Recipe: Acid Tweeker V2.2

created by Bruno Kestemont

Profile

• Name: Acid Tweeker V2.2
• ID: 45675
• Shared with: Public
• Parent: Acid Tweeker V2.1
• Children:
  • Acid Tweeker V2.3
  • Acid Tweeker V2.2 mine
  • Acid Tweeker V2.3
  • gw - AT w/Mutate
  • Acid Tweeker V2.2 reshare
• Created on: September 21, 2013 at 11:08 AM UTC
• Updated on: September 21, 2013 at 11:08 AM UTC
• Description:

  bug fixed on sidechain manipulate and on wiggle selected

Code

--Acid Tweaker v2.2.1
--Acid Tweaker  v1.78 by Steven Pletsch
--modded by rav3n_pl;]
-- modded by BitSpawn, March 2012
-- v2.00: LUAV2, thanks Timo
-- modded by B.Kestemont, March 2013
-- v2.1:  bug fixed on rotamers, set default as in v1.78
-- v2.2 Bug fixed on structure.WiggleAll (replaced by structure.WiggleSelected)
-- managment of slow filters and cleaned BK 8/4/2013
--adding starting score in the log BK 20 Sept 2013
--v2.2.1 adding range of seg in user inputs BK 20 Sept 2013


g_segments = structure.GetCount() -- total number of segments in puzzle
g_total_score = 0 -- recent best to compare to and see if score was improved
g_score = {} -- array of segment scores for comparisons (total for segment)

p=print --a short

segCount=structure.GetCount()
segStart=1
segEnd=segCount
OriginalFilterSetting = behavior.GetSlowFiltersDisabled() -- new BK 8/4/2013
PROBABLEFILTER=false

	--Detect ligands (from Jean-Bob)

function DetectLigand()
	local lastSeg=structure.GetCount()
   while structure.GetSecondaryStructure(lastSeg)=="M" do
		flagligand=true
		lastSeg=structure.GetCount()-1 --corrige l'erreur de compte due au ligand-- c'est un duplicat de setlock. A verifier.
		segCnt=structure.GetCount()-1
	end
	indexligand={lastSeg,segEnd}
	segEnd=segCount
end
DetectLigand()

function Score()
    return current.GetEnergyScore()
end

function ds(val)
    if mutate==true then
		if PROBABLEFILTER then behavior.SetSlowFiltersDisabled(OriginalFilterSetting) end -- new BK 8/4/2013, always back to user settings
        structure.MutateSidechainsSelected(val+1)
    else
        structure.ShakeSidechainsSelected(val)
    end
end

global_ci=1
function CI(val)
    global_ci=val
    behavior.SetClashImportance(global_ci)
end

function detectfilter()
	local descrTxt=puzzle.GetDescription()
	if #descrTxt>0 and (descrTxt:find("filter") or descrTxt:find("filters")) then
		PROBABLEFILTER=true
	end
	return
end
detectfilter()

function WiggleSimple(val,how)
		if PROBABLEFILTER then behavior.SetSlowFiltersDisabled(true) end-- new BK 8/4/2013, always disable filter here
        if how == "s" then ds(1)
            elseif how == "wb" then structure.WiggleSelected(val, true, false) -- backbones
            elseif how == "ws" then structure.WiggleSelected(val, false, true) -- sidechains
            elseif how == "wa" then structure.WiggleSelected(val, true, true) -- all
			elseif how== "lw" then structure.LocalWiggleSelected(val) -- new
        end
		if PROBABLEFILTER then behavior.SetSlowFiltersDisabled(true) end-- new BK 8/4/2013, always disable filter here
end

function WiggleAT(ss, how, iters, minppi)
    local valiter=2
    local val=1
    if fast==true then valiter=1 end
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    minppi=(g_total_score-Score())/100
    if ((minppi==nil) or (minppi<0.001)) then
            minppi=0.001
    end
    if global_ci==1.00 then val=valiter end
    if iters>0 then
        iters=iters-1
        local sp=Score()
		WiggleSimple(val,how)-- new function BK 8/4/2013
        local ep = Score()
        local ig=ep-sp
        if how~="s" then
            if ig > minppi then WiggleAT(ss, how, iters, minppi) end
        end
    end
end

function SelectSphere(sg,radius,nodeselect)
    if nodeselect~=true then selection.DeselectAll() end
    for i=1, segCount do
        if structure.GetDistance(sg,i)<radius then selection.Select(i) end
        if sphere_worst==true then
            if current.GetSegmentEnergyScore(i)<sphere_worst_value then selection.Select(i) end
        end
    end
end

function Fix(sg)
    if fix_band==false then
        return
    end
-- selection.DeselectAll()
    local nb=1
    for i=1, segCount do
        dist=structure.GetDistance(sg,i)
        if (dist<12 and dist>6) then
            local cband=band.GetCount()
            band.AddBetweenSegments(sg, i)
            if cband<band.GetCount() then
                band.SetGoalLength(nb,dist)
                nb=nb+1
            end
-- else if dist>12 then
-- selection.Select(i)
-- end
        end
    end
-- freeze.FreezeSelected(true,true)
-- selection.DeselectAll()
-- SelectSphere(sg,esfera)
    --structure.WiggleSelected(1,true,true)
	WiggleSimple(1,wa) -- new function BK 8/4/2013
    band.DeleteAll()
-- freeze.UnfreezeAll()
end
--L114
function round(x)--cut all afer 3-rd place
    return x-x%0.001
end

bestScore=Score()
function SaveBest()
    local s=Score()
    local g=s-bestScore
    if g>0 then
        p("Gained another ",round(g)," pts.")
        bestScore=s
        save.Quicksave(3)
    end
end

function usableAA(sn)
    local usable=false
---------------------------------------------

        if current.GetSegmentEnergyScore(sn)>minimo then
            return usable
        end
    if rebuild==true then
        selection.DeselectAll()
        selection.Select(sn)
        structure.RebuildSelected(2)
        usable=true
        return usable
    end
---------------------------------------------

    if #useThat>0 then
        for i=1,#useThat do
            if sn==useThat[i] then
                usable=true
                break
            end
        end
    else
        if #useOnly > 0 then
            for i=1,#useOnly do
                local ss=useOnly[i][1]
                local se=useOnly[i][2]
                for s=ss,se do
                    if s==sn then
                        usable=true
                        break
                    end
                end
            end
        else
            usable=true
            if #doNotUse>0 then
                for i=1,#doNotUse do
                    local ss=doNotUse[i][1]
                    local se=doNotUse[i][2]
                    for s=ss,se do
                        if s==sn then
                            usable=false
                            break
                        end
                    end
                    if usable==false then break end
                end
            end

            if #skipAA>0 then
                local aa=structure.GetAminoAcid(sn)
                for i=1,#skipAA do
                    if aa==skipAA[i] then
                        usable=false
                        break
                    end
                end
            end
        end
    end

    local se=segCount
    if ATend~=nil then se=ATend end
    if sn<ATstart or sn>se then usable=false end

    return usable
end

function wiggle_out(ss)
    CI(.6)
    --structure.WiggleSelected(1,true,true)
	WiggleSimple(1,wa) -- new function BK 8/4/2013
    CI(1.)
    WiggleAT(ss)
    WiggleAT(ss,"s",1)
	--selection.SelectAll()
    CI(.6)
    WiggleAT(ss)
    CI(1.)
    WiggleAT(ss)
    recentbest.Restore()
    SaveBest()
end

function getNear(seg)
    if(Score() < g_total_score-1000) then
        selection.Deselect(seg)
        CI(.75)
        --ds(1)
		WiggleSimple(1,s) -- new function BK 8/4/2013
        --structure.WiggleSelected(1,false,true)
		WiggleSimple(1,ws) -- new function BK 8/4/2013
        selection.Select(seg)
        CI(1)
    end
    if(Score() < g_total_score-1000) then
        if fix_band==true then
            Fix(seg)
        else
            recentbest.Restore()
            SaveBest()
            return false
        end
    end
    return true
end

function sidechain_tweak()
    p("Pass 1 of 3: Sidechain tweak")
    for i=segStart, segEnd do
        if usableAA(i) then
            selection.DeselectAll()
            selection.Select(i)
            local ss=Score()
            g_total_score = Score()
            CI(0)
            --ds(2)
			WiggleSimple(2,s) -- new function BK 8/4/2013
            CI(1.)
            p("Try sgmnt ", i)
            SelectSphere(i, esfera)
            if (getNear(i)==true) then
                wiggle_out(ss)
            end
        end
    end
end

function sidechain_tweak_around()
    p("Pass 2 of 3: Sidechain tweak around")
    for i=segStart, segEnd do
        if usableAA(i) then
            selection.DeselectAll()
            for n=1, g_segments do
                g_score[n] = current.GetSegmentEnergyScore(n)
            end
            selection.Select(i)
            local ss=Score()
            g_total_score = Score()
            CI(0)
            --ds(2)
			WiggleSimple(2,s) -- new function BK 8/4/2013
            CI(1. )
            p("Try sgmnt ", i)
            SelectSphere(i,esfera)
            if(Score() > g_total_score - 30) then
               wiggle_out(ss)
            else
                selection.DeselectAll()
                for n=1, g_segments do
                    if(current.GetSegmentEnergyScore(n) < g_score[n] - 1) then
                        selection.Select(n)
                    end
                end
                selection.Deselect(i)
                CI(0.1)
                --ds(1)
				WiggleSimple(1,s) -- new function BK 8/4/2013
                SelectSphere(i,esfera,true)
                CI(1.0)
                if (getNear(i)==true) then
                    wiggle_out(ss)
                end
            end
        end
    end
end


-- debugged:
function sidechain_manipulate()   -- y a un bug, donne des scores negatifs !
    --p("Dernire chance: manipulateur brutal des chaines latrales")
	p("Last chance: bruteforce sidechain manipulate")
    for i=segStart, segEnd do
        if usableAA(i) then
            selection.DeselectAll()
            rotamers = rotamer.GetCount(i)
			save.Quicksave(4)
            if(rotamers > 1) then
                local ss=Score()
				p("Sgmnt: ", i," rotamers: ",rotamers, " Score= ", ss)
                for r=1, rotamers do
					--p("Sgmnt: ", i," position: ",r, " Score= ", ss)
                    save.Quickload(4)
                    g_total_score = Score()
                    rotamer.SetRotamer(i,r)
                    CI(1.)
                    if(Score() > g_total_score - 30) then
                        SelectSphere(i,esfera)
                        wiggle_out(ss) -- ceci peut changer le nombre de rotamers
                    end	
					if rotamers > rotamer.GetCount(i) then break end --si nb de rotamer a change
                end
            end
        end
		recentbest.Restore()-- car les rotamers ont pu tout casser.
    end
end
-- end debugged

--g_segments=g_segments-1 -- uncomment for lingard puzzles only!

--To BE IMPLEMENTED VIA DIALOG BOX
useThat={ --only segments what have to be used OVERRIDES all below
--18,150,151,205,320,322,359,361,425,432,433 --382
}

useOnly={ --ranges what have to be used OVERRIDES BOTH LOWER OPTIONS
--{12,24},
--{66,66},
}
doNotUse={ --ranges that should be skipped
--{55,58},
--{12,33},
}
skipAA={ --aa codes to skip
'a',
'g',
}

--option to easy set start and end of AT work to-- to be implemented in dialog
ATstart=1 --1st segment
ATend=nil --end of protein if nil

sphere_worst=false -- include worst segments in sphere
sphere_worst_value=0
--END TO BE IMPLEMENTED VIA DIALOG BOX

function Run()
    CI(1.00)
    recentbest.Restore()
    save.Quicksave(3)--in save 3 always best solution. Load in case of crash.
    s1=Score()
	sidechain_tweak()
    s2=Score()
    p("Tweak gain: ",round(s2-s1))
	sidechain_tweak_around()
    s3=Score()
    p("Around gain: ",round(s3-s2))
    if manipulate==true then
        sidechain_manipulate()
    end
	s4=Score()
	if s4-s3 <0 then recentbest.Restore() end --against the bug !!!
    selection.SelectAll() -- or 2 lines in one structure.WiggleAll(4,true,true)
	WiggleSimple(4,wa) -- new function BK 8/4/2013
	WiggleSimple(2,ws) -- new function BK 8/4/2013
    selection.SelectAll()
	WiggleSimple(4,wa) -- new function BK 8/4/2013
	recentbest.Restore()
	s5=Score()
    p("Start score: ",round(s1))
    p("Tweak gain: ",round(s2-s1))
    p("Around gain: ",round(s3-s2))
    p("Manipulate gain: ",round(s4-s3))
    p("Total Acid gain: ",round(s5-s1))
    p("End score: ",round(s5))
end

esfera=8
minimo=510 -- score for working with worst segments. Don't use, usually worst segs have no rotts
mutate=false -- Don't use, very bad results yet (TODO)
rebuild=true -- for very end in a puzzle, rebuild segment before tweak
--segStart=1
--segEnd=structure.GetCount()
fix_band=false -- if you want to try with the worst segments
fast=false
manipulate=true -- test rottamers
recentbest.Save()
ini_score=Score()
print("Acid Tweeker starting at score: "..ini_score)

function GetParam()
    local dlg = dialog.CreateDialog("Acid Tweeker 2.2")
    dlg.fast = dialog.AddCheckbox("Fast mode (gain 25% less)", false)
    dlg.fix_band = dialog.AddCheckbox("Fix geometry with bands when score breaks down", false)
    dlg.manipulate = dialog.AddCheckbox("Brute force in phase 3", true)
    dlg.rebuild = dialog.AddCheckbox("Rebuild before search rotts, for very end only", true)
	dlg.segStart=dialog.AddTextbox("From seg ", segStart)
	dlg.segEnd=dialog.AddTextbox("To seg ", segEnd)
    dlg.ok = dialog.AddButton("OK", 1)
    dlg.cancel = dialog.AddButton("Cancel", 0)
    
    if dialog.Show(dlg) > 0 then
        fast = dlg.fast.value
        fix_band = dlg.fix_band.value
        manipulate = dlg.manipulate.value
        rebuild = dlg.rebuild.value
		segStart= dlg.segStart.value
		segEnd= dlg.segEnd.value
        print("Options:\nfast =",fast,"\nfix_band =",fix_band,"\nmanipulate =",manipulate, "\nrebuild =",rebuild, "\nsegs =",segStart,"-",segEnd)
        return true
    end
    return false
end


if GetParam()==false then
    return
end


while(true) do
    Run()
    minimo=minimo+0.5
    print("Score: ", Score(), " Gain: ", Score()-ini_score)
end

--end

Comments

[Bruno Kestemont]

New to ver 2.2: wiggle.selected to get same yield as in ver 1.78.

Now we have less bugs and a dialog for options.

[Bruno Kestemont]

Code cleaning for better performance.
Slow filters management in order to be much faster on filtered puzzles (I think it does not change the velocity on normal puzzles: please do not be disturbed by the strange scoreline appearance: the scores and best scores are well good recorded).

[Bruno Kestemont]

ver 2.2.1: added the possibility to select segments (default = all protein) in the dialog box.
It is still possible to do more complex selection editing the recipe (exclude segments, nominate a list of segments etc). I'll evaluate if it is interesting to put these options into the dialog box.