Recipe: Tvdl VoidCrushers 4.2.2

created by Bruno Kestemont

Profile

• Name: Tvdl VoidCrushers 4.2.2
• ID: 103171
• Shared with: Public
• Parent: Tvdl VoidCrushers 4.1.5
• Children: None
• Created on: May 10, 2021 at 18:12 PM UTC
• Updated on: January 06, 2023 at 19:15 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
BK: 4.2 New commands for symmetrics 22/10/2019
BK: 4.2.1 bands to only one sym is enough (3 times faster than previous version)
BK: 4.2.2 disabling filters during wiggle and during distances


]]--

Version="4.2.2"
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
SYMMETRIC= 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 ')
SymCount=structure.GetSymCount() -- new 22/10/2019
if SymCount>0 then SYMMETRIC = true end


CIfactor=1
filters= false -- disabling filters during wiggle

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 filters then filter.DisableAll()	end--Disables all filters
    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
	if filters then filter.EnableAll()	end--Enables all filters
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
distancessym={} -- a list of distances to symmetric chains
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 getDistSym() -- 1 dim for speed
	if not SYMMETRIC then return end
	local iBand= 0
	local s = 1 -- distance to first sym is enough for all
    if #distancessym<1 or distScore ~= Score() then
        distScore=Score()

        print("Calculating distances to symmetrics... be patient it's very SLOW !")

			distancessym[1]=0
			for i=1,segCnt do --filling table for syms
				for j=i+1,segCnt do --not counting from beginning - no need :)
					iBand=band.AddBetweenSegments(i,j,0,0, s) -- adding a band to symmetrics for measuring distance
					-- (integer segmentIndex1, integer segmentIndex2, [integer atomIndex1], [integer atomIndex2], [integer symnr2])
					distancessym[s*i*segCnt+j]=band.GetLength(iBand)
					band.Delete(iBand)
				end
		end
        print("Done")
    end
end

function distsym(a,b, s) -- reverse becaus we didnt calculate all backward distances for economy
    if a==b then return 0 end
    if a>b then a,b=b,a end
    return distancessym[s*a*segCnt+b]
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 not DIST2USERBANDS then return end
    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
				for j=1,ExistingBands do
					distancesb[i*segCnt+j]=dist2band(i,j)
				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
		if not DIST2USERBANDS then return end
	targetList={} -- reset list of segments and endpoints
    for first = 1,segCnt do
        targetList[#targetList + 1] = {"s",i}
    end

		for i = 1,ExistingBands do
			targetList[#targetList + 1] = {"b",i}
		end
end

function mkBand(a) --make band if found void in area of that segment
    print("Banding segment "..a)
	if filters then filter.DisableAll()	end--Disables all filters
    getDist() -- distances between all segments
	getDist2Band() -- distances between all end band and all segs
	getDistSym() -- distances with symmetrics
    local t={}--there we store possible voids between segments of the monomer
	local ts={}--there we store possible voids between symmetrics (end of band)
	local tssym={}--there we store possible voids between symmetrics
    local first=1
	local voidsym= false
    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 of monomer
      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 SYMMETRIC then -- case with symmetrics, only banding from monomer to a segment from symmetrics
		local s=1 -- no need to band all symetrics, the effetc is the same with only one
			for b=first,segCnt do --test all segments
			  if useRegionBool[a] or useRegionBool[b] then -- case of segments to segments
				local ab=distsym(a,b, s) --distance between segment a and symmetric b
				voidsym=false -- voids between symmetrics
				if ab>minLength and ab < maxLength and math.abs(a-b) >= minDist then --no void if less
					--print(a," ",b," ",ab)
					local void=true -- temp
					for c=1,segCnt do --searching that is any segment between them
						local ac=distsym(a,c, s)
						local bc=distsym(b,c, s)
						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
							tssym[#tssym+1]={a,b, s}
							voidsym=true
							
							print("DEBUG "..tssym[b][1])
							print("DEBUG "..tssym[b][2])
							print("DEBUG "..tssym[b][3])
							
					end
				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 + #tssym
		print("Found "..tt.." possible bands across voids")
	else
		print("No voids found")
	end

    if voids then
        print("Testing "..#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)
			-- (integer segmentIndex1, integer segmentIndex2, [integer atomIndex1], [integer atomIndex2], [integer symnr2])
			
			
            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("Testing "..#ts.." possible bands across voidsb(seg to end of user bands)")
        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
	
    if voidsym then
        print("Testing "..#tssym.." possible bands across symmetrics (seg to first symmetric chain)")
		-- print("Some fake voids are possible if")
		local k=1 -- always 1, we only can band to monomer
			for i=1,#tssym do
				local s=tssym[i][1]
				local e=tssym[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, k)
				-- (integer segmentIndex1, integer segmentIndex2, [integer atomIndex1], [integer atomIndex2], [integer symnr2])
				
				
				local d=distsym(s,e, k)
				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 filters then filter.EnableAll()	end--Enables all filters
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={}
	if filters then filter.DisableAll()	end--Disables all filters
    getDist() --calculate distances now
	getDist2Band() -- calculate distances of all segs with ends of all existing bands
	getDistSym() -- distances with symmetrics
	if filters then filter.EnableAll()	end--Disables all filters
	
    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 SYMMETRIC then 
		ask.SYMMETRIC=dialog.AddCheckbox("Band to symmetric (SLOW !)",SYMMETRIC)
	end
	if DIST2USERBANDS then
		ask.DIST2USERBANDS=dialog.AddCheckbox("Band to end of user bands",DIST2USERBANDS)
	end
    
	ask.mutateOnce = dialog.AddCheckbox("Mutate once",false)
	ask.filters = dialog.AddCheckbox("No filter during wiggle",false)
	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 SYMMETRIC then 
			SYMMETRIC=ask.SYMMETRIC.value
		end
		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
   filters=ask.filters.value
   mutateOnce=ask.mutateOnce.value
		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
		if mutateOnce then structure.MutateSidechainsSelected(1) 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]

Band to symmetric even without user band (it extremely slow at start, but then it's ok)

4.2.1: calculating distances is quicker now

4.2.2: mutate, wiggle no filter (Note: band to symmetric still bugs)