Recipe: CM - Manual DRW V2.0 - 1.0.2

created by ComputerMage

Profile

• Name: CM - Manual DRW V2.0 - 1.0.2
• ID: 44055
• Shared with: Public
• Parent: None
• Children: None
• Created on: October 22, 2012 at 14:09 PM UTC
• Updated on: October 22, 2012 at 14:09 PM UTC
• Description:

  Allows to deep rebuild areas between freeze points. ; Frozen segments unfroze and added to the list to allow properly to rebuild. ; If recipie is cancelled then it loads recent best score. ; If puzzle is mutable it will try to mutate selected part as well.

Code

areas = {}
p=print
CI=behavior.SetClashImportance
segCnt=structure.GetCount()
mutate=false
while structure.GetSecondaryStructure(segCnt)=="M" do
 segCnt=segCnt-1
end

for idx = 1,segCnt do
	if structure.IsMutable(idx) then
		mutate=true
		p("Puzzle has mutable segments. Enabling mutations.")
		break
	end
end

function GetFrozenPairs()
  print("Number of segments is "..structure.GetCount());
  startPos = 0
  endPos = 0
  for idx = 1,structure.GetCount() do
    if freeze.IsFrozen(idx) then
      if startPos == 0 then
        startPos = idx;
      elseif endPos == 0 then
        endPos = idx;
		areas[#areas + 1] = {startPos, endPos}
		freeze.Unfreeze(startPos,true,true)
		freeze.Unfreeze(endPos,true,true)
		startPos = 0
		endPos = 0
      end
    end
  end
end

function Score()
    local s=0
    if normal==true then
        s=current.GetEnergyScore()
    else
        s=current.GetScore()
    end
    return s
end

function round(x)--cut all afer 3-rd place
    return x-x%0.001
end
function abs(x)
    if x<0 then x=-x end
    return x
end

function Wiggle(how, iters, minppi) --score conditioned recursive wiggle/shake
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end

    if iters>0 then
        iters=iters-1
        local sp=Score()
        if how == "s" then structure.ShakeSidechainsAll(1)
            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
        if Score()-sp > minppi then return Wiggle(how, iters, minppi) end
    end
end

SAVEDstructs=false
function AllLoop() --turning entire structure to loops
    local anychange=false
    for i=1,segCnt 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, segCnt do
        for x=ss,se do
            if structure.GetDistance(x,i)<radius then selection.Select(i) break end
        end 
    end
end
function qStab()
    CI(0.1)
    Wiggle("s",1)
	if mutate == true then
		structure.MutateSidechainsSelected(1)
		SaveBest();
	end
    selection.SelectAll()
    if fastQstab==false then 
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
    end
    CI(1)
    Wiggle()
end

function FuzeEnd()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    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()
    selection.SelectAll()
    recentbest.Save()
    Fuze1(0.3,0.6) FuzeEnd()
    scr=reFuze(scr,slot)
    Fuze2(0.3,1) SaveBest()
    scr=reFuze(scr,slot)
    Fuze1(0.05,1) SaveBest()
    scr=reFuze(scr,slot)
    Fuze2(0.7,0.5) FuzeEnd()
    scr=reFuze(scr,slot)
    Fuze1(0.07,1) SaveBest()
    reFuze(scr,slot)
    recentbest.Restore()
    SaveBest()
end

bestScore=Score()
function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        if g>0.01 then p("Gained another ",round(g)," pts.") end
        bestScore=Score()
        save.Quicksave(3)
    end
end
function IsBridge(i)
    return ''..current.GetSegmentEnergySubscore(i,'disulfides') ~= '-0'
end
-- Counts bridges in protein or in rebuild according to globalbridge var
_cyslist = nil
function CountBridges(ss,se)
    if not globalbridge then -- no bridges in a null range
        if ss == nil then return 0 end
        if se == nil then se = ss end
    end
    if _cyslist == nil then -- build initial list
        _cyslist = {}
        for i = 1,segCnt do
            if structure.GetSecondaryStructure(i) ~= 'M' and structure.GetAminoAcid(i) == 'c' then _cyslist[#_cyslist+1] = i end
        end
    end
    local count = 0
    for i = 1,#_cyslist do
        local seg = _cyslist[i]
        if (globalbridge or (seg >= ss and seg <= se)) and
            IsBridge(seg) then count = count + 1 end
    end
    return count
end
function BridgesBroken(n,ss,se)
    return savebridges == true and CountBridges(ss,se) < n
end
function localRebuild(maxiters,ss,se)
    if maxiters==nil then maxiters=3 end
    local s=Score()
    local i=0
    local nbridges = CountBridges(ss,se)
    repeat
        i=i+1
        if i>maxiters then break end
        structure.RebuildSelected(i)
    until Score()~=s and BridgesBroken(nbridges,ss,se) == false
    if Score()~=s then return true else return false end
end
function ReBuild(ss,se,tries)
    Clear() --reser score tables
    if ss>se then ss,se=se,ss end --switch if needed
    p("DR area ",ss,"-",se," ",tries," times.")
	p(" Wait... Current score: ",round(Score()))
    selection.DeselectAll()
    CI(rebuildCI)
    local bcheckss, bcheckse = ss,se
    local nbridges = CountBridges(bcheckss,bcheckse)
    selection.SelectRange(ss,se)
    if rbSkip> 0 then
        p("Skipping ",rbSkip," postitions...")
        structure.RebuildSelected(rbSkip)
        p("Now scoring rebuilds.")
    end
    for try=1,tries do -- perform loop for number of tries
        local extra_rebuilds = savebridges and 3 or 1 -- extra tries if bridges keep breaking
        CI(rebuildCI)
        local done
        repeat
            done=localRebuild(3,bcheckss,bcheckse)
            extra_rebuilds = extra_rebuilds - 1
        until done or extra_rebuilds > 0
        if not BridgesBroken(bcheckss,bcheckse) then SaveBest() end
        if done==true and doShake==true then
            CI(shakeCI)
            if not BridgesBroken(nbridges,bcheckss,bcheckse) then Save(ss,se) end
            Wiggle("s",1)
            if not BridgesBroken(nbridges,bcheckss,bcheckse) then SaveBest() end
        end
		if done == true and mutate == true then
			structure.MutateSidechainsSelected(1)
		end
        if done==true and not BridgesBroken(nbridges,bcheckss,bcheckse) then
			Save(ss,se)
			SaveBest()
		end
    end
    CI(1)
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~=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)-current.GetSegmentEnergySubscore(i, 'reference') --ignore reference part
        end
    end
    return s
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) --p("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 DeepRebuild()
    local ss=Score()
    if struct==false then AllLoop() end
    save.Quicksave(3)
    p("DeepRebuild started at score: ",round(ss))
    for i=1,#areas do
        local ss=Score()
        local s=areas[i][1]
        local e=areas[i][2]
        local nbridges = CountBridges(s,e)
        ReBuild(s,e,rebuilds)
        for r=1,#Scores do
            slot=Scores[r][1]
            if ScoresCheck(slot) then
                p("Stabilizing slot ",slot)
                SelectAround(s,e,12) --local shake after rebuild
				if mutate == true then
					structure.MutateSidechainsSelected(1)
					SaveBest();
				end
                qStab()
				if mutate == true then
					structure.MutateSidechainsSelected(1)
					SaveBest();
				end
            end
        end
        save.Quickload(4)
        recentbest.Save()
        for i=5,10 do
            save.Quickload(i)
        end
        recentbest.Restore()
        p("Fuzing best position.")
        save.Quicksave(4)
		if mutate == true then
			structure.MutateSidechainsSelected(1)
			SaveBest();
		end
        Fuze(4)
		if mutate == true then
			structure.MutateSidechainsSelected(1)
		end
        if not BridgesBroken(nbridges,s,e) then SaveBest() end
        save.Quickload(3)
        if breakOnPoints and Score()>ss then break end --break if points found
    end
    p("DeepRebuild gain: ",round(Score()-ss))
    if struct==false then save.LoadSecondaryStructure() end
end

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


normal = current.GetExplorationMultiplier() == 0

breakOnPoints=true --breaking rebuild after succesfull one to find new worsts
doShake=true --false --shake rebuilded area (only!) every rebuild, slowing down process
shakeCI=0.31 --clash imortance while shaking

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

savebridges=true -- if set, never accepts a rebuild that breaks a disulfide bond
globalbridge=true -- if true count all bridges in protien, else only check in rebuild segments

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

rebuilds=15 --how many rebuilds to try, set at least 10!
rbSkip=0 --skip that many rebuilds b4 scoring (for aunt_deen) ;]
rebuildCI=0 --clash importance while rebuild


-- main proc
function Main()
	p("Manual Deep Rebuild (with disulphide bridges fix) by ComputerMage. Based on DRW Disulphides 3.4.2 code.")
	GetFrozenPairs()

	if #areas ~= 0 then
		while true do --uncomment method/s you want to use
			DeepRebuild() --if set "areas" above by hand
		end
	else
		p("Nothing to rebuild. Please freeze segments. It will rebuild between them")
	end
end

--main call
    xpcall(Main,Cleanup)
--end of scipt