Recipe: Mutators.

created by MurloW

Profile

• Name: Mutators.
• ID: 49144
• Shared with: Public
• Parent: None
• Children:
  • Mutators4
  • Mutators BP
  • Mutators. Hbond
  • Mutators. rm hbond
  • HBond Mutators
  • Mutators. band delete
• Created on: January 19, 2015 at 14:48 PM UTC
• Updated on: January 19, 2015 at 14:48 PM UTC
• Description:

  Four distinctly different methods of mutating the entire structure.

Code

-- Mutators Collection.  
--   MurloW
-- functions sort(part) and allByOne() written mostly by skillful Team AD scripters who wish to remain anonymous. 

-- 23-04-2014 : increased speed and compatibility. 
-- 18-05-2014 : cleanup and public release. 
-- 19-01-2015 : added a mutator; updated wiggle and dialog functions with filter disabling. 


IterationMultiplier = 1.1  -- 2.5  -- 1.4 
ItMu = IterationMultiplier

normal = true 

cival = behavior.GetClashImportance()
nSegs=structure.GetCount()
p=print

function Seed() -- REALLY good seed by Rav3n_pl   
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
--p("Seed is: "..seed)
math.randomseed(seed)
end
Seed()
function score()
local s=0
	if normal==false then
s=current.GetEnergyScore()
	else
s=current.GetScore()
end
	return s
end
function wig(how, it, iters, minppi) 

if DisFil then behavior.SetSlowFiltersDisabled(true) end
if how==nil then how="wa" end
if minppi==nil then minppi=2 end
if iters==nil then iters=2 end 
if it==nil then it=10*ItMu 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)
end
if score()-sp > minppi and how ~= "s" then return wig(how, it, iters, minppi) end 
end
if DisFil then behavior.SetSlowFiltersDisabled(false) end
end

function qStab()
Check()
	setCI(cival/2)
	wig("wa",5)
	setCI(cival)
	wig("s")
	wig()
Check()
	setCI(cival/2)
	wig("wa",5)
	setCI(cival)
	wig()
 Check()
end
function Fuze() 
Check()
	setCI(.05)
	wig("s")
	setCI(cival)
	wig()
  Check()
	setCI(cival/3)
	wig("wa",5)
if Sf == false then
	setCI(.07)
	wig("s")
	setCI(cival)
	wig()
  Check()
	setCI(cival/3)
	wig("wa",5)
end
	setCI(cival)
	wig("s")
	wig()
  Check()
end

function selectsphere(seg, radius)
if seg>nSegs then seg = nSegs end
if seg<1 then seg = 1 end
 for y=1, nSegs do
   if structure.GetDistance(seg,y) <= radius then
   if y >= 1 and y <= nSegs then
     selection.Select(y)
   end
   end
 end
end
function cut(x) 
    return x-x%1
end
function cut1(x) 
    return x-x%0.1
end
function cut3(x)
return x-x%0.001
end
function setCI(ci)
	return behavior.SetClashImportance(ci)
end
function nomuta()
p("")
p(" No mutable residues. ")
end
function End(errmsg)
p("")
    if string.find(errmsg,"Cancelled") then
        p("  User cancel.")
	p("")
		Result()
    else
	p("")
        p(errmsg)
	p("")
	Result()
    end
    return errmsg
end
function Result()
save.Quickload(93)
setCI(cival)
recentbest.Restore()
Tgain = bestscore - startscore
if Tgain>0.008 then
p(" gained: "..cut3(Tgain))
else
p(" No change :/ ")
end
end
function Check()
if (bestscore < score()) then
	gain = score() - bestscore
	bestscore = score()
save.Quicksave(1)
save.Quicksave(93)
else
	gain = 0
end
if gain>0.002 then
p(" ",cut3(gain),"pts.")
end
end

function sort(part)
Mseg = {}
for i = 1, nSegs do
    Mseg[i] = {}
if part ~= 'total' then
    Mseg[i][1] = current.GetSegmentEnergySubscore(i, part)
else
	Mseg[i][1] = current.GetSegmentEnergyScore(i)
end
    Mseg[i][2] = i
end
sW = 1
while sW ~= 0 do
	sW=0
if WF==true then
	for i=1, nSegs-1 do
		if Mseg[i][1] > Mseg[i+1][1] then
			Mseg[i][1],Mseg[i+1][1]=Mseg[i+1][1],Mseg[i][1]
			Mseg[i][2],Mseg[i+1][2]=Mseg[i+1][2],Mseg[i][2]
			sW = sW +1
		end
	end
else
	for i=1, nSegs-1 do
		if Mseg[i][1] < Mseg[i+1][1] then
			Mseg[i][1],Mseg[i+1][1]=Mseg[i+1][1],Mseg[i][1]
			Mseg[i][2],Mseg[i+1][2]=Mseg[i+1][2],Mseg[i][2]
			sW = sW +1
		end
	end
end -- WF
end -- sW 
return Mseg
end

AAs={"a", "c", "d", "e", "f", "g", "h", "i", "k", "l", "m", "n", "p", "q", "r", "s", "t", "v", "w", "y"}
selection.DeselectAll()

startscore = score()
bestscore = startscore
-----------------------------------
-- try all
function AllSorted()
sort(part)
for y=1, loops do
save.Quickload(93)
lscore=score()
p(" ",cut3(score()))
p("")
local nr=0
for i=1, nSegs do
if structure.IsMutable(Mseg[i][2]) then
nr=nr+1
save.Quickload(93)
Tempscore=score()
selection.Select(Mseg[i][2])

	orig_aa = structure.GetAminoAcid(Mseg[i][2])	
for j=1, #AAs do
	if structure.CanMutate(Mseg[i][2], AAs[j]) then
		structure.SetAminoAcid(Mseg[i][2], AAs[j])
if shakeAround == true then
selectsphere(Mseg[i][2],6)
setCI(cival)
structure.ShakeSidechainsSelected(1)
end
Check()
end
selection.DeselectAll()
end
save.Quickload(93)
	new_aa = structure.GetAminoAcid(Mseg[i][2])
if new_aa ~= orig_aa then
print("Residue "..Mseg[i][2].." changed from "..orig_aa.." to "..new_aa)
else 
print("Residue "..Mseg[i][2].." unchanged from "..orig_aa)
end
end
end
if score()>lscore then 
p(" Loop gain:", cut3(score()-lscore))
end 
end-- loops
end
function allByOne()
for c=1, loops do
lscore=score()
if inRevers == true then
 beginS=nSegs
 endS=1
 step=(-1)
else
 beginS=1
 endS=nSegs
 step=1
end
for i=beginS, endS, step do
if structure.IsMutable(i) then
	orig_aa = structure.GetAminoAcid(i)	
for j=1, #AAs do
	if structure.CanMutate(i, AAs[j]) then
		structure.SetAminoAcid(i, AAs[j])
if shakeAround == true then
selectsphere(i,6)
setCI(cival)
structure.ShakeSidechainsSelected(1)
end
Check()
end
selection.DeselectAll()
end
save.Quickload(93)
	new_aa = structure.GetAminoAcid(i)
if new_aa ~= orig_aa then
print("Residue "..i.." changed from "..orig_aa.." to "..new_aa)
else 
print("Residue "..i.." unchanged from "..orig_aa)
end
end
end
if score()>lscore then 
p(" Loop gain:", cut3(score()-lscore))
end
end -- loops
end
function allWalk() 
for c=1, loops do
lscore=score()
if inRevers == true then
 beginS=nSegs
 endS=1
 step=(-1)
else
 beginS=1
 endS=nSegs
 step=1
end
for j=1, #AAs do
for i=beginS, endS, step do
origA = structure.GetAminoAcid(i)
if structure.CanMutate(i, AAs[j]) then 
structure.SetAminoAcid(i, AAs[j]) 
if shakeAround == true then
selectsphere(i,6)
setCI(cival)
structure.ShakeSidechainsSelected(1)
end
Check() --end
selection.DeselectAll()
save.Quickload(93)
	newA = structure.GetAminoAcid(i)
if newA ~= origA then
p("Residue "..i.." changed from "..origA.." to "..newA)
 end 
 end end
 end -- aa 
if score()>lscore then 
p(" Loop gain:", cut3(score()-lscore))
end
 end -- loops
end
-----------------------------------
-- random mutate
function mutateR()
for y=1, Rloops do
lscore=score()
p(" ",cut3(score()))
p("")
local nr=0
if inRevers == true then
 beginS=nSegs
 endS=1
 step=(-1)
else
 beginS=1
 endS=nSegs
 step=1
end
for i=beginS, endS, step do
if structure.IsMutable(i) then
nr=nr+1
save.Quickload(93)
Tempscore=score()
selection.Select(i)
ranci=(math.random(minCI*100, maxCI*100)/100)
setCI(ranci)
p(" #"..nr,"ci: "..ranci)
structure.MutateSidechainsSelected(1)
Check()
selectsphere(i, 6)
setCI(cival)
if shakeAround == true then
structure.ShakeSidechainsSelected(1)
Check()
end
setCI(cival)
structure.WiggleSelected(8, false, true)
selection.DeselectAll()
Check()
--wig('s')
--wig()
--Check()
if qSt == true then qStab() end
if Fuzz == true then Fuze() else
if fzt>=0 then
if score()>(Tempscore-fzt) then
Fuze()
end
else
if score()>=(Tempscore+FFzt) then
Fuze()
end 
end 
end 
end end
if score()>lscore then 
p(" Loop gain:", cut3(score()-lscore))
end end 
end
function mutate()
sort(part)
for y=1, loops do
lscore=score()
p(" ",cut3(score()))
p("")
local nr=0
for i=1, nSegs do
if structure.IsMutable(Mseg[i][2]) then
nr=nr+1
save.Quickload(93)
Tempscore=score()
selection.Select(Mseg[i][2])
ranci=(math.random(minCI*100, maxCI*100)/100)
setCI(ranci)
p(" #"..nr.." seg: "..Mseg[i][2],"ci: "..ranci)
structure.MutateSidechainsSelected(1)
Check()
selectsphere(Mseg[i][2], 6)
setCI(cival)
if shakeAround == true then
structure.ShakeSidechainsSelected(1)
Check()
end
setCI(cival)
structure.WiggleSelected(8, false, true)
selection.DeselectAll()
Check()
--wig('s')
--wig()
--Check()
if qSt == true then qStab() end
if Fuzz == true then Fuze() else
if fzt>=0 then
if score()>(Tempscore-fzt) then
Fuze()
end
else
if score()>=(Tempscore+FFzt) then
Fuze()
end 
end 
end 
end end
if score()>lscore then 
p(" Loop gain:", cut3(score()-lscore))
end 
end end
-----------------------------------
-- dialog 
function dia()
-- puz def 
for i=1, nSegs-1 do
if structure.IsMutable(i) == true then
MM = true
break
end
end
for d=1, nSegs/2 do
if current.GetSegmentEnergySubscore(d, 'density') ~= -0 then
EDpuzzle = true
break
end
end
-- /puzdef 
if MM ~= true then return nomuta() end
p(" Mutator slider:")
p(" 1 = walk mutating with random CI ") -- mutateR
p(" 2 = walk testing all AAs on segment, then next segment ") -- allbyone
p(" 3 = walk testing AA on every segment, then next AA ")  -- allwalk
p(" 4 = mutate worst or best first according to (sub)score ") -- mutateS 

p(" 5 = bruteforce worst or best first according to (sub)score ") -- AllSorted 
opt=dialog.CreateDialog("Choose mutator.")
opt.a=dialog.AddLabel(" See recipe output. ")
opt.Mr=dialog.AddSlider("",1,1,5,0)

opt.dis=dialog.AddCheckbox("Disable slow filters during wiggle.", true)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)

DisFil=opt.dis.value
if opt.Mr.value==1 then RanMut=true
elseif opt.Mr.value==2 then allone=true
elseif opt.Mr.value==3 then allwalk=true
elseif opt.Mr.value==4 then mutateS=true

elseif opt.Mr.value==5 then AllSort=true
end
end
function partDialog()
opt=dialog.CreateDialog("Choose One.")
opt.cl=dialog.AddCheckbox("clashing", false)
opt.p=dialog.AddCheckbox("packing", false)
opt.bo=dialog.AddCheckbox("bonding", false)
if EDpuzzle == true then
opt.d=dialog.AddCheckbox("density", false)
end
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
if opt.bo.value  == true then part="bonding" end
if opt.cl.value  == true then part="clashing" end
if opt.p.value == true then part="packing" end
if EDpuzzle == true then
if opt.d.value  == true then part="density" end
end
if part == nil then return Sdialog() end
end
function allbyoneD()
opt=dialog.CreateDialog("Options")
opt.lo=dialog.AddSlider("Loops: ", 1, 1, 10, 0)
opt.inR=dialog.AddCheckbox(" In reverse, start from end and work to seg #1 ", false)
opt.Sh=dialog.AddCheckbox(" Shake around after mutate ", false)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
inRevers=opt.inR.value
shakeAround=opt.Sh.value
loops=opt.lo.value
end
function allwalkD()
opt=dialog.CreateDialog("Options")
opt.lo=dialog.AddSlider("Loops: ", 1, 1, 10, 0)
opt.inR=dialog.AddCheckbox(" In reverse, start from end and work to seg #1 ", false)
opt.Sh=dialog.AddCheckbox(" Shake around after mutate ", false)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
inRevers=opt.inR.value
shakeAround=opt.Sh.value
loops=opt.lo.value
end
function Sdialog()
opt=dialog.CreateDialog("Options")
opt.wf=dialog.AddCheckbox("Worst first; uncheck is best scoring first.",true)
opt.lo=dialog.AddSlider("Loops: ", 2, 1, 10, 0)
opt.sc=dialog.AddLabel(" Choose one scorepart")
opt.s=dialog.AddCheckbox("sidechain", true)
opt.h=dialog.AddCheckbox("hiding", false)
opt.to=dialog.AddCheckbox("total",false)
opt.o=dialog.AddCheckbox("other",false)
opt.aa=dialog.AddLabel(" Minimum and Maximum mutate CI:")
opt.mic=dialog.AddSlider("minCI :", 0.01, 0.00001, 1, 3)
opt.mac=dialog.AddSlider("maxCI :", 0.94, 0.1, 1, 3)
opt.Sh=dialog.AddCheckbox(" Shake around after mutate ",false)
opt.qst=dialog.AddCheckbox("qStab after mutate",false)
opt.fz=dialog.AddCheckbox("always fuze after mutate",false)
opt.fzt=dialog.AddSlider("  or use threshold: ", -100, -500, 50, 1)
opt.sf=dialog.AddCheckbox("Short fuze",false)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
if opt.to.value == true then part='total' end
if opt.h.value  == true then part="hiding" end
if opt.s.value == true then part='sidechain' end
shakeAround=opt.Sh.value
loops=opt.lo.value
WF=opt.wf.value
minCI = opt.mic.value
maxCI = opt.mac.value
fzt = opt.fzt.value
FFzt = (-1*fzt)
Fuzz = opt.fz.value 
Sf = opt.sf.value 
qSt = opt.qst.value
if opt.o.value == true then partDialog() end
if part == nil then return Sdialog() end
end
function Rdialog()
opt=dialog.CreateDialog("Options.")
opt.rl=dialog.AddSlider("Random mutate loops: ", 2, 1, 50, 0)
opt.inR=dialog.AddCheckbox(" In reverse, start from end and work to seg #1 ", false)
opt.aa=dialog.AddLabel(" Minimum and Maximum mutate CI:")
opt.mic=dialog.AddSlider("minCI :", 0.01, 0.00001, 1, 3)
opt.mac=dialog.AddSlider("maxCI :", 0.94, 0.1, 1, 3)
opt.sha=dialog.AddCheckbox("Shake around after mutate",false)
opt.qst=dialog.AddCheckbox("qStab after mutate",false)
opt.fz=dialog.AddCheckbox("always fuze after mutate",false)
opt.fzt=dialog.AddSlider("  or use threshold: ", -100, -500, 50, 1)
opt.sf=dialog.AddCheckbox("Short fuze",false)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
minCI = opt.mic.value
maxCI = opt.mac.value
inRevers=opt.inR.value
shakeAround = opt.sha.value
fzt = opt.fzt.value
FFzt = (-1*fzt)
Fuzz = opt.fz.value 
Sf = opt.sf.value 
qSt = opt.qst.value
Rloops = opt.rl.value 
end
function AllSoDia()
opt=dialog.CreateDialog("Options")
opt.wf=dialog.AddCheckbox("Worst first; uncheck is best scoring first.",true)
opt.lo=dialog.AddSlider("Loops: ", 2, 1, 10, 0)
opt.sc=dialog.AddLabel(" Choose one scorepart")
opt.s=dialog.AddCheckbox("sidechain", true)
opt.h=dialog.AddCheckbox("hiding", false)
opt.to=dialog.AddCheckbox("total",false)
opt.o=dialog.AddCheckbox("other",false)
opt.Sh=dialog.AddCheckbox(" Shake around after mutate ",false)
opt.ok=dialog.AddButton("Go go!", 1)
dialog.Show(opt)
if opt.to.value == true then part='total' end
if opt.h.value  == true then part="hiding" end
if opt.s.value == true then part='sidechain' end
shakeAround=opt.Sh.value
loops=opt.lo.value
WF=opt.wf.value
if opt.o.value == true then partDialog() end
if part == nil then return Sdialog() end
end
-----------------------------------
p("")
function main()
dia()
p("")
band.DeleteAll()

if DisFil then behavior.SetSlowFiltersDisabled(false) end
startscore = score()
bestscore = startscore
recentbest.Save()
save.Quicksave(1)
save.Quicksave(2)
save.Quicksave(93)
p("")
p(" maxCI = "..cival)
p("")
if RanMut==true then Rdialog()
mutateR() 
elseif allwalk==true then allwalkD()
allWalk() 
elseif allone==true then allbyoneD()
allByOne()  
elseif mutateS==true then Sdialog() 
mutate() 
elseif AllSort==true then AllSoDia()
AllSorted()
end 
end

err = xpcall(main,End)

Comments

[MurloW]

Added a mutator.