Code
--QuakeR - a randomized Quake
recipeTitle='QuakeR & BWF v1.0 '
--v1.0 combined two recpies QuakeR v5.0 with mutate
-- updated and changed some functions!
-- future plans more settings in the gui
-- created 2025-05-22 ZeroLeak7
--[[
Based on "Quake" by Grom
v2.51 -- update 2011-01-15 rav3n_pl
v3.0 -- update 2011-04-18 rav3n_pl
v4.0 -- updated 27 Dec 2014 GaryForbis
v4.5 -- updated 2019-12-30 ZeroLeak7
v5.0 -- updated 2019-12-31
-converted to script v2
-band hydrophobes to beta carbon
-clean up on early exit
-better shake and wiggle ci in Fuze and with mutate now
-updated with a gui
]]
-- original -- behavior wiggle fuze v1 by Bruno Kestemont
--Bravo BWF
--v1 i did a brute force of all single variable behaivor wiggle variations that were reasonable, this script includes all gains that were >0.1
-- it's just a potential script that might see some gains. totally experimental.
-- just a small script that uses recipe scoring mods. works well on ligand / small molecule placement
--v1.1 fixed glitch on Behavior importance
--Wiggle all
Best_Score_slot_num = 3
save.Quicksave(Best_Score_slot_num) --save starting score as best score saved in quick save 3
BestScore = current.GetScore()
StartScore = BestScore
BestBonus = filter.GetBonusTotal()
StartBonus = BestBonus
Importance = 3
global_clashing_importance = 1
behavior_string = "starting"
Behavior_value = 1
print("Make sure RECIPE SCORE MODDING is checked before running")
function SaveBest()
local ss= current.GetScore()
local g = ss - BestScore
local tb = filter.GetBonusTotal()
local bg = tb - BestBonus --dont let the bonus score decrease
if g > 0 then --and bg >= 0 then -- removed bonus requirements
--if g > 0.1 then
print(behavior_string .. Importance)
print("Iteration length: " , iteration_variable , " CI: " , global_clashing_importance)
print("Gained another " .. g.. " Score: "..ss.. " Bonus: "..tb)
print("Total Gain: ".. (ss-StartScore))
--end
BestScore= ss
BestBonus = tb
save.Quicksave(Best_Score_slot_num) --best score saved in quick save 3
else
--print(":( no gain")
end
end
function SidechainsHbondFuze()
--print("SidechainHbond")
behavior_string= "SidechainHbond: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetSidechainHBondImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetSidechainHBondImportance(1)
end
function BackboneHbondFuze()
--print("BackboneHbond")
behavior_string= "BackboneHbond: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetBackboneHBondImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetBackboneHBondImportance(1)
end
function PairWiseFuze()
--print("PairWise")
behavior_string= "PairWise: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetPairwiseImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetPairwiseImportance(1)
end
function PackingFuze()
--print("Packing")
behavior_string= "Packing: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetPackingImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetPackingImportance(1)
end
function HidingFuze()
--print("Hiding")
behavior_string= "Hiding: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetHidingImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetHidingImportance(1)
end
function ClashingFuze()
--print("Clashing importance 0.9")
behavior_string= "Clash: "
recentbest.Save()
--behavior.SetClashImportance(0.9)
behavior.SetClashImportance(global_clashing_importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetClashImportance(1)
end
function DensityFuze()
--print("Density")
behavior_string = "Density: "
recentbest.Save()
behavior.SetClashImportance(global_clashing_importance)
behavior.SetDensityImportance(Importance)
structure.WiggleAll(iteration_variable,true,true) -- wa
Behavior_reset()
structure.WiggleAll(25,true,true)
is_recent_best_better()
SaveBest()
--behavior.SetDensityImportance(1)
end
recent_best_count=0
function is_recent_best_better() --sometime recent best is better than settled score
local score = current.GetScore()
recentbest.Restore()
recent_best_score = current.GetScore()
if (recent_best_score>score and recent_best_score > BestScore) then
print("Recent best restored")
structure.WiggleAll(10,true,true)
if (recent_best_count<4) then --infinite recursion != infinite gain. breaks on 4 failed attemps. might get triggered many times
recent_best_count = recent_best_count + 1
print ("recent_best_count: " .. recent_best_count .. " of 5")
is_recent_best_better() --fixes a bug where the score goes down with these settings
end
score = current.GetScore()
if (score < recent_best_score ) then
recentbest.Restore()
end
end
recent_best_count=0
end
function Behavior_reset()
behavior.SetClashImportance(1)
behavior.SetHidingImportance(1)
behavior.SetPackingImportance(1)
behavior.SetPairwiseImportance(1)
behavior.SetBackboneHBondImportance(1)
behavior.SetSidechainHBondImportance(1)
behavior.SetDensityImportance(1)
end
function brute_force()
while (global_clashing_importance > 0)do
print("global CI: " .. global_clashing_importance)
iteration_variable= 25
while (iteration_variable > 0) do
for importance = 3, 0, -0.5 do
print("Testing Importance: "..importance.. " iteration: ".. iteration_variable .. " CI: " ..global_clashing_importance)
Importance = importance
SidechainsHbondFuze()
BackboneHbondFuze()
PairWiseFuze()
PackingFuze()
HidingFuze()
DensityFuze()
ClashingFuze()
save.Quickload(Best_Score_slot_num) --best score saved in quick save 3
end
for importance = 1.1, .9, -0.01 do
print("Testing Importance: "..importance.. " iteration: ".. iteration_variable .. " CI: " ..global_clashing_importance)
Importance = importance
SidechainsHbondFuze()
BackboneHbondFuze()
PairWiseFuze()
PackingFuze()
HidingFuze()
DensityFuze()
ClashingFuze()
save.Quickload(Best_Score_slot_num) --best score saved in quick save 3
end
if (iteration_variable > 5) then
iteration_variable = iteration_variable-5
else
iteration_variable = iteration_variable-1
end
if (global_clashing_importance > .16) then
global_clashing_importance = global_clashing_importance-.15
else
global_clashing_importance = global_clashing_importance-.01
end
end
end
print("Best Score: ".. BestScore)
print("Total Gain: ".. (BestScore-StartScore))
end
function Bravo_BWF(BWF_string,Behavior_value,Iterationlength,CI)
Importance = Behavior_value
iteration_variable = Iterationlength
global_clashing_importance = CI
if (BWF_string== "SidechainHbond:") then
SidechainsHbondFuze()
elseif (BWF_string== "BackboneHbond:") then
BackboneHbondFuze()
elseif (BWF_string== "PairWise:") then
PairWiseFuze()
elseif (BWF_string== "Packing:") then
PackingFuze()
elseif (BWF_string== "Hiding:") then
HidingFuze()
elseif (BWF_string== "Density:") then
DensityFuze()
elseif (BWF_string== "Clash:") then
ClashingFuze()
else
print("error Bravo_BWF: BWF_string: ".. BWF_string)
end
end
function floor3(x)--cut at 3rd decimal place
return tostring(x-x%0.001)
end
function Score()
local s=0
if normal==true then
s=current.GetEnergyScore()
else
for i=1,segCnt do
s=s+current.GetSegmentEnergyScore(i)
end
end
return s
end
function ScoreRB()
local s=0
if normal==true then
s=recentbest.GetEnergyScore()
else
for i=1,segCnt do
s=s+recentbest.GetSegmentEnergyScore(i)
end
end
return s
end
function SaveBest()
local g=Score()-bestScore
if g>0 then
print("Gained another "..floor3(g).." points.")
bestScore=Score()
save.Quicksave(4) -- under normal conditions retain pose even as recording improvement
recentbest.Restore()
save.Quicksave(3)
save.Quickload(4)
end
return Score()-bestScore
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
function qStab()
behavior.SetClashImportance(0.21)
structure.MutateSidechainsSelected(1)
Wiggle("s",1)
if fastQstab==false then
behavior.SetClashImportance(0.4)
Wiggle("wa",1)
behavior.SetClashImportance(1)
Wiggle("s",1)
end
behavior.SetClashImportance(1)
Wiggle()
return SaveBest()
end
function Fuze1(ci1,ci2)
behavior.SetClashImportance(ci1)
Wiggle("s",1)
behavior.SetClashImportance(ci2)
Wiggle("wa",1)
end
function Fuze2(ci1,ci2)
behavior.SetClashImportance(ci1)
Wiggle("wa",1)
behavior.SetClashImportance(1)
Wiggle("wa",1)
behavior.SetClashImportance(ci2)
Wiggle("wa",1)
end
function FuzeEnd()
behavior.SetClashImportance(1)
Wiggle("wa",1)
Wiggle("s",1)
behavior.SetClashImportance(0.9)
Wiggle()
behavior.SetClashImportance(1)
Wiggle("wa",1)
SaveBest()
end
function reFuze(scr)
local s=ScoreRB()
if s<scr then
recentbest.Restore()
else
scr=s
end
return scr
end
function Fuze()
local scr=Score()
Fuze1(1,0.6) FuzeEnd()
scr=reFuze(scr)
Fuze2(1,1) SaveBest()
scr=reFuze(scr)
Fuze1(1,0.9) SaveBest()
scr=reFuze(scr)
Fuze2(1,1) FuzeEnd()
scr=reFuze(scr)
Fuze1(1,1) SaveBest()
reFuze(scr)
end
function bandstr(str) --set all band strength
for i=1, band.GetCount() do
band.SetStrength(i, str)
end
end
function calcBandAtom()
bandAtom={}
for x = 1,segCnt do
if (structure.GetAminoAcid(x) == 'g') or not structure.IsHydrophobic(x) then
bandAtom[x] = 2 -- center for Glycine and Hydophiles
elseif x == segCnt then
bandAtom[x] = 6 -- beta carbon for terminal segment
else
bandAtom[x] = 5 -- beta carbon
end
end
end
function QuakeR()
math.randomseed(os.time()) math.random() math.random() math.random()
calcBandAtom()
--freeze.UnfreezeAll()
selection.SelectAll()
StartingScore=Score()
bestScore=StartingScore
recentbest.Save()
save.Quicksave(3)
print("Starting "..recipeTitle..tostring(qLoops).." passes. Start score: "..floor3(StartingScore))
for x=1, qLoops do
print("Pass "..tostring(x).." of "..tostring(qLoops))
local start=math.floor(math.random(segCnt/10)) --first band somewhere in first 10% of protein
local len=math.floor(math.random(segCnt/2-5))+10
local step=math.floor(math.random(segCnt/2-5))+10
local loss=math.abs(math.floor(Score()*maxLoss/100))
band.DeleteAll()
print("Bands from segment "..tostring(start).." of length "..tostring(len)
.." every "..tostring(step).." segments.")
print("Pulling until loss of "..tostring(loss).." points.")
for x=start,segCnt, step do
for y=start+len, segCnt, step do
band.AddBetweenSegments(x,y,bandAtom[x],bandAtom[y])
end
end
behavior.SetClashImportance(pullingCI)
recentbest.Save()
local gain
for str=minBS,maxBS,0.07 do--search enough band strength to move
bandstr(str)
repeat
structure.WiggleAll(1,true,false)
gain=SaveBest()
if gain > 0 then
recentbest.Restore()
end
until gain<=0
if gain<-loss then
break
end
end
band.DeleteAll()
behavior.SetClashImportance(1)
recentbest.Save() --after pulling
print("Stabilizing...")
loop_starting_score = current.GetScore()
loop_gain = 1.1
loop_count = 0
while (loop_gain > 1.0) do -- recent best tends to make .01 gains forever. want to avoid that slowness.
print("Starting Score: ".. StartScore)
print("Current Score: ".. loop_starting_score)
loop_starting_score = current.GetScore()
loop_count = loop_count+1
-- these were experimentally determined to make gains. doesn't always work but it's better then brute force.
-- Bravo_BWF(Behavior type,B_v , Iteration length , Clashing Importance)
print ("Starting behavior wiggle fuze (BWF)...")
print ("Density: Fuze...")
print (" ")
Bravo_BWF("Density:",3,25,0.07)
print ("BackboneHbond: Fuze...")
print (" ")
Bravo_BWF("BackboneHbond:",3,25,1)
print ("PairWise: Fuze...")
print (" ")
Bravo_BWF("PairWise:",3,25,1)
print ("Hiding: Fuze...")
print (" ")
Bravo_BWF("Hiding:",3,25,1)
print ("Packing: Fuze...")
print (" ")
Bravo_BWF("Packing:",3,3,0.1)
print ("Clashing: Fuze...")
print (" ")
Bravo_BWF("Clash:",0.5,25,0.07)
loop_gain = current.GetScore() - loop_starting_score
print("Loop " .. loop_count .. " Gain: " .. loop_gain)
end
if qStab() > doFuze then
print("Starting End Round: Fuzing....")
Fuze()
end
end
SaveBest()
save.Quickload(3) --load best state
print("Current score: "..floor3(Score()).." Total gain: "..floor3(Score()-StartingScore))
print("Total QuakeR gain: "..floor3(Score()-StartingScore))
return true
end
function GetParameters ()
local dlog = dialog.CreateDialog ( "QuakeR & BWF v1.0 with mutate" )
dlog.iterations = dialog.AddSlider ( "iterations: " , qLoops , 1 , 1000 , 0 )
dlog.ok = dialog.AddButton ( "OK" , 1 )
dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
if ( dialog.Show ( dlog ) > 0 ) then
qLoops = dlog.iterations.value
return true
else
return false
end
end
function main ()
if ( GetParameters () == false ) then
return -- graceful exit
end
QuakeR()
cleanUp()
end
function CleanUp(err)
if err:find('Cancelled')~=nil then
print "QuakeR & BWF Cancelled"
else
print(err)
end
behavior.SetClashImportance(1)
-- band.DeleteAll()
SaveBest()
save.Quickload(3)
print("Total QuakeR & BWF gain: "..floor3(bestScore-StartingScore))
end
segCnt=structure.GetCount()
while structure.GetSecondaryStructure(segCnt)=="M" do segCnt=segCnt-1 end
--- VVVVVVVVVV OPTIONS
normal=(current.GetExplorationMultiplier()==0)
qLoops=50 -- <<<OVER THERE! do more! much more!
minBS=0.3 --starting minimum bands strength
maxBS=1.0 --maximum band strength
maxLoss=1 --minimum percentage loss when pulling. ie 5% of 10000 is 500pts
pullingCI=1.0 --clash importance while pulling
fastQstab=false --true for 1s1w as stabilize (faster)
doFuze=-10 --run fuze when score after qstabilize is close to best.
xpcall(main,CleanUp)
