Code
-- Toolbox
-- MurloW
p = print
p("")
nSegs=structure.GetCount()
ItMu = 1.4
if ItMu<=0.2 then ItMu=1 end
function wig(how,it,iters,minppi)
if how==nil then how="wa" end
if it==nil then it=10*ItMu else it=it*ItMu end
if iters==nil then iters=2 end
if minppi==nil then minppi=1 end
it=math.ceil(it)
if iters>0 then
iters=iters-1
local sp=score()
if how == "s" then structure.ShakeSidechainsAll(1)
elseif how == "wb" then structure.WiggleAll(it, true, false)
elseif how == "ws" then structure.WiggleAll(it, false, true)
elseif how == "wa" then structure.WiggleAll(it, true, true)
end
if score()-sp > minppi and how ~= "s" then return wig(how,it,iters,minppi) end
end end
function score()
local s=0
if DisFil then behavior.SetSlowFiltersDisabled(false) end
s=current.GetScore()
if DisFil then behavior.SetSlowFiltersDisabled(true) end
return s
end
function Seed()
seed=os.time()/math.abs(current.GetEnergyScore())
seed=seed%0.001
seed=1/seed
while seed<10000000 do seed=seed*10 end
seed=seed-seed%1
math.randomseed(seed)
end
Seed()
function isMovable(seg1, seg2)
local FT = true
for i=seg1, seg2 do
BB, SC = freeze.IsFrozen(i)
if (BB == true) then FT = false end
sl = structure.IsLocked(i)
if ( sl == true ) then FT = false end
end
return FT
end
function Check()
local sc=score()
local gain=0
if (bestscore < sc) then
gain = sc - bestscore
bestscore = sc
save.Quicksave(50)
Delbands()
save.Quicksave(1)
save.Quickload(50)
if cut(gain)>0 then p("",string.format(" %.4f pts, new score: %.4f",gain,sc),os.date("%X")) end
end end
function setCI(ci)
return behavior.SetClashImportance(ci)
end
function qStab()
setCI(cival/2)
wig("wa",5) Check()
setCI(cival)
wig("s") Check()
wig() Check()
setCI(cival/3)
wig("wa",5) Check()
setCI(cival)
wig() Check()
wig("s") Check()
wig() Check()
end
function Fuze()
Check()
setCI(.05)
wig("s") Check()
setCI(cival)
wig() Check()
setCI(cival/3)
wig("wa",5) Check()
if Sf == false then
setCI(.07)
wig("s") Check()
setCI(cival)
wig() Check()
setCI(cival/3)
wig("wa",5) Check()
end
setCI(cival)
wig("s") Check()
wig() Check()
end
function mutaFuze()
Check()
setCI(0.15)
structure.MutateSidechainsAll(1) Check()
setCI(cival/3)
wig("wa",4) Check()
setCI(cival)
wig() Check()
if Sf==false then
setCI(0.2)
wig("s") Check()
setCI(cival/2)
wig("wa",5) Check()
setCI(0.87*cival)
structure.MutateSidechainsSAll(1) Check()
selection.DeselectAll()
end
setCI(cival)
wig() Check()
wig("s") Check()
wig() Check()
end
function Fuzit()
if muta then mutaFuze()
else Fuze() end
recentbest.Restore() Check()
end
function Test()
if (Qscore-score())>(Qscore/4) then
setCI(cival/3)
wig("wa",5) Check()
wig("s") Check()
end
setCI(cival)
wig() Check()
setCI(cival/3)
wig("wa",5) Check()
setCI(cival)
wig() Check()
recentbest.Restore() Check()
if qst then qStab() end
recentbest.Restore() Check()
if fuzt>=0 then
if score()>(Qscore-fuzt) then
Fuzit()
end
else
if score()>=(Qscore+FF) then
Fuzit()
end
end
end
function sort(part)
Mseg = {}
for x=1,nSegs do
Mseg[x]={x,current.GetSegmentEnergySubscore(x, part)}
end
table.sort(Mseg,function(x,y) return x[2]<y[2] end)
return Mseg
end
function cut(x)
return x-x%0.0001
end
function checkLocked()
lockd=0 -- locked seg quantity counter
locklist = {}
for k=1,nSegs do -- k = seg identity counter
if isMovable(k,k) == false then
lockd=lockd+1
locklist[lockd] = k
end end
return lockd,locklist
end
function checkSelected()
selected=0
selList = {}
for k=1, nSegs do
if selection.IsSelected(k) then
selected=selected+1
selList[selected] = k
end end
if selected>0 then sels=true
else sels=false end
return selList,sels
end
function selectsphere(seg, radius)
if seg>nSegs then seg = nSegs end
if seg<1 then seg = 1 end
for i=1, nSegs do
if structure.GetDistance(seg,i) <= radius then selection.Select(i) end end
end
function contains(x, value)
for _, v in pairs(x) do
if v == value then
return true
end
end
return false
end
function Delbands()
if KB then
freshbands = band.GetCount()
for h = oldbands, freshbands-1 do band.Delete(oldbands+1) end
else
band.DeleteAll() end
end
function Disbands()
if KBE then
newbands = band.GetCount()
for i = oldbands, newbands-1 do band.Disable(i+1) end
else
band.DisableAll() end
end
function Rbld()
local sco=score()
local its=0
Disbands()
setCI(0.1)
repeat
its=its+1
if its>4 then break end
structure.RebuildSelected(its)
until cut(score())~=cut(sco)
end
function End(errmsg)
if done then return end
done=true
if string.find(errmsg,"Cancelled") then
p("")
p(" User cancel.")
Result()
p("")
else
p("")
p(errmsg)
Result()
end
return errmsg
end
function Result()
Check()
recentbest.Restore() Check()
save.Quickload(1)
Delbands()
p("",os.date("%X"))
if DisFil then behavior.SetSlowFiltersDisabled(false) end
local Tgain = (score()-startscore)
if Tgain<0.0001 then
p(" No change.. :/ ")
else
p(" Startscore: "..cut(startscore))
p(" Score: "..cut(score()))
p(" Total gain: "..Tgain.." pts.")
end
setCI(cival)
selection.DeselectAll()
for ii=1, #selList do selection.Select(selList[ii]) end
end
function init()
cival=behavior.GetClashImportance()
if cival<0.1 then cival = 1 end
cutlist = { }
checkLocked()
checkSelected()
Qbands=0
for i=1, #selList do
if not isMovable(i,i) then selection.Deselect(i) end
end
checkSelected()
local gc=band.GetCount()
if gc>=1 then bands=true end
oldbands=gc
for i=2, nSegs-1 do -- mutable?
if structure.IsMutable(i) then MM = true break end end
ConP=false
for y = 1, nSegs-2 do -- contact?
for j = y+2, nSegs do
if contactmap.GetHeat(y, j) ~= 0 then ConP=true
break
end
end
if ConP then break end
end
return ConP, plank, MM, locklist, selList, bands, oldbands
end
function dia()
opt=dialog.CreateDialog(" Toolbox. ")
opt.mxc=dialog.AddSlider(" MaxCI:",cival,0.1,1,2)
opt.dfff=dialog.AddLabel(" ")
opt.lb=dialog.AddLabel(" Actions: ")
if sels then
opt.sel=dialog.AddCheckbox(" Rebuild all selected residues simultaneously.",false)
opt.selS=dialog.AddSlider(" ^ x times ",2,1,9,0)
opt.selR=dialog.AddCheckbox(" Rebuild selected residues one area at a time",false)
else
opt.rr=dialog.AddCheckbox(" Rainbow Rebuild",false) end
opt.cuts=dialog.AddCheckbox(" Cut and Wiggle",false)
opt.id=dialog.AddCheckbox(" Idealize",false)
opt.ntw=dialog.AddCheckbox(" Rotamer test",false)
if MM then opt.bfo=dialog.AddCheckbox(" and bruteforce polar AAs",false) end
if ConP then opt.cb=dialog.AddCheckbox(" Contact Bander",true) end
if bands then opt.wb=dialog.AddCheckbox(" Work Existing Bands",false) end
opt.bf=dialog.AddCheckbox(" BandFuze",false)
opt.dff=dialog.AddLabel(" ")
opt.lb2=dialog.AddLabel(" Options: ")
opt.fu = dialog.AddLabel("Fuzing threshold (negative value is gain)")
opt.fuz = dialog.AddSlider("", -50, -200, 100, 1)
opt.qst = dialog.AddCheckbox(" qStab",false)
opt.qu=dialog.AddCheckbox(" Quick quake here and there during Actions",false)
opt.Sf=dialog.AddCheckbox(" Short fuze", true)
if MM then opt.muta=dialog.AddCheckbox(" Mutate (after perturb, during fuze, etc.)",true) end
if sels then
opt.tac=dialog.AddCheckbox(" Target selected residues only with Cut & Wiggle.",true)
opt.tid=dialog.AddCheckbox(" Target selected residues only with Idealize.",true)
opt.sn=dialog.AddCheckbox(" Target selected residues only with Rotamer Test.",true)
end
if bands then
opt.KB=dialog.AddCheckbox(" Keep original bands", true)
opt.KBE=dialog.AddCheckbox(" Keep enabled always",false)
opt.KBSTR=dialog.AddCheckbox(" Keep original strength", false)
end
opt.df=dialog.AddCheckbox(" Disable Filters during operations.",true)
opt.ok = dialog.AddButton("Go go!",1)
opt.can = dialog.AddButton("Cancel.",2)
local res=dialog.Show(opt)
if res==2 then return Cancel()
elseif res~=1 then return dia() end
if sels then
sim=opt.sel.value
simTrs=opt.selS.value
selR=opt.selR.value
tacu=opt.tac.value
tid=opt.tid.value
Snt=opt.sn.value else
rr=opt.rr.value end
DisFil=opt.df.value
QO=opt.qu.value
qst=opt.qst.value
Sf=opt.Sf.value
ide=opt.id.value
cuts=opt.cuts.value
BF=opt.bf.value
NTW=opt.ntw.value
if MM then muta=opt.muta.value
BForce=opt.bfo.value end
if bands then
KB=opt.KB.value
KBE=opt.KBE.value
KBSTR=opt.KBSTR.value
wb=opt.wb.value end
cival=opt.mxc.value
if ConP then CB=opt.cb.value end
fuzt=opt.fuz.value
if fuzt<=0 then
FF = (-1*fuzt)
end
--p(cival, rr, wb, muta, cuts, ide, sim, fuzt, FF, KB, KBE, KBSTR, CB, DisFil, Sf, qst, tacu, tid, selR, simTrs, QO, BF, NTW, Snt, BForce)
return cival, rr, wb, muta, cuts, ide, sim, fuzt, FF, KB, KBE, KBSTR, CB, DisFil, Sf, qst, tacu, tid, selR, simTrs, QO, BF, NTW, Snt, BForce
end
PoAs={"r","n","d","q","e","h","k","y","w","s","t"}
for i=1,#PoAs do --shuffle list
local x=math.random(#PoAs)
PoAs[i],PoAs[x]=PoAs[x],PoAs[i]
end
---- Actions functions
function simul()
p(" Rebuild All Selected",os.date("%X"))
save.Quicksave(80)
Qscore=score()
for i=1, simTrs do
save.Quickload(80)
Rbld() Check()
recentbest.Save()
for x=1, #selList do
selectsphere(selList[x],8) end
setCI(cival*0.8)
if muta then structure.MutateSidechainsSelected(1)
Check()
wig("s") else
structure.ShakeSidechainsSelected(1) end
Check()
selection.DeselectAll()
for k=1, #selList do
selection.Select(selList[k]) end
Test()
if CB then
BandSelectedContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
save.Quicksave(60+i)
end
for yj=1, simTrs do
save.Quickload(60+yj) Check()
end
recentbest.Restore() Check()
end
function selReb()
save.Quickload(1)
Qscore=score()
p(" Rebuild Selected",os.date("%X"))
local Cs=1
local v=0
local tag=2
local tac=1
local tec=0
for i=2, #selList do
if not (selList[i]==selList[i-1]+1) then v=v+1 end
end
for cnt=1, v+1 do
for e=tag, #selList+1 do
if not (selList[e]==selList[e-1]+1) then tec=e break end
end
selection.DeselectAll()
save.Quickload(1)
selStr=selList[tac]
selEnd=selList[tec-1]
for i=selStr, selEnd do
selection.Select(i)
tac=tac+1 end
p(" segs "..selStr.." to "..selEnd,"")
tag=tec+1
Rbld() Check()
recentbest.Save()
setCI(cival*0.8)
for x=selStr, selEnd do
selectsphere(x,8) end
if muta then structure.MutateSidechainsSelected(1)
Check()
wig("s") Check() else
structure.ShakeSidechainsSelected(1) Check() end
selection.DeselectAll()
for i=selStr, selEnd do
selection.Select(i)end
Test()
if CB then
for y = 1, nSegs do
for j = 1, selList[Cs], tac-1 do
if (structure.GetDistance(y,j) <= 10) and (structure.GetDistance(y,j) >= 4) then
if contactmap.GetHeat(y, j) ~=0 then lb=band.AddBetweenSegments(y,j)
band.SetGoalLength(lb, band.GetLength(lb)*(contactmap.GetHeat(y,j)-1)) end end
end
end
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
Cs=tac
end
recentbest.Restore() Check()
for ii=1, #selList do selection.Select(selList[ii]) end
end
function RRdia()
opt=dialog.CreateDialog("Rainbow Rebuild.")
opt.mnlng=dialog.AddSlider("Min. rebuild length",nSegs/4, 2, (nSegs/2)-1,0)
opt.mxlng=dialog.AddSlider("Max. rebuild length", nSegs/4, 2, (nSegs/2)-1,0)
opt.lf=dialog.AddCheckbox("Longest first",true)
if ConP then opt.cb=dialog.AddCheckbox("Contact Bander after Rebuild",true) end
opt.LF=dialog.AddCheckbox("Loop forever (unchecked = 1 cycle through lengths)",false)
opt.ok = dialog.AddButton("Go go!",1)
opt.can = dialog.AddButton("Cancel.",2)
local res=dialog.Show(opt)
if res==2 then return Cancel()
elseif res~=1 then return RRdia() end
if ConP then CB=opt.cb.value end
minlng=opt.mnlng.value
maxlng=opt.mxlng.value
if minlng>maxlng then
Mlng=maxlng
maxlng=minlng
minlng=Mlng end
lFirst=opt.lf.value
LoFo=opt.LF.value
return minlng, maxlng, lFirst, LoFo, CB
end
function RR()
p(" Rainbow Rebuild ",os.date("%X"))
if lFirst then rrlng=maxlng
if minlng~=maxlng then p(" Lengths "..maxlng.." to "..minlng) else
p(" Length "..rrlng,os.date("%X")) end
else rrlng=minlng
if minlng~=maxlng then p(" Lengths "..minlng.." to "..maxlng) else
p(" Length "..rrlng,os.date("%X")) end
end
if LoFo then
xz=1
while true do
for i=xz, nSegs, rrlng do
if (i+rrlng)>nSegs then rrlng=(nSegs-i)+1 end
if isMovable(i,i+(rrlng-1)) then
save.Quickload(1)
Qscore=score()
selection.DeselectAll()
selection.SelectRange(i,i+(rrlng-1))
checkSelected()
p(" segs "..i.." to "..i+(rrlng-1),"")
Rbld() Check()
recentbest.Save()
setCI(cival*0.8)
structure.ShakeSidechainsSelected(1)
Check()
for x=1, #selList do
selectsphere(selList[x],7) end
if muta then structure.MutateSidechainsSelected(1)
Check() end
wig("s")
Check()
selection.DeselectAll()
for k=1, #selList do
selection.Select(selList[k]) end
Test()
if CB then
for y = 1, nSegs-1 do
for j = i, i+(rrlng-1) do
if (structure.GetDistance(y,j) <= 10) and (structure.GetDistance(y,j) >= 4) then
if contactmap.GetHeat(y, j) ~=0 then lb=band.AddBetweenSegments(y,j)
band.SetGoalLength(lb, band.GetLength(lb)*(contactmap.GetHeat(y,j)-1)) end end
end
end
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
end -- isMov
end
if lFirst then rrlng=rrlng-1
if rrlng<minlng then rrlng=maxlng end end
if lFirst==false then rrlng=rrlng+1
if rrlng>maxlng then rrlng=minlng end end
end --while
else
RRc=(maxlng-minlng)+1
for rc=1, RRc do
local rrln=rrlng
--p("",rc,RRc,"rc, RRc")
for i=1, nSegs, rrln do
if (i+rrln)>nSegs then rrln=(nSegs-i)+1 end
if isMovable(i,i+(rrln-1)) then
save.Quickload(1)
Qscore=score()
selection.DeselectAll()
selection.SelectRange(i,i+(rrln-1))
checkSelected()
p(" segs "..i.." to "..i+(rrln-1),"")
Rbld() Check()
recentbest.Save()
setCI(cival*0.8)
structure.ShakeSidechainsSelected(1)
Check()
for x=1, #selList do
selectsphere(selList[x],7) end
if muta then structure.MutateSidechainsSelected(1)
Check() end
wig("s")
Check()
selection.DeselectAll()
for k=1, #selList do
selection.Select(selList[k]) end
Test()
if CB then
for y = 1, nSegs-1 do
for j = i, i+(rrln-1) do
if (structure.GetDistance(y,j) <= 10) and (structure.GetDistance(y,j) >= 4) then
if contactmap.GetHeat(y, j) ~=0 then lb=band.AddBetweenSegments(y,j)
band.SetGoalLength(lb, band.GetLength(lb)*(contactmap.GetHeat(y,j)-1)) end end
end
end
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
end -- isMov
end
if lFirst then rrlng=rrlng-1 end
if lFirst==false then rrlng=rrlng+1 end
--p("",rrlng,"rrlng,","end of rc, RRc")
end
end -- LoFo
end
function Cuts()
save.Quickload(1)
Qscore=score()
if tacu then
cuts=0
for i=1, #selList do
structure.InsertCut(selList[i])
cuts=cuts+1
cutlist[cuts] = selList[i]
end
p("",cuts.." cuts",os.date("%X"))
cutheal()
if CB then
BandSelectedContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
---------
cuts=0
CHu=true
for i=1, #selList do
structure.InsertCut(selList[i])
cuts=cuts+1
cutlist[cuts] = selList[i]
cutheal()
end
CHu=false
if CB then
BandSelectedContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
else -- no tacu
sort('backbone')
cuts=0
local ab=0
while cuts<nSegs/6 do
ab=ab+1
local xi=Mseg[ab][1]
if isMovable(xi,xi) then structure.InsertCut(xi)
cuts=cuts+1
cutlist[cuts] = xi
end end
p("",cuts.." cuts",os.date("%X"))
cutheal()
if CB then
BandAllContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
---------
cuts=0
for xy=1, nSegs do
if (structure.GetSecondaryStructure(xy)=='L') and isMovable(xy,xy) then structure.InsertCut(xy)
cuts=cuts+1
cutlist[cuts] = xy
end
end
p("",cuts.." cuts",os.date("%X"))
cutheal()
if CB then
BandAllContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
---------
sort('backbone')
cuts=0
CHu=true
local ab=0
p("","10 cuts",os.date("%X"))
for ab=1, 10 do
local xi=Mseg[ab][1]
if xi~=nSegs then
if (isMovable(xi,xi) or isMovable(xi+1,xi+1)) then structure.InsertCut(xi)
cuts=cuts+1
cutlist[cuts] = xi
cutheal()
end end
end
CHu=false
if CB then
BandAllContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
end -- tacu
end
function cutheal()
setCI(cival)
wig()
save.Quicksave(90)
for ch=1, #cutlist do structure.DeleteCut(cutlist[ch]) end
Check()
local Csc=score()
recentbest.Save()
wig() Check()
if cut(score())~=cut(Csc) then
Test()
end
if not CHu then
save.Quickload(90)
setCI(cival/3)
wig("wa",5)
setCI(cival)
wig()
for ch=1, #cutlist do structure.DeleteCut(cutlist[ch]) end
Check()
recentbest.Save()
if cut(score())~=cut(Csc) then
Test()
end
end end
function Idia()
opt=dialog.CreateDialog("Idealize.")
opt.iln=dialog.AddSlider(" Length:",3,2,nSegs,0)
opt.uc=dialog.AddCheckbox(" Use Cutpoints.",false)
opt.ok = dialog.AddButton("Go go!",1)
opt.can = dialog.AddButton("Cancel.",2)
local res=dialog.Show(opt)
if res==2 then return Cancel()
elseif res~=1 then return Idia() end
uc=opt.uc.value
if not tid then Ilng=opt.iln.value end
return Ilng, uc
end
function Ide()
save.Quickload(1)
p(" Idealize ",os.date("%X"))
recentbest.Save()
Qscore=score()
if tid then
local Csc=score()
structure.IdealizeSelected()
if cut(score())~=cut(Csc) then
Test()
if CB then
BandSelectedContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
end
else -- tid
if Ilng>nSegs-2 then uc=false end
p(" Length "..Ilng)
for i=1, nSegs, Ilng do
if (i+Ilng)>nSegs then Ilng=(nSegs-i)+1 end
if isMovable(i,i+(Ilng-1)) then
selection.DeselectAll()
selection.SelectRange(i,i+(Ilng-1))
local Csc=score()
if uc then
cuts=0
if (i-1)>=1 then structure.InsertCut(i-1)
cuts=cuts+1
cutlist[cuts] = i-1 end
if (i+Ilng)<nSegs then structure.InsertCut(i+(Ilng-1))
cuts=cuts+1
cutlist[cuts] = i+(Ilng-1) end
end
structure.IdealizeSelected()
if uc then cutheal() else
if cut(score())~=cut(Csc) then
Test() end
end -- uc
if CB then
BandSelectedContacts()
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
if QO then QuakeOnce() end
end --isMov
recentbest.Restore() Check()
end
selection.DeselectAll()
end --if tid
recentbest.Restore() Check()
end
function NetwTest()
p(" Rotamer Test ",os.date("%X"))
lscore=score()
selection.DeselectAll()
local k=0
local targets=0
if Snt then targets=#selList
p(" ",targets.." segs to test") else
targets=nSegs
p(" "," all polar segs") end
for jj=1, targets do
k=k+1
if Snt then st=selList[k] else st=k end
if not Snt then
if contains(PoAs,structure.GetAminoAcid(st)) then Snap() end
else Snap() end
end
if BForce then p(" ","bruteforcing polar AAs ",os.date("%X"))
selection.DeselectAll()
local k=0
local targets=0
if Snt then targets=#selList else targets=nSegs end
for jj=1, targets do
k=k+1
if Snt then st=selList[k] else st=k end
if not Snt then
if contains(PoAs,structure.GetAminoAcid(st)) then BruF() end
else BruF() end
end
end -- BForce
end
function nTest()
setCI(0.01)
structure.WiggleSelected(5,false,true) Check()
structure.ShakeSidechainsSelected(1) Check()
setCI(cival)
structure.WiggleSelected(5,false,true) Check()
structure.ShakeSidechainsSelected(1) Check()
selection.DeselectAll()
wig("ws",3) Check()
end
function Snap()
Check()
selectsphere(st,10)
nTest()
snaps=rotamer.GetCount(st)
for y=1, snaps do
rotamer.SetRotamer(st, y)
Check()
selectsphere(st,10)
selection.Deselect(st)
nTest()
end
end
function BruF()
for i=1, #PoAs do
save.Quickload(1)
origA = structure.GetAminoAcid(st)
BB, SC=freeze.IsFrozen(st)
if structure.CanMutate(st, PoAs[i]) and SC==false then structure.SetAminoAcid(st, PoAs[i])
newA = structure.GetAminoAcid(st)
Nlscore=score()
if newA ~= origA then Snap() end
save.Quickload(1)
newA = structure.GetAminoAcid(st)
if newA ~= origA then p(" seg "..st.." changed from "..origA.." to "..newA) end
end
end -- PoAs--p(os.date("%X"))
end
function WorkExBands()
p(" Work Bands",os.date("%X"))
Qscore=score()
while true do
band.EnableAll()
if band.GetCount()>1 then
if KBE then
for b=oldbands+1, band.GetCount() do
RM=math.random(-100,100)
if RM>=0 then BdOff=false
else BdOff=true end
if BdOff then band.Disable(b) end
end
else
for b=1, band.GetCount() do
RM=math.random(-100,100)
if RM>=0 then BdOff=false
else BdOff=true end
if BdOff then band.Disable(b) end
end
end end
BandTest()
recentbest.Restore()
Disbands() Check()
end -- while
end
function BFdia()
opt = dialog.CreateDialog(" BandFuze. ")
opt.Qq=dialog.AddCheckbox(" Quake.",true)
opt.Bs=dialog.AddCheckbox(" BiS.",false)
opt.Cmb=dialog.AddCheckbox(" Combine Quake and BiS.",false)
opt.Sk=dialog.AddCheckbox(" Shock.",true)
opt.Tg=dialog.AddCheckbox(" Tailgrab.",false)
opt.ok = dialog.AddButton("Go go!",1)
opt.can = dialog.AddButton("Cancel.",2)
local res=dialog.Show(opt)
if res==2 then return Cancel()
elseif res~=1 then return BFdia() end
QQ=opt.Qq.value
BiS=opt.Bs.value
Shock=opt.Sk.value
TG=opt.Tg.value
Combo=opt.Cmb.value
return QQ,BiS,Shock,TG,Combo
end
function BFuze()
p(" BandFuze ",os.date("%X"))
while true do
save.Quickload(1)
Qscore=score()
if QQ or Combo then Quaker() end
BiSs()
if TG then BandAcross() end
end
end
---- Band functions
function bandpull(minBS,maxBS)
local ss=score()
local perc=math.random(80,180)/100
local loss=((perc*ss)/100)
--p("perc,loss",perc,loss)
local lastBS=minBS
for str=lastBS,maxBS, 0.1 do
if KBSTR then
local NNbands = band.GetCount()
for i=oldbands+1, NNbands do band.SetStrength(i, str) end
else
for i=1, band.GetCount() do band.SetStrength(i, str) end
end
wig("wb",5) Check()
save.Quicksave(70)
recentbest.Restore() Check()
save.Quickload(70)
if (ss-score()>=loss) or (score()>bestscore+5) then
if band.GetCount()>(nSegs/10)*2 then
lastBS=str-0.1
if lastBS<minBS then lastBS=minBS end
else
lastBS=minBS
end
break
end
end
end
function BandTest()
if band.GetCount()>0 then
setCI(cival*0.9)
if ZL then wig("wb",5,1)
Check()
save.Quicksave(70)
recentbest.Restore() Check()
save.Quickload(70)
else bandpull(0.2,3) end
Disbands()
recentbest.Save()
Check()
if muta then
save.Quicksave(93)
setCI(math.random(cival*100)/100)
structure.MutateSidechainsAll(1) Check()
setCI(cival)
wig() Check()
setCI(cival/2)
wig("wa",5) Check()
setCI(cival)
wig() Check()
wig("s") Check()
wig() Check()
save.Quickload(93)
end
wig("s") Check()
Test()
end end
function QuakeOnce()
if KB then
band.EnableAll()
if band.GetCount()>1 then
if KBE then
for b=oldbands+1, band.GetCount() do
RM=math.random(-100,100)
if RM>=0 then BdOff=false
else BdOff=true end
if BdOff then band.Disable(b) end
end
else
for b=1, band.GetCount() do
RM=math.random(-100,100)
if RM>=0 then BdOff=false
else BdOff=true end
if BdOff then band.Disable(b) end
end
end end -- KBE
end
local dd = math.floor(nSegs/7)
repeat
local start=math.random(dd)
local len=math.floor(math.random((nSegs-dd)/2)+dd)
local step=math.floor(math.random((nSegs-dd)/2)+dd)
for x=start,nSegs, step do
for y=start+len, nSegs, step do
if (y<=nSegs) and (isMovable(y,y) or isMovable(x,x)) then band.AddBetweenSegments(x,y) end
end end
until (band.GetCount()+oldbands)>(oldbands+3)
BandTest()
recentbest.Restore()
Delbands() Check()
recentbest.Save()
end
function BandAllContacts()
for y = 1, nSegs-2 do
for j = y+2, nSegs do
HT=contactmap.GetHeat(y,j)
if HT >= 0.75 then lb=band.AddBetweenSegments(y,j)
band.SetGoalLength(lb, band.GetLength(lb)*(HT)) end
end
end end
function BandSelectedContacts()
for y = 1, nSegs do
for j = 1, #selList do
if (structure.GetDistance(y,selList[j]) <= 10) and (structure.GetDistance(y,selList[j]) >= 4) then
if contactmap.GetHeat(y,selList[j]) ~=0 then lb=band.AddBetweenSegments(y,selList[j])
band.SetGoalLength(lb, band.GetLength(lb)*(contactmap.GetHeat(y,selList[j]))) end end
end
end
end
function ContactBander()
p(" Band Contacts")
BandAllContacts()
if (band.GetCount()<1) or BF then wb=false else
wb=true end
end
function bandage()
bloat=false
if cival>=0.9 then
RM=math.random(-100,100)
if RM>=0 then bloat=false
else bloat=true end
end
if bloat then
if KBSTR then
local NNbands = band.GetCount()
for i=oldbands+1, NNbands do
band.SetGoalLength(i,band.GetLength(i)+4)
end
else
for i=1, band.GetCount() do
band.SetGoalLength(i,band.GetLength(i)+4)
end
end
else
if KBSTR then
local NNbands = band.GetCount()
for i=oldbands+1, NNbands do
local leng=band.GetLength(i)
local perc=math.random(20,50)
local loss=((perc*leng)/100)
band.SetGoalLength(i,band.GetLength(i)-loss)
end
else
for i=1, band.GetCount() do
local leng=band.GetLength(i)
local perc=math.random(20,50)
local loss=((perc*leng)/100)
band.SetGoalLength(i,band.GetLength(i)-loss)
end
end
end end
function spacebands(amnt)
local zeBands=math.random(amnt)+Qbands
if zeBands<1 then zeBands = 1 end
while band.GetCount()<zeBands do
repeat segO = math.random(nSegs)
until structure.IsLocked(segO)==false
if ZL then
rho=0.2
else
rho=math.random(10)
end
theta = math.random(100,314.159)/100
phi = math.random(100,314.159)/100
if phi<1 then
phi=phi+1
end
if theta<1 then
theta=theta+1
end
if segO<=nSegs and segO>=1 then
if segO==nSegs then
segX = segO-1
segY = segO-2
elseif segO==1 then
segX = segO+1
segY = segO+2
else
segX = segO-1
segY = segO+1
end
if segX>nSegs then segX=nSegs-1 end
if segY>nSegs then segY=nSegs-1 end
if segY<1 then segY=1 end
if segX<1 then segX=1 end
--p(segX,"X",segY,"Y",segO,"O",theta,"theta",phi,"phi")
local lb=band.Add(segO, segX, segY, rho, theta, phi)
if ZL then
band.SetGoalLength(lb,math.random(1))
band.SetStrength(lb,math.random(10))
else
band.SetGoalLength(lb,math.random(band.GetLength(lb)*2))
end end end end
function BiSs()
if Combo==false then
if BiS then
for i=1, 2 do
spacebands(nSegs/2)
BandTest()
Delbands()
end
end--bis
end--combo
if Shock then
ZL=true
for u=1, 2 do
spacebands(nSegs/2)
BandTest()
Delbands()
end
ZL=false
end
end
function BandAcross()
for i=1, nSegs do
if structure.IsLocked(i)==false then first=i break end end
for u=nSegs, 1, -1 do
if structure.IsLocked(u)==false then last=u break end end
band.AddBetweenSegments(first,last)
bandage()
BandTest()
Delbands()
band.AddBetweenSegments(nSegs/2,first)
band.AddBetweenSegments(nSegs/2,last)
bandage()
BandTest()
Delbands()
end
function Quaker()
if Combo then
for i=1, 4 do
nrR=math.random(1, 19)
for u=1, nrR do
repeat
seg1=math.random(1,nSegs)
seg2=math.random(1,nSegs)
until (seg1~=seg2) and (not structure.IsLocked(seg1) or not structure.IsLocked(seg2))
band.AddBetweenSegments(seg1,seg2)
end
bandage()
Qbands=band.GetCount()
spacebands(10)
BandTest()
Delbands()
end
else
for i=1, 2 do
nrR=math.random(1, 19)
for u=1, nrR do
repeat
seg1=math.random(1,nSegs)
seg2=math.random(1,nSegs)
until (seg1~=seg2) and (not structure.IsLocked(seg1) or not structure.IsLocked(seg2))
band.AddBetweenSegments(seg1,seg2)
end
bandage()
BandTest()
Delbands()
end --quake
end --combo
end
---- Container
function main()
init()
if lockd<nSegs-2 then dia() else return end
if DisFil then behavior.SetSlowFiltersDisabled(true) end
Delbands()
Disbands()
save.Quicksave(1)
save.Quicksave(2)
recentbest.Save()
startscore=score()
bestscore=startscore
p(" Startscore: "..cut(score()))
p(" Best score in quicksave slot 1, start in slot 2 ")
p(" maxCI = "..cival," Start time:",os.date("%X"))
p("")
if rr then RRdia() end
if ide then
if not tid then Idia() end end
if BF then BFdia() end
if sim then simul() end
if selR then selReb() end
if rr then RR() end
if cuts then Cuts() end
if ide then Ide() end
if NTW then NetwTest() end
if CB then ContactBander() end
if wb then WorkExBands() end
if BF then BFuze() end
Result()
end
--[[
Toolbox includes:
-A Rebuilder, Rainbow whole structure or Selected residues only;
-a Cut and Wiggle routine, selected residues only or worst backbone scores and all loops;
-an Idealize routine, selected residues only or whole structure variable length with the option to use cutpoints;
-a Rotamer Tester, selected residues only (recommended, you're better off with AcidTweak/Mutators when not targetting specific segs) or all polar residues (hydrophilics + TYR & TRYP), tries all rotamers of current sidechain and local wiggles;
-and bruteforce polar AAs, while testing their rotamers (very lengthy, up to ~30mins/residue), if you pick the right residues this will do wonders for finding HBonds,
e.g.: a network is <75% satisfied -> select promising nearby residues (and/or those already contributing to the network) and run;
-Contact Bander, bands all contacts with a heat >=0.75 and runs WorkExBands;
-Work Existing Bands, randomly disables/enables bands and quakes the structure (needs user created bands, more bands = more profit);
-BandFuze, creates random bands and quakes the structure. Updated/revised, same functionality.
----
If multiple Actions are checked they will happen in consecutive order, top to bottom, as displayed in the dialog (unless loop forever negates this).
A single pull of Contact Bander and/or Quick Quake happen around the same time as qStab/fuze, after the rebuild/cuts/idealize stabilization wiggles.
Contact Bander, Work Exist. Bands and BandFuze loop forever until cancelled.
----
If 'Disable filters during operations' is unchecked, recipe will not touch the filters and leave them as is,
this can be used to run the recipe with only 1 filter enabled, or to keep any filter bonus from locking up the structure, etc.
If it is checked, all filters will be enabled to check score, and disabled during any and all other operations.
Has no effect on puzzles without filters, just ignore the option.
]]
err = xpcall(main,End)
