Recipe: Rav3n_pl GAB v3.6.2 filter Cuts

created by Bruno Kestemont

Profile

• Name: Rav3n_pl GAB v3.6.2 filter Cuts
• ID: 100431
• Shared with: Public
• Parent: Rav3n_pl GAB v3.3 filter Cuts
• Children:
  • Rav3n_pl GAB v3.6.1 band 2 symmetry
  • Rav3n_pl GAB v3.4.10 filter Cuts quiver
  • Rav3n_pl GAB v3.4.10 filter Cuts repost
  • Rav3n_pl GAB v3.7.6 fc binding
• Created on: March 19, 2020 at 17:42 PM UTC
• Updated on: March 19, 2020 at 17:42 PM UTC
• Description:

  GAB in v2 LUA, now banding to 1st atom of sidechain. Now with filter management to gain time, and with cuts in fuze

Code

--[[
GAB - Genetic Algorythm on Bands, with cuts (Bruno Kestemont)
based on Rav3n_pl
based on CartoonVillan and Crashguard303 scripts
Lua V2

Definitions:
band: randomised: start segment, end segment, length, strength
critter: set of bands
herd: set of critters

1.
- randomize needed bands 
- randomly assignig them to criters

2.
- score each critter

3.
- keep critters scoring above score
- breed best critters
- breed bastards (best one + random one)
- forget about rest of critter
- randomize new critters to fill herd

VERSIONS:
2.0.5
2.0.5 Filter => Filter management added Bruno Kestemont 10/10/2013
16/04/2014: only added more score info in the log
3.0 : fuze using cuts 28/05/2014 Bruno Kestemont
3.1: cut bug fixed on deletecut 02/06/2014
3.2: using creditebest
3.3: creditbest bug fixed 02/06/2014 (do not use creditebest)
3.3.1: added Notes management and quicksaves for big gains (for archives when undo's) 4/11/2014
3.3.2: replaced shake by QuickShake  8/11/2014
3.3.3: debugged uncut
3.4.5: generic filter management and debugged segment to itself
3.4.6: detect ligand and always use ligand (optional)
3.4.7: 13/5/2015 changed small possible bugs
	   18/1/2016 log with archive of gains following jeff101 suggestions
	   reduced thresholds on Big Steps
	   Keeps user bands
	   Mutate once 5 days before the deadline or the 3 latest days for HBond puzzles
	   GENERICFILTER only latest days of non HBonds puzzles
	   FILTERMANAGE only on mid game
3.4.8: hide only hydrophobics
3.4.9 undo.SetUndo
3.4.10 fixed unideal loop bug
3.4.11 use ligand on ligand puzzle (not always), new wiggle
3.5 GRRR adapted filter setting to new lua commands: return2GlobalOriginalFilterSetting()
3.5.1 simplified the log
3.6 : added bands to symmetric chains
3.6.1: fixed segMeanScore=10*(800-absolutebest.GetScore())
3.6.2: if badGen<=herd.renew then -- bug fixed thanks to robgee

To Do: Partial filter management, unless end Fuze and end Qstab // to verify
]]--

recipename="Rav3n_pl GAB 3.6.2 filter Cuts"

undo.SetUndo(false)

OriginalFilterSetting = filter.AreAllEnabled() -- new BK 8/4/2013
PROBABLEFILTER=false
HASMUTABLE=false -- NEW BK 10/10/2013
timeLeft=os.difftime(puzzle.GetExpirationTime(),os.time())/86400 -- in days

segCnt=structure.GetCount()
segCnt2=segCnt
SYMMETRIC=  structure.GetSymCount () > 0 -- not used yet
--detect ligand
while structure.GetSecondaryStructure(segCnt2)=="M" do segCnt2=segCnt2-1 end
HASLIGAND=segCnt2<segCnt
startLigand=segCnt2+1
stopLigand=segCnt

	math.randomseed(os.clock()) -- 28/05/2014
	math.random() -- 28/05/2014
	

p=print
userbands=band.GetCount()
p("Starting "..recipename.. " on\n   puzzle "..(puzzle.GetName()))
p('   with puzzle ID '..(puzzle.GetPuzzleID())..' and '..userbands..' user-supplied bands.\n ')

-- START Wiggle Power Setting stuff
function DisplayLongWigglePower ()
	local PowerSetting = behavior.GetWigglePower()
	local result = ""
	if PowerSetting == "l" then result = "Low"
	elseif PowerSetting == "m" then result = "Medium"
	elseif PowerSetting == "h" then result = "High"
	elseif PowerSetting == "a" then result = "Auto"
	end
	return result
end
OriginalWPowerSetting= DisplayLongWigglePower ()
print(OriginalWPowerSetting .. " Wiggle Power")

function CheckWP() -- including Alarm Dialog
	if OriginalWPowerSetting == "Low" or OriginalWPowerSetting == "Auto" then
	   local ask=dialog.CreateDialog("Wiggle Power is ".. OriginalWPowerSetting)
	   ask.l1=dialog.AddLabel("Are you sure ?")
	   ask.continue=dialog.AddButton("Continue",1)
	   ask.stop=dialog.AddButton("Cancel",0)
	   askresult=dialog.Show(ask)
	   if askresult < 1 then return false end
   end
   return true
end

-- STOP Wiggle Power Setting stuff

function return2GlobalOriginalFilterSetting()
	if OriginalFilterSetting then -- if true, all filters are default enabled
		filter.EnableAll()	--Enables all filters
	else
		filter.DisableAll()	--Disables all filters
	end

end

--START Generic Filter Management by BitSpawn 21/12/2014
--Source: http://fold.it/portal/node/1998917

--identifying filtered puzzles and all properties
OriginalFilterSetting = filter.AreAllEnabled()
PROBABLEFILTER= false
GENERICFILTER=false
FILTERMANAGE= false
HASMUTABLE= false
IDEALCHECK= false
PROBABLESYM= false
SEPSIS= false
ELECTRON= false
CENTROID= false
HOTSPOT= false
HBOND=false
sym=1
--START extraction of information from puzzle metadata	--Extrait des infos

function detectfilterandmut() -- Bruno Kestemont 10/10/2013; 13/2/2015; 5/1/2019
	local descrTxt=puzzle.GetDescription()
	local puzzletitle=puzzle.GetName()
	local function SymetryFinder() -- by Bruno Kestemont 7/2/2013, 25/8/2013
		local segMeanScore=10*(800-absolutebest.GetScore()) -- top score pour eviter les debuts de puzzle
		--p("Score moyen par segment= "..segMeanScore)
		if PROBABLESYM then
			 if       segMeanScore<33.39 then sym=1
				PROBABLESYM=false
				elseif segMeanScore<85  then sym=2 
				elseif segMeanScore<132 then sym=3 
				elseif segMeanScore<197 then sym=4
				else sym=5
			 end
		else sym=1
		end
		return
	end
	
	
	
	
	if #descrTxt>0 and (descrTxt:find("filter") or descrTxt:find("filters") or descrTxt:find("bonus") or descrTxt:find("bonuses") and not descrTxt:find("disabled"))then
		PROBABLEFILTER=true
		FILTERMANAGE=true -- default yes during wiggle (will always be activate when scoring)
		GENERICFILTER=false -- to be evaluated
	end
	if #descrTxt>0 and (descrTxt:find("H-bond networks") or descrTxt:find("Hydrogen Bond Networks") or descrTxt:find("H-bond Networks") 
		or descrTxt:find("H-bond Network") and not descrTxt:find("disabled"))then
		PROBABLEFILTER=true
		FILTERMANAGE=false -- default no
		GENERICFILTER=false -- to be evaluated
	end	
	if #descrTxt>0 and (descrTxt:find("design") or descrTxt:find("designs")) then
		HASMUTABLE=true
		IDEALCHECK=true
		HANDFOLD=true
	end
	if #descrTxt>0 and (descrTxt:find("De-novo") or descrTxt:find("de-novo") or descrTxt:find("freestyle")
		or descrTxt:find("prediction") or descrTxt:find("predictions")) then
		IDEALCHECK=true
		HANDFOLD=true
	end

	if #puzzletitle>0 then
		if (puzzletitle:find("Sym") or puzzletitle:find("Symmetry") or puzzletitle:find("Symmetric")
				or puzzletitle:find("Dimer") or puzzletitle:find("Trimer") or puzzletitle:find("Tetramer")
				or puzzletitle:find("Pentamer")) then
			PROBABLESYM=true
			if puzzletitle:find("Dimer") and not puzzletitle:find("Dimer of Dimers") then sym=2		
			elseif puzzletitle:find("Trimer") or puzzletitle:find("trimer") then sym=3
			elseif puzzletitle:find("Dimer of Dimers") or puzzletitle:find("Tetramer") then sym=4
			elseif puzzletitle:find("Pentamer") then sym=5
			else SymetryFinder()
			end
		end
	end
	if #descrTxt>0 and (descrTxt:find("Sym") or descrTxt:find("Symmetry") or descrTxt:find("Symmetric")
			or descrTxt:find("sym") or descrTxt:find("symmetry") or descrTxt:find("symmetric")) then
		PROBABLESYM=true
		if (descrTxt:find("Dimer") or descrTxt:find("dimer") or descrTxt:find("C2 symmetry") or descrTxt:find("twoo symmetric"))
			and not (descrTxt:find("Dimer of Dimers") or descrTxt:find("dimer of dimers")) then sym=2 
		elseif descrTxt:find("Trimer") or descrTxt:find("trimer") or descrTxt:find("C3 symmetry") or descrTxt:find("three symmetric") then sym=3
		elseif (descrTxt:find("Dimer of Dimers") or descrTxt:find("Tetramer") or descrTxt:find("C4 symmetry") or descrTxt:find("four symmetric"))
			and not (descrTxt:find("dimer of dimers") or descrTxt:find("tetramer"))then sym=4 
		elseif descrTxt:find("Pentamer") or descrTxt:find("pentamer") or descrTxt:find("C5 symmetry") or descrTxt:find("five symmetric") then sym=5
		else SymetryFinder()
		end
	end
	--print resulting sym info
	if PROBABLESYM then
		print("Symmetric")
		if sym==2 then
			print("Dimer")
		elseif sym==3 then
			print("Trimer")
		elseif sym==4 then
			print("Tetramer")
		elseif sym==5 then
			print("Pentamer")
		elseif sym>5 then
			print("Terrible polymer")
		end
	else print("Monomer")
	end

	if #puzzletitle>0 and puzzletitle:find("Sepsis") then -- new BK 17/6/2013
		SEPSIS=true
		HANDFOLD=true
		--p(true,"-Sepsis")
		print("Sepsis")
	end
	if #puzzletitle>0 and puzzletitle:find("Electron Density") then -- for Electron Density
		--p(true,"-Electron Density")
		ELECTRON=true
		HANDFOLD=true
		print("Electron density")
	end
	if #puzzletitle>0 and puzzletitle:find("Centroid") then -- New BK 20/10/2013
		--p(true,"-Centroid")
		CENTROID=true
		print("Centroid")
	end
	if #puzzletitle>0 and puzzletitle:find("Hotspot") then -- New BK 21/01/2014
	HOTSPOT=true
	print("Hotspot")
	end
	return
end
detectfilterandmut()

--END extraction of information from puzzle metadata	--Extrait des infos

-- function to copy class/table


function CopyTable(orig)

    local copy = {}

    for orig_key, orig_value in pairs(orig) do

        copy[orig_key] = orig_value  

    end

    return copy

end

-- functions for filters

function FiltersOn()

    if filter.AreAllEnabled() then

        filter.EnableAll()

    end

end

function FiltersOff()

    if filter.AreAllEnabled() and GENERICFILTER then -- 18/1/2016

        filter.DisableAll()

    end

end

-- function to overload a funtion

function mutFunction(func)

    local currentfunc = func

    local function mutate(func, newfunc)

        local lastfunc = currentfunc

        currentfunc = function(...) return newfunc(lastfunc, ...) end

    end

    local wrapper = function(...) return currentfunc(...) end

    return wrapper, mutate

end

-- function to overload a class

-- to do: set the name of function

classes_copied = 0

myclcp = {}

function MutClass(cl, filters)

    classes_copied = classes_copied+1

    myclcp[classes_copied] = CopyTable(cl)

    local mycl =myclcp[classes_copied]

    for orig_key, orig_value in pairs(cl) do

        myfunc, mutate = mutFunction(mycl[orig_key])

        if filters==true then

            mutate(myfunc, function(...)

                FiltersOn()

                if table.getn(arg)>1 then

                    -- first arg is self (function pointer), we pack from second argument

                    local arguments = {}

                    for i=2,table.getn(arg) do

                        arguments[i-1]=arg[i] 

                    end

                    return mycl[orig_key](unpack(arguments))

                else

                    --print("No arguments")

                    return mycl[orig_key]()

                end

            end)   

            cl[orig_key] = myfunc

        else

            mutate(myfunc, function(...)

                FiltersOff()

                if table.getn(arg)>1 then

                    local arguments = {} 

                    for i=2, table.getn(arg) do

                        arguments[i-1]=arg[i]  

                    end

                    return mycl[orig_key](unpack(arguments))

                else

                    return mycl[orig_key]()

                end

            end)   

            cl[orig_key] = myfunc
        end
    end
end

-- how to use:
--setting default options if filters BK 4/2/2015
--MutClass(structure, false)
--MutClass(band, false)
--MutClass(current, true)
if GENERICFILTER then -- WARNING: TO VERIFY !! (may be it's irreversible for several funtions bellow)
	MutClass(structure, false)
	MutClass(band, true)
	MutClass(current, true)
	MutClass(recentbest, true) -- otherwise, it remembers cut solutions
	MutClass(save, true) -- better to save with full score
end
			
--STOP Generic Filter Management

-- options:
energy = false --set true to seek energy in exploration puzzles; false works on all puzzles
pullCI = 0.9 --Clash Importance during pull
maxCI = 1 --maximum CI used by script
fastQstab = true -- only 1s1w after pull if true
fuzeThresh = 1 -- run fuze if we are close to best score (negative=new best score)
qstabThresh = 1 -- run qstab if score drops more than... wiggle only in other case
useLigand = false --use ligand if true
AlwaysUseLigand=false -- Warning: don't set true by default because there are some erroneous ligands
onlyMutable = false --if true use ONLY all mutable aas, no matter of always use
mutateOnce = false --if true use mutate(1) instead of shake in qstab
mutateOnceCI = 0.21 --mutate on what clashing importance
mutateAlwas = false --if true use mutate(1) instead of all shakes
mingps= 80 -- in wiggle sequence, this is the minimum gain per iteration needed to do the wiggle again (not zure it's very usefull to save time).
cut=structure.InsertCut -- 28/05/2014
--uncut=structure.DeleteCut -- 28/05/2014
if HASMUTABLE and not HBOND and timeLeft>4 and timeLeft<6 then mutateOnce = true print ("Option: mutate(1) instead of shake in qstab") end -- It's an option !
--if HASMUTABLE  and not HBOND and timeLeft>4 then mutateAlwas = true print ("Option: mutate(1) instead of all shakes") end -- It's an option !
--Don't mutate just after hand fold (because of filters on AAs, better to mutate by purpose using recipes like MNW or Maaa)
--Don't mutate the last 4 days, it's slow and it will not gain.
if HASMUTABLE and HBOND and timeLeft<4 then mutateOnce = true print ("Option: mutate(1) instead of shake in qstab") end
--with HBonds, mutate a little bit later
if HASMUTABLE and HBOND and timeLeft<3 then FILTERMANAGE = true print ("Option: wiggle with filter disabled") end

--SLOTS:
--[[
3	 is best
4  used in recipe
5  used in recipe
50-100 used to record each big steps for movie at the end

]]--
SlotStepStart=50 -- New 4/11/2014
SlotStep=SlotStepStart

herd= --herd options
{ 
breedBest = 5, --breed best 4 critters - all combinations => 6 kids form 4 critters, 3 form 3, 1 form 2, 9 form 5 ;]
keepBest = 3, --save up to 3 best scoring critters, rest are forgotten
breedBastards = 8, --number of best will have one random bastard
newRandom = 10, --adding new random ones each generation
maxGen= 100, --maximum generations 
shuffle = true, --set true to run critters in random order
renew=4, --create totally fresh herd after that many gens w/o improvement
}
critter= --critter options
{
minBands=2, --minimum bands
maxBands=7, --maximum bands
keepScore = 0 , --survive to next gen only if score higher than
breedScore= -20, --will breed kids only if score higher. Basttards always breed
maxLoss=30, --maximum loss by critter. set 0 to disable
}

bands= --bands options
{
minStr=0.3, --minimum band str
maxStr=1.1, --maximum band str
minChng = 3, -- minimum length change of band (negative length pull or positive length push)
maxUp = 6.1, -- maximum length change up (push)
maxDn = 6.9, -- maximum length change down (pull)(will be used negative)
minSkip = 5, --minimum segment distance (not banding segments that are too proximate)
minDist = 4, --minimum spatial distance
minLen = 2, --minimum length of created band
}

DoNotUse={--just comment lines below or add more areas to avoid
--{segCnt,segCnt}, --ligand cant be used
--{120,134},
--{1,10},
}
AlwaysUse={ --areas should be always used
--{236,236}--ligand need to be at one end
--{308,311}, --loopy
--{272,319}, --loopy
}
UseSegments= --use ONLY this segments
{
--2,3,4,5
}

-- bands by secondary structure
use=
{
Sheet=true, --set false to not band sheets
Helix=true, --set false to not band helices
Loop=true, --set false to not band loops
}
checkBoth=false --check both ends to above, if false only one end need to be true

--end of options


if HASLIGAND then useLigand=true end

if useLigand==false then
    segCnt=segCnt2
end

if HASLIGAND and AlwaysUseLigand then
	AlwaysUse={ --areas should be always used
{startLigand,stopLigand}--ligand need to be at one end
--{308,311}, --loopy
--{272,319}, --loopy
}
end

function uncut(seg) -- new BK 02/06/2014
	for i=1, structure.GetCount() do
		structure.DeleteCut(i)
	end
end

function CI(c)
if c>maxCI then c=maxCI end
behavior.SetClashImportance(c)
end
function round(x)--cut all afer 3-rd place
    return x-x%0.001
end
function down(x)
    return x-x%1
end

function Score()--return score, exploration too
    if energy==true then
        return current.GetEnergyScore()
    else
        return current.GetScore()
    end
end 
--local seed=recipe.GetRandomSeed() --NOT WORKING on windowz!!!
--calculate REALLY good seed from current score
seed=os.time()
seed=1/seed
while seed<10000000 do seed=seed*10 end
seed=seed-seed%1
p("Seed is: "..seed)
math.randomseed(seed)
math.random(100) -- Because the first is not random
format=string.format

--START Archive in Notes, -- New 4/11/2014

function SelectNote(recipename)
	store={}
	store.label=recipename or "" -- edit here the recipe name
	store.note_number=structure.GetCount()
	for seg=structure.GetCount(),1,-1 do
	  if structure.GetNote(seg)~="" then break end
	  store.note_number=seg
	end
	print(string.format("Recording results in Note for segment %i",store.note_number))
	store.starting_score=current.GetScore()
	--structure.SetNote(store.note_number,string.format("(%s) %.3f + FSP",user.GetPlayerName(),store.starting_score))
end

SelectNote(recipename)

function WhriteNote(loop_nb) -- all inits are in SelectNote function
	local loop_count= loop_nb or 1
	structure.SetNote(store.note_number,string.format("(%s) %.3f + %s(%i) %.3f",user.GetPlayerName(),store.starting_score,store.label,loop_count,current.GetScore()))
end

--END Archive in Notes

--START quick save algorithm

function QuickShake()
--[[------------------------------------------------------------------------------------------------
-- Algorithm for faster shake

REFERENCES
1. N/A

Copyright (C) 2014 Seagat2011 <http://fold.it/port/user/1992490>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

$Id$

------------------------------------------------------------------------------------------------]]--

--[[

v1
- Inception

1.2
- Loops until nogain 

]]--

local idx  = 1
local idx2 = structure.GetCount ()
local hash = {}
local cs   = current.GetScore ()

--print ( 'Quick Shake Algorithm v1.2 SG2011 - Current Score: '..cs )

local function New ( obj )
  return obj -- pass-new-obj-by-value
end

local _gses = New ( current.GetSegmentEnergySubscore )

local function SmartShake ( iters ) 
  local gain = true
  while (gain) do
    gain = false
    for i=idx,idx2 do
      local ci = _gses ( i,'clashing' ) 
      if ci <  _gses ( i,'hiding'   ) and
         ci <  _gses ( i,'packing'  ) and
         ci <  _gses ( i,'ideality' ) and
         ci <  _gses ( i,'sidechain') and
         ci <  _gses ( i,'bonding'  ) and
         ci <  _gses ( i,'other'    ) and
         ci <  _gses ( i,'reference') then
        selection.Select ( i )
      end -- test ci --
    end -- loop --
    if selection.GetCount () then
      local css = current.GetScore ()
      structure.ShakeSidechainsSelected ( iters )
      selection.DeselectAll () 
      if current.GetScore () > css then 
        gain = true 
      end -- test --
    end -- test --
  end -- loopf --
end

structure.SmartShake = SmartShake

structure.SmartShake ( 1 )

--print ( 'Done.' )
end

--END quick save algorithm

function WiggleOld(how, iters, minppi)
	if FILTERMANAGE then filter.DisableAll() end-- new BK 8/4/2013, always disable filter here
    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
        sp=Score()
        if how == "s" then 
				if FILTERMANAGE then return2GlobalOriginalFilterSetting() end -- new BK 8/4/2013, always back to user settings
                if mutateAlwas==true then structure.MutateSidechainsSelected(1) 
                                    --else structure.ShakeSidechainsSelected(1) end
									else QuickShake() end
            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)
        end
        ep = Score()
        ig=ep-sp
        if how~="s" then
            if ig > minppi then return Wiggle(how, iters, minppi) end --tail call
        end
    end
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() end -- new BK 10/10/2013, always back to user settings
end

function Wiggle(how, iters, minppi, valit, mingps) -- NEW one, with filter management, 17/4/2016
	if FILTERMANAGE then filter.DisableAll() end-- new BK 8/4/2013, always disable filter here
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end
	if valit==nil then valit= 1 end
	if mingps==nil then mingps= 80 end -- the goal here is to save time
    local loops = 0  -- only for log, no other use
	
    if iters>0 then
		startRecTime=os.clock ()
        iters=iters-1
		loops=loops+1 -- only for log, no other use
		
        sp=Score()
        if how == "s" then 
				if FILTERMANAGE then return2GlobalOriginalFilterSetting() end -- new BK 8/4/2013, always back to user settings
                if mutateAlwas==true then structure.MutateSidechainsSelected(1) 
                                    --else structure.ShakeSidechainsSelected(1) end
									else QuickShake() end
            elseif how == "wb" then structure.WiggleAll(valit, true,false)
            elseif how == "ws" then structure.WiggleAll(valit, false,true)
            elseif how == "wa" then structure.WiggleAll(valit)
        end
        ep = Score()
        ig=ep-sp
		timeperiteration =os.clock ()-startRecTime
		tppii=ig/timeperiteration
		--print("g/s: "..ig.." / "..timeperiteration.." = "..tppii)
        if how~="s" then
            if ig > minppi
			--and tppii > mingps --Test DEBUG for gaining time, but is this loosing gains ?
			then
			--print("Repeating Wiggle. Gain per second was "..tppii)
			return Wiggle(how, iters, minppi, valit) end --tail call
        end
    end
	
	if loops > 1 then
	print("Wiggled "..loops.." times") -- for DEBUG
	end
	
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() end -- new BK 10/10/2013, always back to user settings
end

wiggle=structure.WiggleAll -- 28/05/2014 No filter management

function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        if g>0.01 then p("Gained another "..round(g).." pts. Score: "..round(Score()).. " from "..round(ss)) end
        bestScore=Score()
        save.Quicksave(3)
    end
end

function SaveRB()
	if Score()>bestScore then
		save.Quicksave(4)
		recentbest.Restore() -- WARNING: it took the best including cuts
		SaveBest()
		save.Quickload(4)
	end
end

function SaveCB() -- cut version 02/06/2014 , recent save no increment
	if Score()>bestScore then
		save.Quicksave(4)
		recentbest.Restore() -- OK only is recentbest saved after deleting cuts
		SaveBest()
		save.Quickload(4)
	end
end

function Qstab()
    selection.SelectAll()
    CI(0.1)
    if mutateOnce==true then
		CI(mutateOnceCI)
        structure.MutateSidechainsSelected(1)
    else
        Wiggle("s",1)
    end
    if fastQstab==false then 
        CI(0.4)
        Wiggle("wa",1)
        CI(1)
        Wiggle("s",1)
    end
    CI(1)
    Wiggle()
end

function FuzeCuts(ci1) -- 28/05/2014 by pauldunn NB: no filter management here . 02/06/2014 recentbest bug fixed
	  local seg=math.random(structure.GetCount())
	  cut(seg)
	  CI(1)
	  wiggle(15,true,true)
	  CI(ci1) --ci(0.01)
	  wiggle(1,true,true)
	  CI(1)
	  wiggle(25,true,true)  
	  uncut(seg)
	  recentbest.Save() -- NEW 02/06/2014 important to avoid recentbest in cut bug
	  wiggle(25,true,true)
	  CI(ci1) --ci(0.01)
	  wiggle(2,true,true)
	  CI(1)
	  wiggle(25,true,true)	  
end
function FuzeEnd()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    srb()
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 srb()
    recentbest.Restore()  -- IMPORTANT: recentbest must be saved after deleting cut
    SaveBest()
end
function scb()
    recentbest.Restore() -- IMPORTANT: recentbest must be saved after deleting cut
    SaveBest()
end

function FuzeWithCuts()
    p("Fuzing with cuts...")
    local scr=Score()
    selection.SelectAll()
    recentbest.Save()
    Fuze1(0.3,0.6) FuzeEnd()
	FuzeCuts(0.01) scb() -- NEW 28/05/2014, 02/06/2014
    Fuze2(0.3,1) srb()
    Fuze1(0.05,1) srb()
    Fuze2(0.7,0.5) FuzeEnd()
	FuzeCuts(0.1) scb() -- NEW 28/05/2014, 02/06/2014
    Fuze1(0.07,1)
    srb()
end

function random(n1,n2) --random function returns int or float depends on input vars
    if n2==nil and n1==nil then
        return math.random() --float
    else
        if n2==nil then
            if n1%1==0 then
                return math.random(n1) --integer
            else
                return math.random()*n1 --float
            end
        else
            if n1%1==0 and n2%1==0 then
                return math.random(n1,n2) --integer between 
            else
                return math.random()*(n2-n1)+n1 --float between
            end
        end
    end
end

function FillHerd() --fill up herd
    local n=#critters
    if n>0 then --fill up
        n=herd.newRandom
    else --fresh herd
        n=herd.breedBest + herd.keepBest + herd.breedBastards 
    end
    p("Randomizing "..n.." new critters...")
    for i=1,n do
        AddCritter()
    end
end
function AddCritter() --create new random critter
    local c={}
    critterID=critterID+1
    c.no=critterID
    c.name=c.no..'-rnd'
    c.bands={}
    local r=random(critter.minBands, critter.maxBands)
    for i=1,r do
        c.bands[#c.bands+1]=AddBand()
    end
    critters[#critters+1]=c
    --p(c.name.." bands: "..#c.bands) -- suppressed from the log, I don't see the use of this
end
function AddBand() --create one random band (random push or pull)
    local cnt=0
    local b={}
    while true do --try till die
        cnt=cnt+1
        local s1=random(segCnt)
		local branch= random(structure.GetSymCount ()+1)-1 -- 0 if monomer, equal probability for each branch
        if onlyMutable==true or #UseSegments>0 then
            s1=UseSegments[random(#UseSegments)]
        end
        local s2=random(segCnt)
        if s1>s2 then s1,s2=s2,s1 end --swap
        if #UseSegments>0 or CanBeUsed(s1,s2) then
            local str=random(bands.minStr,bands.maxStr)
            local len=0
            while true do --randomize correct distance
                len=random(-bands.maxDn,bands.maxUp) -- the goal change from pull to push
                if len<-bands.minChng or len>bands.minChng then break end
            end
            b={s1,s2,str,len, branch}
            break
        end
        
        if cnt>100 then
            p("Sorry! Cant create band! Breaking script!")
            --BreakScript() --there is no such function, so it crashes script
			break
        end
    end
    return b
end

function CanBeUsed(sg1,sg2) --checking end of bands
    function ssCheck(ss)
        local good=false
            if use.Sheet and ss=="E" then good=true end
            if use.Helix and ss=="H" then good=true end
            if use.Loop and ss=="L"  then good=true end
        return good
    end
    function AreGood(s1,s2) --check that s1 and s2 can be used
        local ok=true
        if s2-s1<bands.minSkip then ok=false end
        if ok==true and structure.GetDistance(s1,s2)<bands.minDist then ok=false end
        return ok 
    end
    
    local ok=AreGood(sg1,sg2)
    if ok==true and #DoNotUse>0 then --none of 2 can be in that area
        for i=1, #DoNotUse do
            local r=DoNotUse[i]
            for x=r[1],r[2] do
                if x==sg1 or x==sg2 then
                    ok=false
                    break
                end
            end
            if ok==false then break end
        end
    end
    if ok==false then 
        return false --if false can`t be used
    else
        ok=false
        if #AlwaysUse>0 then --at least one have to be there
            for i=1, #AlwaysUse do
                local r=AlwaysUse[i]
                for x=r[1],r[2] do
                    if x==sg1 or x==sg2 then
                        ok=true
                        break
                    end
                end
                if ok==true then break end
            end
        else
            ok=true
        end
    end 
    
    if ok==true then --check structure
        ok=false
        local ss1=structure.GetSecondaryStructure(sg1)
        local ss2=structure.GetSecondaryStructure(sg2)
        if checkBoth then
            if ssCheck(ss1) and ssCheck(ss2) then ok=true end
        else
            if ssCheck(ss1) or ssCheck(ss2) then ok=true end
        end
    end
    return ok
end
function deletebands() --leave user bands intact
    nbands=band.GetCount()
    if nbands>userbands then
        for i=nbands,userbands+1,-1 do -- count down from nbands to userbands+1
            band.Delete(i)
        end -- for i
    end -- if nbands
end -- function
function ScoreHerd() --makes the bands and score all critters from herd
    save.Quickload(3)
    p("Scoring "..#critters.." critters...")
    save.Quicksave(5)
    local herdScore=Score()
    for i=1,#critters do
        deletebands()
        local crt=critters[i] --critter
        local s=Score() --start score
        local bnds=crt.bands -- b={s1,s2,str,len, branch} (len is the random push or pull difference of length)
        for b=1,#bnds do
            local bnd=bnds[b]
			if bnd[1] ~= bnd[2] then -- new debugging, no band to itself
				local a1=5
				local a2=5
				if bnd[1]== structure.GetCount() then a1=6 end
				if bnd[2]== structure.GetCount() then a2=6 end  -- changed a1 to a2 13/5/2015
				if structure.GetAminoAcid(bnd[1])=='g' then a1=0 end
				if structure.GetAminoAcid(bnd[2])=='g' then a2=0 end
				if not structure.IsHydrophobic(bnd[1]) and bnd[4]<0 then a1=0 end -- only hiding hydrophobics
				if not structure.IsHydrophobic(bnd[2]) and bnd[4]<0 then a2=0 end
				if structure.IsHydrophobic(bnd[1]) and bnd[4]>0 then a1=0 end -- don't push hydropobics to water
				if structure.IsHydrophobic(bnd[2]) and bnd[4]>0 then a2=0 end				
				
				band.AddBetweenSegments(bnd[1],bnd[2],a1,a2, bnd[5]) -- 5 is the branch for symmetrics
				local bc=band.GetCount()
				band.SetStrength(bc,bnd[3])
				local len=structure.GetDistance(bnd[1],bnd[2])+bnd[4] -- distance between segments + band length change (+ or -)
				if len<bands.minLen then len=bands.minLen end
				band.SetGoalLength(bc,len)
				--print("Band: "..bnd[1].."-"..bnd[2].." a1: "..a1.." a2: "..a2.." str: "..round3(bnd[3]).." length= "..round3(length))
			end
        end
        selection.SelectAll()
        CI(pullCI)
        recentbest.Save()
		local seg=math.random(structure.GetCount()) -- new 28/05/2014
		cut(seg) -- new 28/05/2014
        Wiggle("wb",1)
		uncut(seg)-- new 28/05/2014 PROBLEM here, recentbest includes cuts
		recentbest.Save() -- NEW 02/06/2014 to avoid recent best in cuts
		
        deletebands()
        CI(1)
        if math.abs(s-Score()) > qstabThresh then
            Qstab()
        else
            Wiggle()
        end
        if Score()-bestScore>fuzeThresh then 
            SaveRB()
            FuzeWithCuts() -- new 02/06/2014
        else
            SaveRB()
        end
        
        crt.score=Score()-s
        -- p("Critter "..crt.name.." : "..round(crt.score)) -- eliminated ! I don't see the use of publishing this !
        
        if critter.maxLoss>0 then
            if Score()>herdScore-critter.maxLoss then
                save.Quicksave(5)
                herdScore=Score()
            else
                save.Quickload(5)
            end
        else
            save.Quickload(3)
        end
    end
    save.Quickload(3)
    if band.GetCount()>0 then --clean bands from best solution (if any)
        deletebands()
        save.Quicksave(3)
    end
end
function BreedCritters(mom,dad,t) --breed 2 critters. bands are taken randomly
    local kid={}
    critterID=critterID+1
    kid.no=critterID
    kid.name=kid.no.."-"..t..mom.no..'/'..dad.no
    kid.bands={}
    local mb=#mom.bands
    local db=#dad.bands
    if mb>db then mb,db=db,mb end --kid have bands count between mom and dad bands
    local bn=random(mb,db)
    for i=1,bn,2 do
        kid.bands[#kid.bands+1]=mom.bands[random(#mom.bands)]
        kid.bands[#kid.bands+1]=dad.bands[random(#dad.bands)]
    end
    --p(kid.name.." bands: "..#kid.bands) -- suppressed, I don't see the use of this info
    return kid
end
function KeepGood() --copy best scoring critters form last gen if score above
    local newHerd={}
    for i=1,herd.keepBest do
        if critters[i].score>critter.keepScore and (math.abs(critters[i].score)>0.1 or critters[i].score>0) then
            newHerd[#newHerd+1]=critters[i]
        end
    end
    return newHerd
end
function SortCritters() --bubble sort
    for i=1,#critters do
        for j=i+1,#critters do
            if critters[i].score<critters[j].score then
                critters[i],critters[j]=critters[j],critters[i] --love lua :)
            end
        end
    end
end
function BreedHerd()
    p("Breeding...")
    SortCritters()
    newHerd=KeepGood()
    for i=1, herd.breedBest do
        local mom=critters[i]
        if mom.score>critter.breedScore or i<2 then --breed only good ones, 1st is always breed anyway
            for j=i+1, herd.breedBest do
                local dad=critters[j]
                newHerd[#newHerd+1]=BreedCritters(mom,dad,"kid-")
                newHerd[#newHerd+1]=BreedCritters(dad,mom,"kid-")
            end
        end
    end
    for i=1, herd.breedBastards do --they will always appear ;]
        local mom=critters[i]
        local j=random(herd.breedBastards+1,#critters)
        local dad=critters[j]
        newHerd[#newHerd+1]=BreedCritters(mom,dad,"bas-")
        newHerd[#newHerd+1]=BreedCritters(dad,mom,"bas-")
    end
    critters=newHerd
    FillHerd()
end
function ShuffleHerd()
    if herd.shuffle==true then 
        for i=1,#critters do
            local r=random(#critters)
            if r~=i then
                critters[i],critters[r]=critters[r],critters[i]
            end
        end
    end
end
function GAB()
    if onlyMutable==true then
        for i=1,segCnt do
			if structure.IsMutable(i) then
				UseSegments[#UseSegments+1]=i
			end
		end
    end
	if #AlwaysUse>0 then
		for i=1,#AlwaysUse do
			local ss=AlwaysUse[i][1]
			local se=AlwaysUse[i][2]
			if ss>se then ss,se=se,ss end
			for j=ss,se do
				UseSegments[#UseSegments+1]=j
			end
		end
		AlwaysUse={} --added to list, no need to check later
	end
    bestScore=Score()
    critterID=0
    gen=0
    ss=Score()
	ssstr=(round(ss))
    save.Quicksave(3)
    recentbest.Save()
    p("Starting "..recipename.." score: "..round(ss))
    critters={}
    FillHerd()
    badGen=0
    while true do --this is (almost) endless script ;]
		undo.SetUndo(false) -- reset if gain before end of loop
        genScore=Score()
        gen=gen+1
        p()
		p("Generation: "..gen..", score: "..round(Score())..", gain: "..round(Score()-ss).." ("..(os.date())..")")
        ShuffleHerd()
        ScoreHerd()
        save.Quickload(3)
        if gen==herd.maxGen then break end --end of script
        
        if genScore<=Score() then badGen=badGen+1 else badGen=0 end
        if badGen<=herd.renew then -- bug fixed thanks to robgee
            p("Creating fresh random herd...")
            critters={}
            FillHerd()
            badGen=0
        else
            BreedHerd()
        end
        genEndScore=Score()
        genGain=genEndScore-genScore
        if gen>1 and (gen-1)==5*down((gen-1)/5) then -- New 18/1/2016 jeff101 log display
            ssstr=(ssstr..'\n  ') -- start new line every 5 generations
        end
        if genGain>=0 then
            ssstr=(ssstr..' + '..round(genGain))
			undo.SetUndo(true)
        else
            ssstr=(ssstr..' - '..(-round(genGain)))
        end
        p(ssstr..' = '..round(genEndScore))
		WhriteNote(gen)  -- New 4/11/2014
		SaveBigSteps() -- New 4/11/2014 for movie at the end
    end
    p("Final score: "..round(Score()).." Total gain: "..round(Score()-ss))
end

--START Movie store big steps
	StepScore= Score() -- New 4/11/2014
function StoreBigStep()
	StepScore= Score()
	save.Quicksave(SlotStep)
	SlotStep=SlotStep+1
end	

function SaveBigSteps() -- in order to be able to display big steps afterwards in undos
	local g=Score()-StepScore
	local s= Score()
	if s >0 and ( (s <7000 and g>500) or (s <9000 and g>200) or (s <10000 and g>100) or (s >10000 and g>50)) then
		StoreBigStep()
	end
end

function MovieSteps()
	undo.SetUndo(true)
	for i= SlotStepStart, SlotStep do
		save.Quickload(SlotStep)
	end
	--save.Quickload(3)
	print("See remembering of big steps in undos")
end

--END Movie store big steps

function Cleanup(err) -- NEW BK 10/10/2013
    print("Restoring CI, best result, filter and structures")
    CI(1)
	undo.SetUndo(true)
	if FILTERMANAGE then return2GlobalOriginalFilterSetting() end -- new BK 8/4/2013, always back to user settings
    MovieSteps() -- New 4/11/2014
	save.Quickload(3)
	MovieSteps()
	WhriteNote(gen)  -- New 4/11/2014
	deletebands()
    print(err)
end

-- main call
--GAB()

xpcall(GAB,Cleanup) -- NEW BK 10/10/2013

--end of script

Comments

[Bruno Kestemont]

When there is a ligand (molecule), it now always uses the ligand (optional editing the recipe)

[Bruno Kestemont]

3.4.7: 13/5/2015 changed small possible bugs
18/1/2016 log with archive of gains following jeff101 suggestions
reduced thresholds on Big Steps
Keeps user bands
Mutate once 5 days before the deadline or the 3 latest days for HBond puzzles
GENERICFILTER only latest days of non HBonds puzzles
FILTERMANAGE only on mid game

[Bruno Kestemont]

Hide only hydrophobics
Default not always use ligand

[Bruno Kestemont]

Optimized undo chart in order to save time and memory on old computers

[Bruno Kestemont]

Now that this recipe matured enough within my group, I suppose it's time to share it to public. Enjoy !

[Bruno Kestemont]

Translated discarded filter commands (grr !)

[Bruno Kestemont]

Simplified the log and the wiggle part.

[Bruno Kestemont]

Band to symmetrics as well

[Bruno Kestemont]

A rare bug fixed

[Bruno Kestemont]

if badGen<=herd.renew then – bug fixed thanks to robgee