Recipe: DRW A 35

created by karstenw

Profile

• Name: DRW A 35
• ID: 44401
• Shared with: Public
• Parent: DRW C 35
• Children:
  • DRW A 55
• Created on: October 22, 2012 at 13:20 PM UTC
• Updated on: October 22, 2012 at 13:20 PM UTC
• Description:

  This DRW is preset for longest rebuilds first. It will rebuild 10 segments then 9,8,7. It will perform 35 rebuilds on each attempt! When you are not confident that your protein is quite right and it is in it's early stages, run this. Trust me.

Code

--[[
    Based on Tvdl Rav3n_pl Deep Rebuild v3.x
    WARNING!
    1) Script uses save slots 3-10!!!
    2) Best score are always in slot 3

Description:
This is a long run rebuilder. Idea is to rebuild given/found area so many tyimes to found better position.
Each rebuild is scored on 7 different ways and saved if better.
After rebuild finishes script trying to stabilize and fuze each saved position (up to 7).
Because some positions are best in more than 1 way sometimes it is only 2 positions to stabilize.

Changed by: Timo van der Laan 17-12-2011 till 5-8-2012
Overview:

This version of Rav3n_pl DRW has several new features.

First of all it is made totally V2 and uses option dialogs.
It has an optimised fuze and qStab, and will run a lot faster as the original.
The main optimalisation is that futile shakes are skipped. Another one is that unprommissing fuzes can be skipped.

Feature 1.
Can be used in design puzzles, has mutate options for that.

Feature 2.
It will continue with the next segments of the same length if there is a win unless the gain reaches a threshold (default number of segments/4). Else it will continue with the next length or main cycle.

Feature 3.
It will not try to rebuild the exact same segments for a second time unless the gain reaches a threshold (default number of segments)

Feature 4.
It will not try a fuze if the loss is too great depending on the size of the rebuild

Feature 5.
It will not try to rebuild frozen or locked parts

Feature 6.
You can specify where to work on, based on secondary structure and/or selected or non selected parts.

Feature 7.
If you want it can keep disulfide bridges intact (thanks Brow42)

Feature 8.
If the starting score is negative, default is that no wiggles will be done to avoid exploding the protein.

Feature 9.
If stopped, it will reset CI, best score and secondary structures.

Some of the smaller features:
You can skip cycles, handy after a crash. It breaks off rebuild tries if no chance of success. It works on puzzles even if the score is < -1000000 (but will be slower).
Fuze and qStab can be suppressed (default if score is negative from the start)
You can specify to disable bands when rebuilding and enable them afterwards.
And several minor bugfixes.

Version 1.0.1 Fixed Selections, and minor text changes
Version 1.0.2 Added textbox to selections and a printout of what is selected
              and replaced the comment above
Version 1.0.3 Fixed bridgekeeping after fuze
Version 1.0.4 Did some more work on the bridgekeeping feature
Version 1.1.0 Included the BridgeFuze, and rearranged the bridgekeeping
              plus some minor changes
Version 1.1.1 Corrected a minor bug (mutating after a rebuild with a big selection gave problems)
Version 1.1.2 Made CI on mutate settable and also the sphere mutate uses
Version 1.1.3 Auto exploration detection
Version 1.1.4 Fixed Score function for exploration when negative
Version 1.2.0 CI is now dependend on the start CI
Version 1.2.1 With running on low CI there is an increased risk of losing best
              score during qStab. Fixed that.
Version 1.2.2 Put in a warning when running not on CI 1 and a last chance
]]--

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

-- On request of gmn
CIfactor=1
function CI(CInr)
    behavior.SetClashImportance(CInr*CIfactor)
end

function CheckCI()
   local ask=dialog.CreateDialog("Clash importance is not 1")
   ask.l1=dialog.AddLabel("Last change to change it")
   ask.l2=dialog.AddLabel("CI settings will be multiplied by set CI")
   ask.continue=dialog.AddButton("Continue",1)
   dialog.Show(ask)
end

if behavior.GetClashImportance() < 0.99 then CheckCI() end
CIfactor=behavior.GetClashImportance()

-- Score functions
function Score(pose)
    if pose==nil then pose=current end
    local total= pose.GetEnergyScore()
    -- FIX for big negatives

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

    if normal then
        return total
    else
        return total*pose.GetExplorationMultiplier()
    end
end

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

function RBScore()
    return Score(recentbest)
end

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

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()
        save.Quicksave(3)
    end
end

-- Wiggle function
-- Note the extra parameter to be used if only selected parts must be done
function Wiggle(how, iters, minppi,onlyselected)
    --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=6 end
    if minppi==nil then minppi=0.1 end
    if onlyselected==nil then onlyselected=false end

    if iters>0 then
        iters=iters-1
        local sp=Score()
        if onlyselected then
            if how == "s" then
                -- Shake is so slow on big ones, so first try one round
                structure.ShakeSidechainsSelected(1)
                if math.abs(Score()-sp) > minppi then structure.ShakeSidechainsSelected(1) end
            elseif how == "wb" then structure.WiggleSelected(2,true,false)
            elseif how == "ws" then structure.WiggleSelected(2,false,true)
            elseif how == "wa" then structure.WiggleSelected(2,true,true)
            end
        else
            if how == "s" then
                -- Shake is so slow on big ones, so first try one round
                structure.ShakeSidechainsAll(1)
                if math.abs(Score()-sp) > minppi then structure.ShakeSidechainsAll(1) end
            elseif how == "wb" then structure.WiggleAll(2,true,false)
            elseif how == "ws" then structure.WiggleAll(2,false,true)
            elseif how == "wa" then structure.WiggleAll(2,true,true)
            end
        end
        if math.abs(Score()-sp) > minppi then return Wiggle(how, iters, minppi,onlyselected) end
    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

-- 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

-- Start of module for bridgechecking
Cyslist={}
savebridges=false --default no bridgechecking
nrofbridges=0

function setCyslist()
    Cyslist=FindAminotype("c")
    nrofbridges=CountBridges()
end

function IsBridge(i)
    return ''..current.GetSegmentEnergySubscore(i,'disulfides') ~= '-0'
end

function CountBridges()
    local count = 0
    for i = 1,#Cyslist do
        if IsBridge(Cyslist[i]) then count = count + 1 end
    end
    return count
end

function BridgesBroken()
    return savebridges == true and CountBridges() < nrofbridges
end
-- End module bridgechecking

-- Position stack module 1.0
-- uses slot 50 and higher
Stackmin=50
StackMarks={}
StackPos=50
function PushPosition()
    if StackPos==100 then
        print("Position stack overflow, exiting")
        exit()
    end
    save.Quicksave(StackPos)
    StackPos=StackPos+1
end

function PopPosition()
    if StackPos==50 then
        print("Position stack underflow, exiting")
        exit()
    end
    StackPos=StackPos-1
    save.Quickload(StackPos)
end
function PushMarkPosition()
    StackMarks[#StackMarks+1]=StackPos
    PushPosition()
end
function PopMarkPosition()
    if #StackMarks == 0 then
        print("No marked position found, just popping")
    else
        StackPos=StackMarks[#StackMarks]+1
        StackMarks[#StackMarks]= nil
    end
    PopPosition()
end
function ClrTopPosition()
    if StackPos > 50 then StackPos=StackPos-1 end
end
-- Bridgekeeping Fuze module
-- Picks up all gains by using recentbest
-- But makes sure no bridges are broken

function BridgeFuzeEnd()
    PushPosition()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    if RBScore()> Score() then BridgerestoreRB() end
    if not BridgesBroken() then
        SaveBest()
        ClrTopPosition()
    else
        PopPosition()
    end
end
function BridgeFuze1(ci1,ci2)
    PushPosition()
    CI(ci1)
    Wiggle("s",1)
    CI(ci2)
    Wiggle("wa",1)
    if not BridgesBroken() then
        ClrTopPosition()
    else
        PopPosition()
    end
end
function BridgeFuze2(ci1,ci2)
    PushPosition()
    CI(ci1)
    Wiggle("wa",1)
    CI(1)
    Wiggle("wa",1)
    CI(ci2)
    Wiggle("wa",1)
    if not BridgesBroken() then
        ClrTopPosition()
    else
        PopPosition()
    end
end
function reBridgeFuze(scr,slot)
    local s=Score()
    if s<scr then
        save.Quickload(slot)
    else
        scr=s
        save.Quicksave(slot)
    end
    return scr
end
function BridgerestoreRB()
    PushPosition()
    recentbest.Restore()
    if BridgesBroken() then
        PopPosition()
    else ClrTopPosition() end
end
function BridgeFuze(slot)
    local scr=Score()

    recentbest.Save()
    BridgeFuze1(0.3,0.6) BridgeFuzeEnd()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze2(0.3,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze1(0.05,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze2(0.7,0.5) BridgeFuzeEnd()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze1(0.07,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    reBridgeFuze(scr,slot)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
end
-- end bridgekeeping Fuze module

SAVEDstructs=false
function AllLoop() --turning entire structure to loops
    local anychange=false
    for i=1,segCnt2 do
        if structure.GetSecondaryStructure(i)~="L" then
            anychange=true
            break
        end
    end
    if anychange then
        save.SaveSecondaryStructure()
        SAVEDstructs=true
        selection.SelectAll()
        structure.SetSecondaryStructureSelected("L")
    end
end

function SelectAround(ss,se,radius,nodeselect)
    if nodeselect~=true then selection.DeselectAll() end
    for i=1, segCnt2 do
        for x=ss,se do
            if structure.GetDistance(x,i)<radius then selection.Select(i) break end
        end
    end
end

function qStab()
    recentbest.Save()
    CI(0.1)
    Wiggle("s",1,nil,true) --shake only selected part
    if InQstab then
        CI(1)
        doMutate()
    end
    if fastQstab==false then
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
    end
    CI(1)
    Wiggle()
    recentbest.Restore()
end

function Sort(tab,items) --BACWARD bubble sorting - lowest on top, only needed items
    for x=1,items do --items do
        for y=x+1,#tab do
            if tab[x][1]>tab[y][1] then
                tab[x],tab[y]=tab[y],tab[x]
            end
        end
    end
    return tab
end

function FindWorst()
    if sEnd==nil then sEnd=segCnt2 end
    print("Searching worst scoring parts of len "..len)
    wrst={}
    GetSegmentScores()
    local skiplist=""
    local nrskip=0
    for i=sStart,sEnd-len+1 do
        if (not donotrevisit or not donotrevisitlist[i+(i+len-1)*segCnt2])
             and MustWorkon(i,i+len-1)
        then
            if scrPart==nil then scrPart='local' end
            s=getAreaScore(i,i+len-1,scrPart)
            wrst[#wrst+1]={s,i}
        else
            if (donotrevisit and donotrevisitlist[i+(i+len-1)*segCnt2])
            then
                if nrskip==0 then print("Skipping") end
                nrskip=nrskip+1
                skiplist=skiplist..i.."-"..(i+len-1).." "
                if nrskip%7==0 then
                    print(skiplist)
                    skiplist=""
                end
            end
        end
    end
    if nrskip%7 ~= 0 then print(skiplist) end
    if nrskip > 0 then print("Number of skips: "..nrskip) end
    wrst=Sort(wrst,reBuild)
    areas={}
    local rb=reBuild
    if rb>#wrst then rb=#wrst end
    for i=1,rb do
        local w=wrst[i]
        local ss=w[2]
        areas[#areas+1]={ss,ss+len-1}
    end
end

function localRebuild(maxiters)
    if maxiters==nil then maxiters=3 end
    local s=Score()
    local i=0
    if bandflip then band.DisableAll() end
    if savebridges then PushPosition() end
    repeat
        i=i+1
        if i>maxiters then break end
        structure.RebuildSelected(i)
    until Score()~=s and BridgesBroken() == false
    if bandflip then band.EnableAll() end
    if savebridges then
        if BridgesBroken() then PopPosition() else ClrTopPosition() end
    end
    if Score()~=s then return true else return false end
end

function ReBuild(ss,se,tries)
    Clear() --reset score tables
    if ss>se then ss,se=se,ss end --switch if needed
    local Foundone=false
    for try=1,tries do -- perform loop for number of tries
        selection.DeselectAll()
        CI(rebuildCI)
        selection.SelectRange(ss,se)
        local extra_rebuilds = 1
        if savebridges then extra_rebuilds=3 end --extra if bridges keep breaking
        local done
        repeat
            done=localRebuild(nil)
            extra_rebuilds = extra_rebuilds -1
        until done or extra_rebuilds == 0
        SaveBest()
        if done==true and doShake==true then
            CI(shakeCI)
            Foundone=true
            if savebridges then PushPosition() end
            Wiggle("s",1,nil,true)
            if savebridges then
                if BridgesBroken() then PopPosition() else ClrTopPosition() end
            end
        end
        if done==true and AfterRB then doMutate() end
        if done==true then
            Foundone=true
            Save(ss,se)
            SaveBest()
        end
        if (try > 3 or savebridges) and Foundone==false then
            print("No valid rebuild found on this section")
            print("After 9 or more rebuild attempts, giving up")
            break
        end
    end
    CI(1)
    return Foundone
end

function getPartScore(segments,attr)--using partial scoring
    local score = 0
    for i=1,#attr do
        score = score + current.GetSegmentEnergySubscore(segments,attr[i])
    end
    return score
end
function getAreaScore(ss,se,attr)
    local s=0
    if attr=='local' then --this one for evaluation of worst scores
        for i=ss,se do
            s=s+SegmentScores[i]
        end
    elseif attr~=nil then --local scoring
        for i=ss,se do
            s=s+getPartScore(i,attr)
        end
    else --total segment scores
        for i=ss,se do
            s=s+current.GetSegmentEnergyScore(i)
        end
    end
    return s
end
WORKONbool={}
function InitWORKONbool()
    WORKONbool=SegmentSetToBool(WORKON)
end
function MustWorkon(i,j)
    for k=i,j do if not WORKONbool[k] then return false end end
    return true
end
SegmentScores={}
lastSegScores=0
function GetSegmentScores()
    if lastSegScores~=Score() then
        lastSegScores=Score()
        for i=1,segCnt2 do
            if WORKONbool[i] then SegmentScores[i]=current.GetSegmentEnergyScore(i)-current.GetSegmentEnergySubscore(i,'reference') --ignore reference part
            end
        end
    end
end

Scores={} --{save_no,points}
function Clear()
    Scores={
    {10,-99999999},
    {9,-99999999},
    {8,-99999999},
    {7,-99999999},
    {6,-99999999},
    {5,-99999999},
    {4,-99999999},
    }
    slotScr={}
end

function Save(ss,se) --there you can change scoring methods for each save
    local scr=
    {
    {10,getAreaScore(ss,se,{'backbone'})},
    {9,getAreaScore(ss,se,{'sidechain'})},
    {8,getAreaScore(ss,se,{'clashing'})},
    {7,getAreaScore(ss,se,{'hiding'})},
    {6,getAreaScore(ss,se,{'bonding'})},
    {5,getAreaScore(ss,se)},
    {4,Score()}
    }
    for i=1,#Scores do
        local s=scr[i][2]
        if s>Scores[i][2] then
            local slot=scr[i][1]
            save.Quicksave(slot) --print("Saved slot ",slot," pts" ,s) --debug
            Scores[i][2]=s
        end
    end
    SaveBest()
end

slotScr={}
function ScoresCheck(slot)
    save.Quickload(slot)
    local s=Score()
    local ok=true
    if #slotScr > 0 then
        for i=1,#slotScr do
            if slotScr[i]==s then ok=false break end
        end
    end
    slotScr[#slotScr+1]=s
    return ok
end

function PrintAreas()
    if #areas<19 then
        local a=""
        local x=0
        for i=1,#areas do
            x=x+1
            a=a..areas[i][1].."-"..areas[i][2].." "
            if x>6 then
                print(a)
                a=""
                x=0
            end
        end
        if x>0 then print(a) end
    else
        print("It is "..#areas.." places, not listing.")
    end
end

function AddLoop(sS)
    local ss=sS
    local ssStart=structure.GetSecondaryStructure(ss)
    local se=ss
    for i=ss+1,segCnt2 do
        if structure.GetSecondaryStructure(i)==ssStart then se=i
        else break end
    end
    if se-ss+2>minLen and loops==true then
        areas[#areas+1]={ss,se}
    end
    return se
end

function AddOther(sS)
    local ss=sS
    local ssStart=structure.GetSecondaryStructure(ss)

    local se=ss
    if ss>1 then
        for i=ss-1,1,-1 do --search bacward for start
            local sec=structure.GetSecondaryStructure(i)
            if sec=="L" then ss=i
            else break end
        end
    end
    if se<segCnt2-1 then --now forward to find end
        local change=false
        repeat
            se=se+1
            if se==segCnt2 then break end
            local sec=structure.GetSecondaryStructure(se)
            if change==false then
                if sec~=ssStart then change=true end
            end
        until change==true and sec~="L"
        if se<segCnt2 then se=se-1 end
    end
    if sheets==false and ssStart=="E" then return se end
    if helices==false and ssStart=="H" then return se end
    if se-ss+2>minLen then
        areas[#areas+1]={ss,se}
    end
    return se
end
function FindAreas()
    if loops then
        local done=false
        local ss=0
        repeat--loops
            ss=ss+1
            local ses=structure.GetSecondaryStructure(ss)
            if ses=="L" then
                ss=AddLoop(ss)
            end
            if ss==segCnt2 then done=true end
        until done~=false
    end
    if sheets or helices then
        local done=false
        local ss=0
        repeat--other
            ss=ss+1
            local ses=structure.GetSecondaryStructure(ss)
            if ses~="L" then
                ss=AddOther(ss)
            end
            if ss==segCnt2 then done=true end
        until done~=false
    end
end

firstRBseg=0
lastRBseg=0

function doMutate()
    CI(MutateCI)
    if savebridges then PushPosition() end
    if MUTRB then
        selection.DeselectAll()
        selection.SelectRange(firstRBseg,lastRBseg)
        structure.MutateSidechainsSelected(1)
    elseif MUTSur then
        SelectAround(firstRBseg,lastRBseg,MutSphere)
        structure.MutateSidechainsSelected(1)
    else
        structure.MutateSidechainsAll(1)
    end
    if savebridges then
        if BridgesBroken() then PopPosition() else ClrTopPosition() end
    end
end

function DeepRebuild()
    if sEnd==nil then sEnd=segCnt2 end
    local ss=Score()
    if struct==false then AllLoop() end
    save.Quicksave(3)
    recentbest.Save()
    print("DeepRebuild started at score: "..round3(ss))
    for i=1,#areas do
        local ss1=Score()
        local s=areas[i][1]
        local e=areas[i][2]
        firstRBseg=s
        lastRBseg=e
        save.Quicksave(11) -- for uncaught bridge breaks
if Runnr > nrskip then
        print("DR "..Runnr.."."..(e-s+1).."."..i.." "..s.."-"..e.." "..
              rebuilds.." times. Wait... Current score: "..round3(Score()))
        if ReBuild(s,e,rebuilds) then
            for r=1,#Scores do
                slot=Scores[r][1]
                if ScoresCheck(slot) then
                    print("Stabilizing slot "..slot)
                    SelectAround(s,e,12) --local shake after rebuild
                    if savebridges then PushPosition() end
                    if not skipqstab then qStab()
                    else
                        CI(1)
                        Wiggle("s",1,nil,true)
                        Wiggle("ws",1,nil,true)
                    end
                    if savebridges then
                        if BridgesBroken() then
                            PopPosition()
                        else ClrTopPosition() end
                    end
                    if AfterQstab then doMutate() end
                    save.Quicksave(slot)
                    SaveBest()
                end
            end
            save.Quickload(4)
            recentbest.Save()
            for i=5,10 do
                save.Quickload(i)
            end
            recentbest.Restore()
            local scorebeforefuze=Score()
            if not skipfuze and ss1-Score() < maxlossbeforefuze*(e-s+1)/3 then
                print("Fuzing best position.")
                if not AfterQstab and BeFuze then doMutate() end
                save.Quicksave(4)
                if savebridges then BridgeFuze(4) else Fuze(4) end
            end
            if AfterFuze then doMutate() end
            SaveBest()
            save.Quickload(3)
        else save.Quickload(3) end
end --skip section
        if BridgesBroken() then
            -- THIS SHOULD NOT HAPPEN
            print("Unexpected bridge broken, pls report\n")
            print("Restoring a good position, discarding wins\n")
            save.Quickload(11)
            save.Quicksave(3)
            bestScore=Score()
        end
        donotrevisitlist[s+e*segCnt2] = true
        nrremember=nrremember+1
        remembernottorevisit[nrremember] = s+e*segCnt2
        if Score()-scorebefore > clearnottorevisitgain then
            scorebefore=Score()
            clearrevisitlist()
        end
        if Score()-ss > minGain then break end
    end
    print("DeepRebuild gain: "..round3(Score()-ss))
    if struct==false and SAVEDstructs then save.LoadSecondaryStructure() end
end

function clearrevisitlist()
    for i=1,nrremember do
        donotrevisitlist[remembernottorevisit[i]] = false
    end
    nrremember=0
end

function DRcall(how)
    if sEnd==nil then sEnd=segCnt2 end
    if how=="drw" then
        for i=minLen,maxLen do --search from minl to maxl worst segments
            len=i
            if longfirst then len=maxLen-i+minLen end
            FindWorst() --fill areas table. Comment it if you have set them by hand
            PrintAreas()
            DeepRebuild()
        end
    elseif how=="fj" then --DRW len cutted on pieces
        FindWorst() --add to areas table worst part
        areas2={}
        for a=1,#areas do
            local s=areas[a] --{ss,se}
            local ss=s[1] --start segment of worst area
            local se=s[2] --end segment of worst area
            for i=ss,se do
                for x=1,len do
                    if i+x<=se then
                        areas2[#areas2+1]={i,i+x}
                    end
                end
            end
        end
        areas=areas2
        PrintAreas()
        DeepRebuild()
    elseif how=="all" then
        areas={}
        for i=minLen,maxLen do
            for x=sStart,sEnd do
                if i+x-1<=sEnd then
                    areas[#areas+1]={x,x+i-1}
                end
            end
        end
        PrintAreas()
        DeepRebuild()
    elseif how=="simple" then
        FindWorst()
        PrintAreas()
        DeepRebuild()
    elseif how=="areas" then
        areas={}
        FindAreas()
        PrintAreas()
        DeepRebuild()
    end
end

function AskMoreOptions()
    local ask=dialog.CreateDialog("More DRW options")
    ask.l1=dialog.AddLabel("Clear no revisit list if gain is more")
    ask.revlist=dialog.AddSlider("Cleargain:",clearnottorevisitgain,0,250,0)
    ask.l2=dialog.AddLabel("Number of rebuilds each pass")
    ask.nrrebuilds=dialog.AddSlider("Rebuilds:",rebuilds,10,20,0)
    ask.l3=dialog.AddLabel("Number of full cycles")
    ask.nrcycles=dialog.AddSlider("Cycles:",maxnrofRuns,1,40,0)
    ask.l4=dialog.AddLabel("Skip first cycles (crash resume)")
    ask.nrskip=dialog.AddSlider("Skip cycles:",nrskip,0,10,0)
    ask.reBuild=dialog.AddSlider("# to do in first cycle:",reBuild,1,6,0)
    ask.longfirst=dialog.AddCheckbox("Longest rebuild first",longfirst)
    ask.doShake=dialog.AddCheckbox("Shake after rebuild (rebuilds only)",doShake)
    ask.shakeCI=dialog.AddSlider("Shake CI:",shakeCI,0,1,2)
    ask.bandflip=dialog.AddCheckbox("Disable bands before rebuild",bandflip)
    ask.skipqstab=dialog.AddCheckbox("Local shake instead of Qstab",skipqstab)
    ask.skipfuze=dialog.AddCheckbox("Skip Fuze",skipfuze)
    ask.OK = dialog.AddButton("OK",1)
    dialog.Show(ask)
    clearnottorevisitgain=ask.revlist.value
    rebuilds=ask.nrrebuilds.value
    maxnrofRuns=ask.nrcycles.value
    nrskip=ask.nrskip.value
    reBuild=ask.reBuild.value
    longfirst=ask.longfirst.value
    doShake=ask.doShake.value
    shakeCI=ask.shakeCI.value
    bandflip=ask.bandflip.value
    skipqstab=ask.skipqstab.value
    skipfuze=ask.skipfuze.value
end

AfterRB=false
InQstab=false
AfterQstab=false
BeFuze=false
AfterFuze=false
MutateCI=0.9
MutSphere=10
MUTRB=false
MUTSur=false
function AskMutateOptions()
    local ask = dialog.CreateDialog("Mutate Options")
    ask.AfterRB = dialog.AddCheckbox("Mutate after rebuild",AfterRB)
    ask.InQstab = dialog.AddCheckbox("Mutate during Qstab",InQstab)
    ask.AfterQstab = dialog.AddCheckbox("Mutate after Qstab",AfterQstab)
    ask.BeFuze = dialog.AddCheckbox("Mutate before Fuze",BeFuze)
    ask.AfterFuze = dialog.AddCheckbox("Mutate after Fuze",AfterFuze)
    ask.l1=dialog.AddLabel("-----What to rebuild or all")
    ask.OnlyRB=dialog.AddCheckbox("Mutate only rebuild part",MUTRB)
    ask.OnlySur=dialog.AddCheckbox("Mutate rebuild and surround",MUTSur)
    ask.l2=dialog.AddLabel("Sphere size to use with surround")
    ask.SurSize=dialog.AddSlider("Sphere:",MutSphere,3,15,0)
    ask.MutateCI=dialog.AddSlider("MutateCI:",MutateCI,0.1,1,2)
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    if dialog.Show(ask) > 0 then
        AfterRB=ask.AfterRB.value
        InQstab=ask.InQstab.value
        AfterQstab=ask.AfterQstab.value
        BeFuze=ask.BeFuze.value
        AfterFuze=ask.AfterFuze.value
        MutateCI=ask.MutateCI.value
        MutSphere=ask.SurSize.value
        MUTRB=ask.OnlyRB.value
        MUTSur=ask.OnlySur.value
    end
end

function printOptions(title)
    print(title)
    print("Based on rav4pl DRW 3.4")
    print("Length of rebuilds: "..minLen.." until "..maxLen)
    print("Rebuild area: "..SegmentSetToString(WORKON))
    if AfterRB then print("Mutates after each rebuild") end
    if InQstab then print("Mutates inside qStab") end
    if AfterQstab then print("Mutates after qStab") end
    if BeFuze then print("Mutates before Fuzing") end
    if AfterFuze then print("Mutates after Fuzing") end
    print("Nr of rebuilds each try: "..rebuilds)
    if not struct then print("Convert everything to loops") end
    if donotrevisit then
        print("Will not retry already tried rebuilds")
        print("Clear done list if gain raises above "..clearnottorevisitgain.." pts")
    end
    if doShake then
        print("Do an initial shake on rebuild part after rebuild")
        print("With CI="..shakeCI)
    end
    if skipqstab then print("Local shake instead of qStab") end
    if skipfuze then print("Skipping Fuzes") end
    print("Nr of full cycles: "..maxnrofRuns)
    if nrskip > 0 then print("SKIPPING "..nrskip.." CYCLES") end
end

-- 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
WORKON={{1,structure.GetCount()}}

function AskDRWOptions()
    local askresult
    local ask = dialog.CreateDialog("Tvdl enhanced DRW "..DRWVersion)
repeat
    ask.l1 = dialog.AddLabel("Minimum length to rebuild")
    ask.minLen = dialog.AddSlider("Minimum:",minLen,1,10,0)
    ask.l2 = dialog.AddLabel("Maximum length to rebuild")
    ask.maxLen = dialog.AddSlider("Maximum:",maxLen,1,10,0)
    ask.l3 = dialog.AddLabel("Force next round if gain is more")
    ask.minGain = dialog.AddSlider("MinGain:",minGain,0,100,0)
    ask.fastQstab=dialog.AddCheckbox("Do a fast qStab",fastQstab)
    ask.l4 = dialog.AddLabel("Skip fuze if loss is more")
    ask.l5 = dialog.AddLabel("Threshold used is RBlength*threshold/3")
    ask.maxLoss = dialog.AddSlider("Skip fuze:",maxlossbeforefuze,-5,200,0)
    ask.donotrevisit = dialog.AddCheckbox("Do not things twice",donotrevisit)
    ask.SEL= dialog.AddCheckbox("(Re)select where to work on ",false)
    ask.MUTS = dialog.AddCheckbox("(Re)set Mutate Options",false)
    ask.bridge = dialog.AddCheckbox("Keep sulfide bridges intact",savebridges)
    ask.struct = dialog.AddCheckbox("Do not change all to loop",struct)
    ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0)
    ask.Options = dialog.AddButton("More options",2)
    -- TODO ask.Presets = dialog.AddButton("Presets",3)
    askresult=dialog.Show(ask)
    if askresult > 0 then
        minLen=ask.minLen.value
        maxLen=ask.maxLen.value
        minGain=ask.minGain.value
        fastQstab=ask.fastQstab.value
        maxlossbeforefuze=ask.maxLoss.value
        donotrevisit=ask.donotrevisit.value
        struct=ask.struct.value
        savebridges=ask.bridge.value
        if ask.SEL.value then
            local SelMode={}
            SelMode.askignorefrozen=false
            SelMode.defignorefrozen=true
            SelMode.askignorelocks=false
            SelMode.defignorelocks=true
            SelMode.askligands=false
            SelMode.defligands=false
            WORKON=AskForSelections("Tvdl enhanced DRW "..DRWVersion,SelMode)
            print("Selection is now, reselect if not oke:")
            print(SegmentSetToString(WORKON))
            if askresult==1 then askresult=4 end --to force return to main menu
        end
        -- Do not try to rebuild frozen or locked parts or ligands
        WORKON=SegmentSetMinus(WORKON,FindFrozen())
        WORKON=SegmentSetMinus(WORKON,FindLocked())
        WORKON=SegmentSetMinus(WORKON,FindAAtype("M"))
        if ask.MUTS.value then
            AskMutateOptions()
            if askresult==1 then askresult=4 end --to force return to main menu
        end
        if askresult==2 then AskMoreOptions() end
   --TODO if askresult==3 then AskPresets() end
    end
until askresult < 2
    return askresult > 0
end
-- Quick fix for failing first rebuild
for i=3,10 do save.Quicksave(i) end

function Cleanup(err)
    print("Restoring CI, best result and structures")
    CI(1)
    save.Quickload(3)
    if SAVEDstructs then save.LoadSecondaryStructure() end
    print(err)
end

--[[
    USAGE
1. 'drw' - need 'minLen' and 'maxLen'; finding worst scores by len betwen that 2
2. 'fj' - need 'len'; searching len then cutting in pieces 2->len and rebuilds pieces
3. 'all' - need 'minLen' and 'maxLen'; rebuilding ENTIRE prorein (from min to max) like in WalkinRebuild script
4. 'simple' - need 'len'; find and rebuild worst scoring parts of that lenght
5. 'areas' - need secondary structure set and 'true' on at least one of structure
]]--
----------------- options below VVVV

areas={ --start segment, end segment. use for last line call
--{1,10},
--{20,30},
--{32,35},
}
scrPart=nil --{'backbone','sidechain','clashing'} --change there to find worst scoring parts by partial scoring

--options for (5)"areas" setting
loops=true --rebuild loops alone
sheets=false --rebuild sheets + surrounding loops
helices=true --false --rebuild helices + surrounding loops

doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
shakeCI=0.31 --clash imortance while shaking

struct=false --set in all loop (if true work in structure mode)

fastQstab=true --false --if true faster stabilize, but longer

sStart=1 --start segment to search worsts
sEnd=segCnt2 --end segment to search worst

reBuild=4 --up to worst parts to look at
rebuilds=35 --how many rebuilds to try, set at least 10!
rebuildCI=0 --clash importance while rebuild

len=6 --find worst segments part
minLen=7 --or specify minimum len
maxLen=10 --and maximim len

-- New options
maxnrofRuns=40 -- Set it very high if you want to run forever
Runnr=0
donotrevisitlist={}
remembernottorevisit={}
nrremember=0
donotrevisit=true -- If you do not want a second try at the same part
clearnottorevisitgain=segCnt2 -- If there is enough change clear revisitlist
minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute
if minGain < 40 then minGain=40 end
longfirst=true --true -- Reverse the search, long ones first
skipqstab=false
skipfuze=false
bandflip=false
maxlossbeforefuze=(segCnt2-segCnt2%4)/4 -- if loss is more no fuze is done
if maxlossbeforefuze < 30 then maxlossbeforefuze=30 end
scorebefore=Score()
nrskip=0
Cyslist={}

DRWVersion="1.2.3"

-- MAIN PROGRAM
function Doit()
    printOptions("Tvdl enhanced DRW "..DRWVersion)
    InitWORKONbool()
    if savebridges then setCyslist() end
    for nrofRuns=1,maxnrofRuns do --uncomment method/s you want to use
         Runnr=nrofRuns
         print("Main cycle nr ",nrofRuns)
-- DRcall("areas")
     DRcall("drw")
-- DRcall("fj")
-- DRcall("all")
-- DRcall("simple")
-- DeepRebuild() --if set "areas" above by hand
        if Score()-scorebefore > clearnottorevisitgain then clearrevisitlist() end
        reBuild=reBuild+3 --three worst places more every loop
    end
end

-- Change defaults if the startscore is negative
if Score() < 0 then
    print("Score Negative, adjusting defaults")
    print("Now skipping Fuzes, replacing qStab")
    print("Can be changed in More options")
    skipfuze=true
    skipqstab=true
end

if AskDRWOptions() then
    xpcall(Doit,Cleanup)
end

Comments

[karstenw]

The "More Options" window is not available to you. 35 rebuilds is not an amount of rebuilds provided in that window, so script will cancel if you try to use it. Ps. you don't need that window anyway, I set it all up pretty for you ;)

[karstenw]

This script is meant to be used very early on. It is not meant to propel you to the top like a magic wand (hides magic wand). It will prep your protein very well for the next stage of game play (promise).