Icon representing a recipe

Recipe: TvdL DRW Compressor 2.0.0

created by Timo van der Laan

Profile


Name
TvdL DRW Compressor 2.0.0
ID
49664
Shared with
Public
Parent
TvdL DRW Compressor 1.0.1
Children
Created on
August 23, 2017 at 06:10 AM UTC
Updated on
August 23, 2017 at 06:10 AM UTC
Description

Small update. Tx LociOiling

Best for


Code


-- Combi compressor and DRW -- When to change from DRW and when from Compressor is gain & cycles based -- If compressor did not gain enough then DRW will skip done parts -- TvdL, 8-2-2013 -- Fixed: DRW now stops immediate after big enough gain -- Compressor stops if gain is enough and last cycle is a loss --[[ Based on Rav3n_pl Deep Rebuild v3.x WARNING! 1) Script uses a lot of save slots 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 in different ways and saved if better. After rebuild finishes script is trying to stabilize each different saved position. Because some positions are best in more than 1 way sometimes it is only 1 positions to stabilize. On the best position a fuze is run if it looks promissing enough. Changed by: Timo van der Laan 17-12-2011 till 28-12-2012 ]]-- -- 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 maxCI=true function CI(CInr) if CInr > 0.99 then maxCI=true else maxCI=false end 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 -- Module Filteractive Filterscore=Score() behavior.SetSlowFiltersDisabled(true) FilterOffscore=Score() behavior.SetSlowFiltersDisabled(false) maxbonus=Filterscore-FilterOffscore CURBONUS=maxbonus function Filter() local ask=dialog.CreateDialog("Slow filters seem to be active") ask.disable=dialog.AddCheckbox("Run with disabled slow filters",Filteractive) ask.l1=dialog.AddLabel("Current bonus is: "..maxbonus) ask.l2=dialog.AddLabel("If this is not the maximum bonus put in a number") if maxbonus < 0 then maxbonus=0 end ask.maxbonus=dialog.AddTextbox("Set maxbonus:",maxbonus) ask.l3=dialog.AddLabel("Scores will only be checked for real gains if") ask.l4=dialog.AddLabel("Score with filter off+maxbonus is a potential gain") ask.continue=dialog.AddButton("Continue",1) dialog.Show(ask) maxbonus=ask.maxbonus.value if maxbonus=="" then maxbonus=0 end Filteractive=ask.disable.value end BetterRecentBest=false function FilterOff() -- Filters off but restore a better recentbest with filter off behavior.SetSlowFiltersDisabled(true) if BetterRecentBest then save.Quicksave(99) save.Quickload(98) recentbest.Save() save.Quickload(99) end end function FilterOn() -- Filter on but remember recent best if better than current BetterRecentBest= Score(recentbest) > Score() if BetterRecentBest then save.Quicksave(99) recentbest.Restore() save.Quicksave(98) save.Quickload(99) end behavior.SetSlowFiltersDisabled(false) end Filteractive=(math.abs(maxbonus) > 0.1) if Filteractive then --Filters active, give people a choice --And ask what the maximum bonus is. Filter() end -- End of module Filteractive bestScore=Score() if Filteractive then FilterOff() end function SaveBest() if (not Filteractive) or (Score()+maxbonus>bestScore) then if Filteractive then FilterOn() end 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 if Filteractive then FilterOff() end 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) --score conditioned recursive wiggle/shake --fixed a bug, absolute difference is the threshold now if how==nil then how="wa" end if iters==nil then iters=3 end if minppi==nil then minppi=0.1 end if onlyselected==nil then onlyselected=false end local wf=1 if maxCI then wf=WF end --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 math.abs(Score()-sp) > minppi then return Wiggle(how, iters, minppi,onlyselected) end --end end -- end of handy shorts 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 SegmentInvertList(list) table.sort(list) local result={} for i=1,#list-1 do for j=list[i]+1,list[i+1]-1 do result[#result+1]=j end end for j=list[#list]+1,segCnt2 do result[#result+1]=j 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 FindMutablesList() local result={} for i=1,segCnt2 do if structure.IsMutable(i) then result[#result+1]=i end end return result end function FindMutables() return SegmentListToSet(FindMutablesList()) end function FindFrozenList() local result={} for i=1,segCnt2 do if freeze.IsFrozen(i) then result[#result+1]=i end end return result end function FindFrozen() return SegmentListToSet(FindFrozenList()) end function FindLockedList() local result={} for i=1,segCnt2 do if structure.IsLocked(i) then result[#result+1]=i end end return result end function FindLocked() return SegmentListToSet(FindLockedList()) end function FindSelectedList() local result={} for i=1,segCnt do if selection.IsSelected(i) then result[#result+1]=i end end return result end function FindSelected() return SegmentListToSet(FindSelectedList()) end function FindAAtypeList(aa) local result={} for i=1,segCnt2 do if structure.GetSecondaryStructure(i)== aa then result[#result+1]=i end end return result end function FindAAtype(aa) return SegmentListToSet(FindAAtypeList(aa)) end function FindAminotype(at) --NOTE: only this one gives a list not a set local result={} for i=1,segCnt2 do if structure.GetAminoAcid(i) == at then result[#result+1]=i end end return result end -- end Module Find Segment Types -- Module to compute subscores -- TvdL, 14-12-2012 function GetSubscore(types,seg1,seg2,pose) local result=0 if type(types) == "table" then for i=1,#types do result=result+GetSubscore(types[i],seg1,seg2,pose) end else if types==nil and seg1==nil and seg2==nil then return Score(pose) end if seg1==nil then seg1=1 end if seg2==nil then seg2=segCnt end --includes ligands! if seg1>seg2 then seg1,seg2=seg2,seg1 end if pose==nil then pose=current end if types==nil then for i=seg1,seg2 do result=result+pose.GetSegmentEnergyScore(i) end else for i=seg1,seg2 do result=result+pose.GetSegmentEnergySubscore(i,types) end end end if normal then return result else return result*pose.GetExplorationMultiplier() end end function FindActiveSubscores(show) local result={} local Subs=puzzle.GetPuzzleSubscoreNames() local Showlist ="Computing Active Subscores" if show then print(Showlist) end for i=1,#Subs do local total=0 for j=1,segCnt do if Subs[i] == 'disulfides' and nrofbridges>0 then total=11 end total=total+math.abs(current.GetSegmentEnergySubscore(j,Subs[i])) if total>10 then result[#result+1]=Subs[i] if show then print("Active subscore: "..Subs[i]) end break end end end return result end -- End module to compute subscores -- Position stack module 1.0 -- uses slot 60 and higher Stackmin=60 StackMarks={} StackPos=60 function PushPosition() if StackPos==100 then print("Position stack overflow, exiting") exit() end save.Quicksave(StackPos) StackPos=StackPos+1 end function PopPosition() if StackPos==60 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 GetTopPosition() if StackPos==60 then print("No top position on the stack, exiting") exit() end save.Quickload(StackPos-1) end function ClrTopPosition() if StackPos > 60 then StackPos=StackPos-1 end end -- Start of module for bridgechecking Cyslist={} savebridges=false --default no bridgechecking nrofbridges=0 function setCyslist() Cyslist=FindAminotype("c") nrofbridges=CountBridges() end function IsBridge(i) if structure.IsLocked(i) then return false end 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 function Bridgesave() if savebridges then PushPosition() end end function Bridgerestore() if savebridges then if BridgesBroken() then PopPosition() else ClrTopPosition() end end end -- End module bridgechecking -- Module find puzzle properties -- Tvdl 14-12-2012 HASMUTABLE=false HASDENSITY=false HASLIGAND= (segCnt2<segCnt) DENSITYWEIGHT=0 PROBABLESYM=false FREEDESIGN=false ISAUNTDEEN=false function SetPuzzleProperties() print("Computing puzzle properties") -- Find out if the puzzle has mutables local MutList=FindMutablesList() HASMUTABLE= (#MutList>0) if HASMUTABLE then print("Mutables found") end FREEDESIGN= (segCnt2/2 < #MutList) if FREEDESIGN then print("Design puzzle") end -- Find out if the puzzle has possible bridges setCyslist() if #Cyslist > 1 then print("Puzzle has more than 1 cystine") if nrofbridges > 0 then print("Puzzle has bridges") savebridges=true end end -- Find out is the puzzle has Density scores and their weight if any local Densitytot=GetSubscore("density") local segtot=GetSubscore(nil,1,segCnt) HASDENSITY= math.abs(Densitytot) > 0.0001 if normal and HASDENSITY then print("Puzzle has Density scores") DENSITYWEIGHT=(Score()-CURBONUS-segtot-8000)/Densitytot print("The Density component has an extra weight of "..round3(DENSITYWEIGHT)) end -- Check if the puzzle is a probable symmetry one if normal and not HASDENSITY then PROBABLESYM=math.abs(Score()-segtot-8000) > 2 if PROBABLESYM then print("Puzzle is a symmetry puzzle or has bonuses") end end -- Check to see if the player is auntdeen if user.GetPlayerName() == "auntdeen" then print("Hello auntdeen") ISAUNTDEEN=true end end SetPuzzleProperties() -- End of module find puzzle properties -- Standard Fuze module -- Picks up all gains by using recentbest function GetRB(prefun,postfun) if RBScore()> Score() then if prefun ~= nil then prefun() end recentbest.Restore() if postfun ~= nil then postfun() end end end function FuzeEnd(prefun,postfun) if prefun ~= nil then prefun() end CI(1) -- Wiggle("wa",1) -- Wiggle("s",1) Wiggle() GetRB(prefun,postfun) if postfun ~= nil then postfun() end SaveBest() end function Fuze1(ci1,ci2,prefun,postfun,globshake) if prefun ~=nil then prefun() end if globshake==nil then globshake=true end CI(ci1) Wiggle("s",1,nil,globshake) CI(ci2) Wiggle("wa",1) if postfun ~= nil then postfun() end end function Fuze2(ci1,ci2,prefun,postfun) if prefun ~= nil then prefun() end CI(ci1) Wiggle("wa",1) CI(1) Wiggle("wa",1) CI(ci2) Wiggle("wa",1) if postfun ~= nil then postfun() end 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,prefun,postfun,globshake) local scr=Score() if slot == nil then slot=4 save.Quicksave(slot) end recentbest.Save() Fuze1(0.3,0.6,prefun,postfun,globshake) FuzeEnd(prefun,postfun) scr=reFuze(scr,slot) Fuze2(0.3,1,prefun,postfun) GetRB(prefun,postfun) SaveBest() scr=reFuze(scr,slot) Fuze1(0.05,1,prefun,postfun,globshake) GetRB(prefun,postfun) SaveBest() scr=reFuze(scr,slot) Fuze2(0.7,0.5,prefun,postfun) FuzeEnd() scr=reFuze(scr,slot) Fuze1(0.07,1,prefun,postfun,globshake) GetRB(prefun,postfun) SaveBest() reFuze(scr,slot) GetRB(prefun,postfun) SaveBest() end -- end standard Fuze module -- Module setsegmentset -- Tvdl, 11-05-2012 Free to use for noncommercial purposes function SetSelection(set) selection.DeselectAll() if set ~= nil then for i=1,#set do selection.SelectRange(set[i][1],set[i][2]) end 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 SetAAtype(set,aa) local saveselected=FindSelected() SetSelection(set) structure.SetSecondaryStructureSelected(aa) SetSelection(saveselected) end -- Module AllLoop 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 qStab() -- Do not accept qstab losses local curscore=Score() PushPosition() 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,nil,localshakes) end CI(1) recentbest.Save() Wiggle() recentbest.Restore() if Score() < curscore then PopPosition() else ClrTopPosition() end end function Cleanup(err) print("Restoring CI, initial selection, best result and structures") CI(1) save.Quickload(3) if Filteractive then FilterOn() end if SAVEDstructs==true then save.LoadSecondaryStructure() end selection.DeselectAll() if SAFEselection ~= nil then SetSelection(SAFEselection) end print(err) 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 progname="DRW " action="rebuild" 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 AddDone(first,last) if donotrevisit then Donepart[first+(last-first)*segCnt2]=true Blocked[#Blocked+1]=first+(last-first)*segCnt2 end if disjunct then for i=first,last do Disj[i]=true end end end function CheckDone(first,last) if not donotrevisit then return false end local result=Donepart[first+(last-first)*segCnt2] if disjunct then for i=first,last do if Disj[i] then result=true end end end return result end function ChkDisjunctList(n) if not disjunct then return end local maxlen=0 for i=1,segCnt2 do if Disj[i] then maxlen=0 else maxlen=maxlen+1 end if maxlen == n then return end end -- No part is big enough so clear Disjunctlist print("Clearing disjunct list") for i=1,segCnt2 do Disj[i]=false end end function ClearDoneList() --clear donelist for i=1,#Blocked do Donepart[Blocked[i]]=false end if disjunct then --clear disjunctlist also for i=1,segCnt2 do Disj[i]=false end end Blocked={} curclrscore=Score() end function ChkDoneList() if not donotrevisit and not disjunt then return end if Score() > curclrscore+clrdonelistgain then if donotrevisit then ClearDoneList() end end end --end of administration part function FindWorst(firsttime) print("Searching worst scoring parts of len "..len) ChkDisjunctList(len) wrst={} GetSegmentScores() local skiplist="" local nrskip=0 for i=1,segCnt2-len+1 do if not CheckDone(i,i+len-1) and MustWorkon(i,i+len-1) then local s=getPartscore(i,i+len-1) wrst[#wrst+1]={s,i} else if CheckDone(i,i+len-1) 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 if firsttime and #wrst == 0 then print("No possibilities left so clearing Done list") ClearDoneList() FindWorst(false) end end -- Rebuild section function localRebuild(maxiters) if maxiters==nil then maxiters=3 end local s=Score() local i=0 if bandflip then band.DisableAll() end Bridgesave() 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 Bridgerestore() if Score()~=s then return true else return false end end function ReBuild(ss,se,tries) ClearScores() --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 then Foundone=true Bridgesave() if doSpecial==true then SelectAround(ss,se,9) CI(1) Wiggle("s",1,nil,true) Wiggle("ws",2,nil,true) selection.DeselectAll() selection.SelectRange(ss,se) Wiggle("wb",4,nil,true) SelectAround(ss,se,9) elseif doShake==true then CI(shakeCI) Wiggle("s",1,nil,true) end Bridgerestore() if AfterRB then PushPosition() --save the current position for next round doMutate() end SaveScores(ss,se,try) if AfterRB then PopPosition() end 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 -- end rebuild section -- section to compute segmentscore(part)s function getPartscore(ss,se,attr) local s=0 if attr=='total' then s=Score() elseif attr==nil then --is only called from findWorst for i=ss,se do s=s+SegmentScores[i] end elseif attr=='loctotal' then --total segment scores s=GetSubscore(nil,ss,se) elseif attr=='ligand' then --ligand score for i=segCnt2+1,segCnt do s=s+current.GetSegmentEnergyScore(i) end else s=GetSubscore(attr,ss,se) end return s end 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 function GetSegmentScores() if lastSegScores~=Score() then lastSegScores=Score() for i=1,segCnt2 do if WORKONbool[i] then if #scrPart==0 then -- if nothing specified by user default is -- segmentenergy - reference + extra Density score SegmentScores[i]=current.GetSegmentEnergyScore(i) if not structure.IsMutable(i) then --ignore reference part but NOT for mutables) SegmentScores[i]=SegmentScores[i]-current.GetSegmentEnergySubscore(i,'reference') end if math.abs(DENSITYWEIGHT) > 0 then --the Density component has extra weight SegmentScores[i]=SegmentScores[i]+DENSITYWEIGHT*current.GetSegmentEnergySubscore(i,'density') end else SegmentScores[i]=GetSubscore(scrPart,i,i) end end end end end -- end section segmentscore(part)s -- Administration of the different slots and best scores Scores={} --{save_no,points,totscore,showlist,todo,rbnr} -- Compute which scoreparts to use ActiveSub=FindActiveSubscores(true) ScoreParts={ --{save_no,name,active,longname} {4,'total',true,'4(total)'}, {5,'loctotal',true,'5(loctotal)'} } nextslot=6 if HASLIGAND then ScoreParts[#ScoreParts+1] = { nextslot,'ligand',true,nextslot..'(ligand)'} nextslot=nextslot+1 print("Ligand slot enabled") end for i=1,#ActiveSub do if ActiveSub[i] ~='Reference' then ScoreParts[#ScoreParts+1] = { nextslot,ActiveSub[i],true,nextslot..'('..ActiveSub[i]..')' } nextslot=nextslot+1 end end function ClearScores() Scores={} for i=1,#ScoreParts do if ScoreParts[i][3] then Scores[#Scores+1]={ScoreParts[i][1],-9999999,-9999999,'',false,-1} end end slotScr={} end function SaveScores(ss,se,RBnr) local scr={} for i=1,#ScoreParts do if ScoreParts[i][3] then scr[#scr+1]={ScoreParts[i][1],getPartscore(ss,se,ScoreParts[i][2])} end end local totscore=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 Scores[i][3]=totscore Scores[i][6]=RBnr end end SaveBest() end function ListSlots() --Give overview of slot occupation --And sets which slots to process local Donelist={} for i=1,#Scores do Donelist[i]=false end local Report="" for i=1,#Scores do if not Donelist[i] then local Curlist=" "..Scores[i][1] Scores[i][5]=true --This one we have to process -- Now find identical filled slots for j=i+1,#Scores do if Scores[j][3] == Scores[i][3] then Curlist=Curlist.."="..Scores[j][1] Donelist[j]=true end end Scores[i][4]=Curlist Report=Report.." "..Curlist end end print("Slotlist:"..Report) end -- end of administration of slots and scores 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 MutateSel(maxitter) if maxitter == nil then maxitter=2 end structure.MutateSidechainsSelected(maxitter) end function MutateAll(maxitter) selection.SelectAll() MutateSel(maxitter) end function doMutate() if not HASMUTABLE then return end -- Do not accept loss if mutating local curscore=Score() PushPosition() CI(MutateCI) Bridgesave() if MUTRB then selection.DeselectAll() selection.SelectRange(firstRBseg,lastRBseg) MutateSel() elseif MUTSur then SelectAround(firstRBseg,lastRBseg,MutSphere) MutateSel() else MutateAll() end Bridgerestore() if Score() < curscore then PopPosition() else ClrTopPosition() end end function DeepRebuild() local ss=Score() print("Deep"..action.." started at score: "..round3(ss)) if struct==false then AllLoop() end save.Quicksave(3) recentbest.Save() for i=1,#areas do local ss1=Score() local s=areas[i][1] local e=areas[i][2] local CurrentHigh=0 local CurrentAll="" -- to report where gains came from local CurrentHighScore= -99999999 firstRBseg=s lastRBseg=e Bridgesave() if Runnr > 0 then --Runnr 0 is to skip worst parts print("DR "..Runnr.."."..(e-s+1).."."..i.." "..s.."-"..e.." ".. rebuilds.." times. Wait... Current score: "..round3(Score())) if ReBuild(s,e,rebuilds) then -- Make sure we do not miss an improvement during rebuild if RBScore() > bestScore then Bridgesave() recentbest.Restore() Bridgerestore() if Score() > bestScore+0.00001 then print("Found a missed gain!!!") SaveScores(s,e,0) end end ListSlots() for r=1,#Scores do if Scores[r][5] then local slot=Scores[r][1] save.Quickload(slot) SelectAround(s,e,12) --local shake after rebuild/remix Bridgesave() if not skipqstab then qStab() else CI(1) Wiggle("s",1,nil,true) Wiggle("ws",1,nil,true) end Bridgerestore() if AfterQstab then doMutate() end save.Quicksave(slot) if Score() > CurrentHighScore then CurrentHigh=slot CurrentAll=Scores[r][4].."(RB"..Scores[r][6]..")" CurrentHighScore=Score() end SaveBest() print("Stabilized score: "..round3(Score()).." from slot "..ScoreParts[slot-3][4]) end end save.Quickload(CurrentHigh) 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 Fuze(4,Bridgesave,Bridgerestore,localshakes) else Fuze(4,nil,nil,localshakes) end if AfterFuze then doMutate() end end SaveBest() save.Quickload(3) else save.Quickload(3) end end --skip section if savebridges then if BridgesBroken() then -- THIS SHOULD NOT HAPPEN print("Unexpected bridge broken, pls report\n") print("Restoring a good position, discarding wins\n") Bridgerestore() save.Quicksave(3) bestScore=Score() else Bridgerestore() end else Bridgerestore() end if ss1+0.00001 < Score() then print("Gain from slots ",CurrentAll) end AddDone(s,e) ChkDoneList() if Score()-ss > minGain then break end if Score()-DRWstartscore > drwgain then break end end print("Deep"..action.." gain: "..round3(Score()-ss)) if struct==false and SAVEDstructs then save.LoadSecondaryStructure() end end function DRcall(how) if how=="drw" then local stepsize=1 if minLen>maxLen then stepsize= -1 end for i=minLen,maxLen,stepsize do --search from minl to maxl worst segments len=i FindWorst(true) --fill areas table. Comment it if you have set them by hand PrintAreas() DeepRebuild() if Score()-DRWstartscore > drwgain then break end end elseif how=="fj" then --DRW len cutted on pieces FindWorst(true) --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=1,segCnt2 do if i+x-1<=segCnt2 then areas[#areas+1]={x,x+i-1} end end end PrintAreas() DeepRebuild() elseif how=="simple" then FindWorst(true) PrintAreas() DeepRebuild() elseif how=="areas" then areas={} FindAreas() PrintAreas() DeepRebuild() end end function AskMoreOptions() local ask=dialog.CreateDialog("More "..progname.." options") ask.fastQstab=dialog.AddCheckbox("Do a fast qStab",fastQstab) ask.ll3 = dialog.AddLabel("Force next round if gain is more") ask.minGain = dialog.AddSlider("MinGain:",minGain,0,500,0) ask.ll4 = dialog.AddLabel("Skip fuze if loss is more") ask.ll5 = 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.l1=dialog.AddLabel("Clear no revisit list if gain is more") ask.revlist=dialog.AddSlider("Cleargain:",clrdonelistgain,0,500,0) ask.l2=dialog.AddLabel("Number of "..action.." each pass") ask.nrrebuilds=dialog.AddSlider(action..":",rebuilds,1,100,0) ask.reBuild=dialog.AddSlider("#in first cycle:",reBuild,1,segCnt2,0) ask.reBuildm=dialog.AddSlider("#add each cycle:",reBuildmore,0,4,0) ask.doSpecial=dialog.AddCheckbox("Local cleanup after "..action.." SLOW",doSpecial) ask.doShake=dialog.AddCheckbox("Or Shake after "..action,doShake) ask.shakeCI=dialog.AddSlider("Shake CI:",shakeCI,0,1,2) 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) fastQstab=ask.fastQstab.value minGain=ask.minGain.value maxlossbeforefuze=ask.maxLoss.value clrdonelistgain=ask.revlist.value rebuilds=ask.nrrebuilds.value reBuild=ask.reBuild.value reBuildmore=ask.reBuildm.value doShake=ask.doShake.value doSpecial=ask.doSpecial.value shakeCI=ask.shakeCI.value skipqstab=ask.skipqstab.value donotrevisit=ask.donotrevisit.value skipfuze=ask.skipfuze.value end function AskMutateOptions() local ask = dialog.CreateDialog("Mutate Options") ask.AfterRB = dialog.AddCheckbox("Mutate after "..action,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, last one counts or all") ask.OnlyRB=dialog.AddCheckbox("Mutate only "..action.." part",MUTRB) ask.OnlySur=dialog.AddCheckbox("Mutate "..action.." 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 if MUTSur then MUTRB=false end end end function printOptions(title) print(title.." Based on rav4pl DRW 3.4") print("Length of "..action..": "..minLen.." to "..maxLen) print(action.." area: "..SegmentSetToString(WORKON)) print("Nr of "..action.." each try: "..rebuilds) if WF>1 then print("Wiggle factor "..WF) end if not struct then print("Convert everything to loops") end if not donotrevisit then print("Will retry already tried "..action) else print("Clear retry blockings if gain raises above "..clrdonelistgain.." pts") end if doSpecial then print("Local cleanup after "..action) elseif doShake then print("Initial shake after "..action.." 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.." worst segmentparts") end if disjunct then print("Running in disjunct mode") end end function AskSubScores() local ask = dialog.CreateDialog("Slot selection "..progname..DRWVersion) ask.l1=dialog.AddLabel("Specify which slots based on scorepart to use") for i=1,#ScoreParts do ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][1].." "..ScoreParts[i][2],ScoreParts[i][3]) end ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0) if dialog.Show(ask) > 0 then for i=1,#ScoreParts do ScoreParts[i][3]=ask[ScoreParts[i][2]].value end end end function AskSelScores() local ask = dialog.CreateDialog("Set worst searching "..progname..DRWVersion) ask.l1=dialog.AddLabel("Specify which worst subscoretotal(s) to count") for i=3,#ScoreParts do ask[ScoreParts[i][2]]=dialog.AddCheckbox(ScoreParts[i][2],false) end ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0) scrPart={} if dialog.Show(ask) > 0 then for i=3,#ScoreParts do if ask[ScoreParts[i][2]].value then scrPart[#scrPart+1]=ScoreParts[i][2] end end end end function AskDRWOptions() local askresult local askmutable=HASMUTABLE local ask = dialog.CreateDialog("Tvdl enhanced "..progname..DRWVersion) if askmutable then print("Setting default mutate options") AfterQstab=true AfterFuze=true MutSur=true end repeat ask.l1 = dialog.AddLabel("Length to rebuild, From can be bigger than To") ask.minLen = dialog.AddSlider("From length:",minLen,1,10,0) ask.maxLen = dialog.AddSlider("To length:",maxLen,1,10,0) ask.lll=dialog.AddLabel("Wiggle more when CI is on its maximum") ask.WF = dialog.AddSlider("WiggleFactor:",WF,1,5,0) ask.slotl=dialog.AddLabel("Slot selection, last choice counts") ask.selall=dialog.AddCheckbox("All slots",SlotAll) ask.sel4=dialog.AddCheckbox("4 main slots, faster",Slot4) ask.selSP= dialog.AddCheckbox("(Re)select slots",false) ask.ll4=dialog.AddLabel("Skip first worst parts (crash resume)") ask.nrskip=dialog.AddSlider("Skip parts:",nrskip,0,segCnt2,0) ask.SEL= dialog.AddCheckbox("(Re)select where to work on ",false) if HASMUTABLE then ask.MUTS = dialog.AddCheckbox("(Re)set Mutate Options",askmutable) end ask.localshakes=dialog.AddCheckbox("Do shakes only local",localshakes) ask.worst= dialog.AddCheckbox("(Re)set worst search params",false) if nrofbridges > 1 then ask.bridge = dialog.AddCheckbox("Keep sulfide bridges intact",savebridges) end ask.struct = dialog.AddCheckbox("Do not change all to loop",struct) ask.l6=dialog.AddLabel("Search only for disjunct from previous done") ask.disjunct=dialog.AddCheckbox("Disjunct",disjunct) ask.bandflip=dialog.AddCheckbox("Disable bands during rebuild AND enable after",bandflip) ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0) ask.Options = dialog.AddButton("More options",2) askresult=dialog.Show(ask) if askresult > 0 then minLen=ask.minLen.value maxLen=ask.maxLen.value nrskip=ask.nrskip.value bandflip=ask.bandflip.value disjunct=ask.disjunct.value struct=ask.struct.value WF=ask.WF.value SlotAll=ask.selall.value if SlotAll then for i=1,#ScoreParts do ScoreParts[i][3]=true end end Slot4=ask.sel4.value if Slot4 then for i=1,#ScoreParts do if ScoreParts[i][1] == 4 then ScoreParts[i][3]=true elseif ScoreParts[i][2] == 'Backbone' then ScoreParts[i][3]=true elseif ScoreParts[i][2] == 'Hiding' then ScoreParts[i][3]=true elseif ScoreParts[i][2] == 'Packing' then ScoreParts[i][3]=true else ScoreParts[i][3]=false end end end localshakes=ask.localshakes.value if nrofbridges > 1 then savebridges=ask.bridge.value end if ask.SEL.value then Slot4=false SlotAll=false local SelMode={} SelMode.askignorefrozen=false SelMode.defignorefrozen=true SelMode.askignorelocks=false SelMode.defignorelocks=true SelMode.askligands=false SelMode.defligands=false WORKON=AskForSelections("Tvdl enhanced "..progname..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 if ask.selSP.value then AskSubScores() if askresult==1 then askresult=4 end end for i=1,#ScoreParts do if ScoreParts[i][3] then print("Active slot "..ScoreParts[i][1].." is "..ScoreParts[i][2]) end end if ask.worst.value then AskSelScores() if askresult==1 then askresult=4 end 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 HASMUTABLE then if ask.MUTS.value then AskMutateOptions() askmutable=false if askresult==1 then askresult=4 end --to force return to main menu end end if HASMUTABLE then print("Mutate options are now:") local Mess="Mutates " if AfterRB then Mess=Mess.."after each rebuild, " end if InQstab then Mess=Mess.."inside qStab, " end if AfterQstab then Mess=Mess.."after qStab, " end if BeFuze then Mess=Mess.."before Fuzing, " end if AfterFuze then Mess=Mess.."after Fuzing." end print(Mess) Mess="Mutate area " if MUTRB then Mess=Mess.."is Rebuild parts only" elseif MUTSur then Mess=Mess.."is Rebuild part and surroundings" else Mess=Mess.."is the whole protein" end print(Mess) end if askresult==2 then AskMoreOptions() end end until askresult < 2 return askresult > 0 end -- Quick fix for failing first rebuild for i=3,12 do save.Quicksave(i) 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={} --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 doSpecial=false -- local shake, wiggle sidec, wiggle backbone, even slower 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 reBuild=4 --up to worst parts to look at reBuildmore=1 --increased by every main cycle rebuilds=15 --how many rebuilds to try, set at least 10! function askAUNT() local ask=dialog.CreateDialog("HI Auntdeen") ask.l1=dialog.AddLabel("Set number of rebuilds") ask.l2=dialog.AddLabel("Low 15") ask.l3=dialog.AddLabel("Medium 25") ask.l4=dialog.AddLabel("High 40") ask.low=dialog.AddButton("Low",1) ask.med=dialog.AddButton("Medium",2) ask.high=dialog.AddButton("High",3) local result=dialog.Show(ask) if result==1 then rebuilds=15 elseif result==2 then rebuilds=25 else rebuilds=40 end end if ISAUNTDEEN then askAUNT() end rebuildCI=0 --clash importance while rebuild len=6 --find worst segments part minLen=2 --or specify minimum len maxLen=4 --and maximim len -- New options maxnrofRuns=40 -- Set it very high if you want to run forever Runnr=0 minGain=(segCnt2-segCnt2%4)/4 -- If less gain then try the next one, else recompute if minGain < 40 then minGain=40 end skipqstab=false skipfuze=false bandflip= band.GetCount() > 0 maxlossbeforefuze=(segCnt2-segCnt2%4)/4 -- if loss is more no fuze is done if maxlossbeforefuze < 30 then maxlossbeforefuze=30 end nrskip=0 localshakes=true AfterRB=false InQstab=false AfterQstab=false BeFuze=false AfterFuze=false MutateCI=0.9 MutSphere=8 MUTRB=false MUTSur=false if HASMUTABLE then AfterQstab=true AfterFuze=true MUTSur=true end Slot4=false SlotAll=true WORKON={{1,segCnt2}} -- part to administrate what has been done Donepart={} --To find fast if to be skipped Blocked={} --A simple list so we can clear Donepart Disj={} --To administrate which segments have be touched disjunct=false donotrevisit=true clrdonelistgain=segCnt curclrscore=Score() WORKONbool={} SegmentScores={} --Optimalisation for fast worst search lastSegScores=0 DRWVersion="3.0.2" -- MAIN PROGRAM firstDRWcall=true DRWstartscore=0 function DRW() if firstDRWcall then printOptions("Tvdl enhanced "..progname..DRWVersion) firstDRWcall=false end InitWORKONbool() DRWstartscore=Score() if nrskip > 0 then local sreBuild=reBuild reBuild=nrskip Runnr=0 DRcall("drw") nrskip=0 reBuild=sreBuild end maxnrofRuns=drwcycles for nrofRuns=1,maxnrofRuns do --uncomment method/s you want to use Runnr=Runnr+1 print("Main cycle nr ",Runnr) -- DRcall("areas") DRcall("drw") -- DRcall("fj") -- DRcall("all") -- DRcall("simple") if Score()-DRWstartscore > drwgain then break end ChkDoneList() reBuild=reBuild+reBuildmore end end -- Change defaults if the startscore is negative if Score() < 4000 then local adjust=true if HASDENSITY then local oscore=GetSubscore("density") if Score()-oscore*(DENSITYWEIGHT+1) > 4000 then adjust=false print("ED puzzle, score high enough not counting ED") print("so no auto blocking of qstab and fuze") end end if adjust then print("Score < 4000, adjusting defaults") print("Now skipping Fuzes, replacing qStab") print("Can be changed in More options") skipfuze=true skipqstab=true end end SAFEselection=FindSelected() function MakeBands(num) local done=false local s1=math.random(segCnt2) local s2=math.random(segCnt2) if s1>s2 then s1,s2=s2,s1 end local d=structure.GetDistance(s1,s2) if s2-s1>=minSkip and d>=minDist and d<=maxDist then done=true end if done then num=num-1 mkBand(s1,s2) bands[#bands+1]={s1,s2} end if num>0 then return MakeBands(num) end --tail call end function mkBand(s1,s2) band.AddBetweenSegments(s1, s2) local len=structure.GetDistance(s1,s2) if decomp==true then len=len+compressFrac else len=len-compressFrac end if len<3.5 then len=3.5 end if len>20 then len=20 end band.SetGoalLength(band.GetCount(),len) end bands={} function Repeat_bands(bands) band.DeleteAll() for i=1,#bands do local s1=bands[i][1] local s2=bands[i][2] mkBand(s1,s2) end end function Bandstr(str) --set all band strength if str<0.1 then str=0.1 end if str>10 then str=10 end for i=1, band.GetCount() do band.SetStrength(i,str) end end function Compressor(numTries) if numTries == nil then numTries=1000 end local sscore=Score() --starting score print("Starting Compressor v2 "..numTries.." loops.") if normal==false then print("Using exploration options") end if decomp==true then print("Decompressing") minDist=7 maxDist=20-compressFrac else minDist=10 --minimum spatial distance between banding segments maxDist=20+compressFrac --maximum spatial distance between banding segments end save.Quicksave(3) badOnes=0 recentbest.Save() local best=false for i=1,numTries do local ls=Score() local lastbest=bestScore loss=Score()*percLoss/100 --pulling till we lost some points band.DeleteAll() PushPosition() --save state for losing if best==true and repeatGood==true then print("Repeating last bands.") Repeat_bands(bands) else bands={} MakeBands(numBands) end print("Loop "..i.." of "..numTries.." started. Current score: "..round3(ls)) CI(pullingCI) selection.SelectAll() recentbest.Save() if slowBands then for str=minStr,maxStr,0.07 do--search enough band strenght to move if normal==true then recentbest.Restore() end--because sometimes it makes points during pull :D local ss=Score() Bandstr(str) Wiggle("wb",1) if ss-Score()>loss then minStr=str-0.1 break end end else Bandstr(maxStr) Wiggle("wb",1) end band.DeleteAll() -- Save gains during pull PushPosition() recentbest.Restore() band.DeleteAll() SaveBest() PopPosition() --back to the position after Pull qStab() if useFuze and Score()> (bestScore-fuzeScore) then SaveBest() Fuze(4) end local afterscore=Score() SaveBest() if maxLoss>0 then if Score()>bestScore-maxLoss then ClrTopPosition() best= (Score() > ls) else best=false badOnes=badOnes+1 if badOnes >=reloadBest then badOnes=0 save.Quickload(3) ClrTopPosition() else PopPosition() end end else ClrTopPosition() save.Quickload(3) end local es=Score() print("Loop "..i.." gain "..round3(es-ls).." ;total gain "..round3(bestScore-sscore)) -- Stop if gain is enough but only after a loss if Score() - sscore > compgain and es-ls < 0 then break end end save.Quickload(3) print("Total compress gain: "..round3(Score()-sscore)) end ----------- options below VVVVV --------------------- useRegions={ --set regions that have to be used in all bands --{1,20} --{25,55} --{100,210} } compressFrac=4 --make bands shorter by that much points minSkip=15 --minimum segment distance between banded segments numBands=9 --how many bands use at once useFuze=true -- use Fuze after qStab fuzeScore=-1 --how close we have to be to run Fuze minStr=0.3 --starting band str maxStr=1.0 -- max band strenght slowBands=true --bands strenght are raised few times till score drops by % percLoss=2 --pulling stops when score drops by that percent (ie 2=200pts when 10k pts) repeatGood=true --repeating good bands pullingCI=0.9 --clash importance during pull maxLoss=50 --maximum acceptable LOSS after pull/stabilize reloadBest=5 --reload best solution after that many worst ones decomp=false --true --true for DeCompression instead of compression function AskCompOptions() local ask=dialog.CreateDialog("Set Compressor options") ask.compFrac=dialog.AddSlider("Compress by",compressFrac,1,10,0) ask.minSkip=dialog.AddSlider("Min seg dist",minSkip,1,20,0) ask.numBands=dialog.AddSlider("Nr of bands",numBands,3,12,0) ask.minStr=dialog.AddSlider("Min band str",minStr,0.1,1,1) ask.maxStr=dialog.AddSlider("Max band str",maxStr,0.3,2,1) ask.pullingCI=dialog.AddSlider("PullingCI",pullingCI,0,1,1) ask.maxLoss=dialog.AddSlider("Max loss",maxLoss,10,100,0) ask.reloadBest=dialog.AddSlider("Max big loss",reloadBest,0,10,1) ask.l1=dialog.AddLabel("Run fuze if score is close enough") ask.fuzeScore=dialog.AddSlider("Fuze limit",fuzeScore,-5,10,0) ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0) local result=dialog.Show(ask) if result > 0 then compressFrac=ask.compFrac.value minSkip=ask.minSkip.value numBands=ask.numBands.value minStr=ask.minStr.value maxStr=ask.maxStr.value pullingCI=ask.pullingCI.value maxLoss=ask.maxLoss.value reloadBest=ask.reloadBest.value fuzeScore=ask.fuzeScore.value end return result end DCVersion="2.0.0" askdrw=true askcomp=true drwgain=50 compgain=50 drwcycles=2 compcycles=20 clrdone=100 function SetSwitchParams() local ask=dialog.CreateDialog("Tvdl DRW Compressor combi "..DCVersion) ask.l1=dialog.AddLabel("Switch if one of the bounds is reached") ask.drwcycles=dialog.AddSlider("DRW cycles:",drwcycles,1,10,0) ask.drwgain=dialog.AddSlider("DRW gain:",drwgain,1,200,0) ask.compcycles=dialog.AddSlider("Comp cycles:",compcycles,1,50,0) ask.compgain=dialog.AddSlider("Comp gain:",compgain,1,200,0) ask.l2=dialog.AddLabel("Change defaults") ask.askdrw=dialog.AddCheckbox("DRW settings",askdrw) ask.askcomp=dialog.AddCheckbox("Comp settings",askcomp) ask.l3=dialog.AddLabel("Clear donelist of DRW if Comp gained more") ask.clrdone=dialog.AddSlider("Clear gain",clrdone,-1,300,0) ask.OK = dialog.AddButton("OK",1) ask.Cancel = dialog.AddButton("Cancel",0) if dialog.Show(ask) > 0 then drwcycles=ask.drwcycles.value drwgain=ask.drwgain.value compcycles=ask.compcycles.value compgain=ask.compgain.value askdrw=ask.askdrw.value askcomp=ask.askcomp.value clrdone=ask.clrdone.value return true end return false end function MainProg() if SetSwitchParams() then local nrtries=0 if askdrw then AskDRWOptions() end if askcomp then AskCompOptions() end repeat DRW() local compscore=Score() Compressor(compcycles,compgain) if Score() - compscore > clrdone then ClearDoneList() end nrtries=nrtries+1 until nrtries > 50 --Just to prevent looping on nothing end Cleanup() end xpcall(MainProg,Cleanup)

Comments