh, sorry. I forgot to ask whether or not adding mutate at potentially helpful spots would be possible too as an option.

[Bruno Kestemont]

I probably will implement them in further versions