Recipe: TEST JF + Walk MarathoN + MULTILOCKONES

created by Vincera

Profile

• Name: TEST JF + Walk MarathoN + MULTILOCKONES
• ID: 104985
• Shared with: Public
• Parent: TEST JF Rav3n_pl WalkeR MarathoN
• Children: None
• Created on: July 07, 2021 at 00:08 AM UTC
• Updated on: December 30, 2024 at 19:54 PM UTC
• Description:

  JOSH'S FUZE + WALKER MARATHON + MULTI WALK LOCKED ONES

Code

--[[
WalkeR v1.0
a randomatic LWS script
set from-to
set min-max len of lws
ser minimum points per iter
optiona at end
]]--


--[[
Tlaloc`s math library
------------------------------------------------------------------------
The original random script this was ported from has the following notices:
Copyright (c) 2007 Richard L. Mueller
Hilltop Lab web site - http://www.rlmueller.net
Version 1.0 - January 2, 2007
You have a royalty-free right to use, modify, reproduce, and
distribute this script file in any way you find useful, provided that
you agree that the copyright owner above has no warranty, obligations,
or liability for such use.
------------------------------------------------------------------------
]]--

-- Updated to Script V2 and given some repeat options (StackOverflow)

local lngX = 1000
local lngC = 48313

local function _MWC()
    local S_Hi
    local S_Lo
    local C_Hi
    local C_Lo
    local F1
    local F2
    local F3
    local T1
    local T2
    local T3

    local A_Hi = 63551
    local A_Lo = 25354
    local M = 4294967296

    local H = 65536

    local S_Hi = math.floor(lngX / H)
    local S_Lo = lngX - (S_Hi * H)
    local C_Hi = math.floor(lngC / H)
    local C_Lo = lngC - (C_Hi * H)

    local F1 = A_Hi * S_Hi
    local F2 = (A_Hi * S_Lo) + (A_Lo * S_Hi) + C_Hi
    local F3 = (A_Lo * S_Lo) + C_Lo

    local T1 = math.floor(F2 / H)
    local T2 = F2 - (T1 * H)
    lngX = (T2 * H) + F3
    local T3 = math.floor(lngX / M)
    lngX = lngX - (T3 * M)

    lngC = math.floor((F2 / H) + F1)

    return lngX
end
local function _abs(value)
    if value < 0 then
        value = -value
    end
    return value
end
local function _floor(value)
    return value - (value % 1)
end
local function _randomseed(x)
    lngX = x
end
local function _random(m,n)
    if n == nil and m ~= nil then
        n = m
        m = 1
    end
    if (m == nil) and (n == nil) then
        return _MWC() / 4294967296
    else
        if n < m then
            return nil
        end
        return math.floor((_MWC() / 4294967296) * (n - m + 1)) + m
    end
end
math=
{
    abs = _abs,
    floor = _floor,
    random = _random,
    randomseed = _randomseed,
}
--[[ End math library ]]--

function Score()
    return current.GetScore ()
end 
function seed()
    local s=math.abs(Score())
    s=s%0.001
    s=1/s
    while s<10000000 do s=s*10 end 
    s=s-s%1
    math.randomseed(s) 
end
seed()

segCnt=structure.GetCount ()
p=print

function round(x)--cut all afer 3-rd place
    return x-x%0.001
end
function down(x)
    return x-x%1
end

function ShuffeleTable()
    p("Mixing LWS table...")
    local tl=#lwsTable
    for i=1,tl do
        local n=math.random(tl)
        lwsTable[i],lwsTable[n]=lwsTable[n],lwsTable[i]
    end
    --p("Mixing done.") --save some screen space, redundant message (Stack)
end

lwsTable={}
function CreateTable()
    p("Preparing LWS table...")
    lwsTable={}
    if segEnd==nil then segEnd=segCnt end
    
    for sn=segStart,segEnd do
        for l=minLen, maxLen do
            if (sn+l-1)<=segEnd then
                lwsTable[#lwsTable+1]={sn,l}
            end
        end
    end
    p("We have LWS ",#lwsTable," starts to do.")
end
function lws()
    repeat
        local s=Score()
        structure.LocalWiggleSelected(2)
        local g=Score()-s
        if g<0 then recentbest.Restore() end
    until g<minPpi
end
function WalkeR()
    recentbest.Save ()
    save.Quicksave(3)
    local ss=Score()
    p("Starting WalkeR, Score=",round(ss))
    local tl=#lwsTable
    for i=1, tl do
        local sc=Score()
        local s=lwsTable[i][1]
        local l=lwsTable[i][2]
        selection.DeselectAll ()
        selection.SelectRange(s,s+l-1)
        lws()
        save.Quicksave(3)
        print("Iter " ..i .. "/" .. tl .. " (" .. s .. ":" .. l .. ") g: " .. round(Score()-sc) .. " score: " .. round(Score()) .. plus() )
    end
    p("Total gain: ",round(Score()-ss))
end

segStart=1 --start from
segEnd=nil --end seg: nil=end of protein
minLen=1 --minimum lws len
maxLen=7 --maximum lws len
minPpi=0.01 --minimum points gain per 2 wiggles, set 0.0001 in endgame :)

function go ()
    CreateTable()
    ShuffeleTable()
    WalkeR()
end

function main () -- main added by StackOverflow
    startScore = current.GetScore ()
    local mf = dialog.CreateDialog ( "Rav3n Marathon WalkeR" )
    mf.chk1 = dialog.AddCheckbox ( "Run specified number of times" , true )
    mf.sldr = dialog.AddSlider ( "Times" , 3 , 1 , 10 , 0 )
    mf.chk2 = dialog.AddCheckbox ( "Run until no more gains are achieved" , false )
    mf.chk3 = dialog.AddCheckbox ( "Run forever" , false )
    mf.btnGo = dialog.AddButton ( "Start" , 1 )
    mf.btnExit = dialog.AddButton ( "Exit" , 0 )
    local cmd = dialog.Show ( mf )
    if ( cmd == 1 ) then
        if (  mf.chk3.value == true ) then
            local iter1 = 1
            while ( true ) do
                print ( "Run " .. iter1 .. " (will run forever!)" )
                go ()
                iter1 = iter1 + 1
                print ( newscore () )
            end
        elseif ( mf.chk2.value == true ) then
            local ssc = current.GetScore () - 1
            local iter2 = 1
            while ( flr ( current.GetScore () , 3 ) > flr ( ssc , 3 ) ) do
                print ( "Run " .. iter2 .. " (will run until no gains are achieved)" )
                ssc = current.GetScore ()
                go ()
                iter2 = iter2 + 1
                print ( newscore () )
            end
        elseif ( mf.chk1.value == true ) then
            for r = 1 , mf.sldr.value do
                print ( "Run " .. r .. " of " .. mf.sldr.value )
                go ()
                print ( newscore () )
            end
        else
            print ( "no valid repeat options specified, running once only" )
            go ()
        end
    else
        print ( "user cancelled" )
    end
end
function newscore ()
    return "New Score: " .. flr ( current.GetScore() , 3 ) .. plus ()
end
function plus ()
    return " (+" .. flr((current.GetScore() - startScore),3) .. ")"
end
function flr(num, idp)
  local mult = 10^(idp or 0)
  return math.floor(num * mult) / mult
end

main ()
--

--  Josh's Fuse - 6 Nov 2020 - see notes at end

--

print ( "Josh's Fuse" )

startScore = current.GetEnergyScore ()      -- Get the current energy score. 

print ( "starting score = " .. startScore ) -- print the starting score



recentbest.Save ()                          -- Save the current pose as the recent best pose.




behavior.SetPackingImportance(0.17)

seventeen = behavior.GetPackingImportance()

behavior.SetPackingImportance(0.18)

eighteen = behavior.GetPackingImportance()

modding = true

if (seventeen == eighteen) then
  modding = false
end

local ask = dialog.CreateDialog("Josh's Fuse")

ask.Clashing = dialog.AddCheckbox("Clashing", true)

ask.SidechainHBonds = dialog.AddCheckbox("Sidechain HBonds", true)

ask.BackboneHBonds = dialog.AddCheckbox("Backbone HBonds", true)

ask.Packing = dialog.AddCheckbox("Packing", true)

ask.Hiding = dialog.AddCheckbox("Hiding", true)
ask.Pairwise = dialog.AddCheckbox("Pairwise", true)

if (modding == false) then
ask.Warning = dialog.AddLabel("WARNING: Recipe Modding is currently OFF\nPlease turn it on before running this recipe.")
end
ask.OK = dialog.AddButton("OK", 1)

ask.Cancel = dialog.AddButton("Cancel", 0)



function resetBehavior()

    behavior.SetClashImportance ( 1.0 )

    behavior.SetSidechainHBondImportance ( 1.0 )

    behavior.SetBackboneHBondImportance ( 1.0 )

    behavior.SetPackingImportance ( 1.0 )

behavior.SetHidingImportance ( 1.0 )
    behavior.SetPairwiseImportance ( 1.0 ) 



end




resetBehavior()

if (dialog.Show(ask) > 0) then



    if (ask.Clashing.value) then

        behavior.SetClashImportance ( 0.05 )        -- Set the clashing importance.

    end

    if (ask.SidechainHBonds.value) then

        behavior.SetSidechainHBondImportance ( 3.0 )        -- Set the schbonds importance.

    end

    if (ask.BackboneHBonds.value) then

        behavior.SetBackboneHBondImportance ( 3.0 )        -- Set the bbhbonds importance.

    end

    if (ask.Packing.value) then

        behavior.SetPackingImportance ( 3.0 )        -- Set the packing importance.

    end

if (ask.Hiding.value) then

        behavior.SetHidingImportance ( 3.0 )        -- Set the hiding importance.

    end
    if (ask.Pairwise.value) then

        behavior.SetPairwiseImportance ( 3.0 )        -- Set the pairwise importance.

    end

    structure.ShakeSidechainsAll ( 1 )          -- Shake all sidechains. 

    resetBehavior()

    structure.WiggleAll ( 8 )                   -- Global wiggle all segments.

    print ( "after first shake/wiggle, score = " .. current.GetEnergyScore () ) 



    if (ask.Clashing.value) then

        behavior.SetClashImportance ( 0.07 )        -- Set the clashing importance.

    end

    if (ask.SidechainHBonds.value) then

        behavior.SetSidechainHBondImportance ( 2.0 )        -- Set the schbonds importance.

    end

    if (ask.BackboneHBonds.value) then

        behavior.SetBackboneHBondImportance ( 2.0 )        -- Set the bbhbonds importance.

    end

    if (ask.Packing.value) then

        behavior.SetPackingImportance ( 2.0 )        -- Set the packing importance.

    end

    if (ask.Hiding.value) then

        behavior.SetHidingImportance ( 2.0 )        -- Set the hiding importance.

    end
    if (ask.Pairwise.value) then

        behavior.SetPairwiseImportance ( 2.0 )        -- Set the pairwise importance.

    end

    structure.ShakeSidechainsAll ( 1 )          -- Shake all sidechains. 

    

    resetBehavior()

    

    structure.WiggleAll ( 8 )                   -- Global wiggle all segments.

    print ( "after second shake/wiggle, score = " .. current.GetEnergyScore () ) 



    recentbest.Restore ()                       -- Load the recent best pose.

    print ( "after restoring recent best, score = " .. current.GetEnergyScore () ) 



    if (ask.Clashing.value) then

        behavior.SetClashImportance ( 0.3 )        -- Set the clashing importance.

    end

    if (ask.SidechainHBonds.value) then

        behavior.SetSidechainHBondImportance ( 1.5 )        -- Set the schbonds importance.

    end

    if (ask.BackboneHBonds.value) then

        behavior.SetBackboneHBondImportance ( 1.5 )        -- Set the bbhbonds importance.

    end

    if (ask.Packing.value) then

        behavior.SetPackingImportance ( 1.5 )        -- Set the packing importance.

    end

if (ask.Hiding.value) then

        behavior.SetHidingImportance ( 1.5 )        -- Set the hiding importance.

    end
    if (ask.Pairwise.value) then

        behavior.SetPairwiseImportance ( 1.5 )        -- Set the pairwise importance.

    end

    structure.WiggleAll ( 1 )                   -- Global wiggle all segments.

    

    resetBehavior()

    

    if (ask.Clashing.value) then

        behavior.SetClashImportance ( 0.5 )        -- Set the clashing importance.

    end

    if (ask.SidechainHBonds.value) then

        behavior.SetSidechainHBondImportance ( 0.3 )        -- Set the schbonds importance.

    end

    if (ask.BackboneHBonds.value) then

        behavior.SetBackboneHBondImportance ( 0.3 )        -- Set the bbhbonds importance.

    end

    if (ask.Packing.value) then

        behavior.SetPackingImportance ( 0.3 )        -- Set the packing importance.

    end

if (ask.Hiding.value) then

        behavior.SetHidingImportance ( 0.3 )        -- Set the hiding importance.

    end
    if (ask.Pairwise.value) then

        behavior.SetPairwiseImportance ( 0.3 )        -- Set the pairwise importance.

    end

    structure.WiggleAll ( 3 )                   -- Global wiggle all segments.

    

    resetBehavior()

    

    print ( "after third wiggle, score = " .. current.GetEnergyScore () ) 



    recentbest.Restore ()                -- Load the recent best pose.

    

    structure.WiggleAll ( 8 )                   -- Global wiggle all segments.

    print ( "after final wiggle, score = " .. current.GetEnergyScore () ) 



    recentbest.Restore ()                -- Load the recent best pose.



    finalScore = current.GetEnergyScore ()      -- Get the current energy score.

    print ( "final score = " .. finalScore )    -- print the final score

    gain = finalScore - startScore              -- calculate the gain

    print ( "gain = " .. gain )                 -- print the gain

end

print ( "Josh's Fuse complete" )





--

--  original: Blue Fuse v1.1 by Vertex 3 January 2010 - https://fold.it/portal/recipe/2052

--

--  BlueFuse 2020a - LociOiling - 21 March 2020

--  + converted to Foldit Lua interface V1 to V2

--  + added printing scores and gain

--  + dropped "select_all", not needed with ShakeSidechainsAll and WiggleAll

--

--  Some potential improvements:

--

--  TODO: round the score to three decimals

--  TODO: repeat the process if there's a gain

--  TODO: try different values for clashing importance

--  TODO: try a different number of iterations for wiggle

--  TODO: turn off filters during shake and wiggle for better performance

--  TODO: add a dialog to control settings

--




--
--  original: Blue Fuse v1.1 by Vertex 3 January 2010 - https://fold.it/portal/recipe/2052
--
--  BlueFuse 2020a - LociOiling - 21 March 2020
--  + converted to Foldit Lua interface V1 to V2
--  + added printing scores and gain
--  + dropped "select_all", not needed with ShakeSidechainsAll and WiggleAll
--
-- -- ZeroLeak7 Multiwalker for locked ones v0.9
-- converted scripts to Lua "V2"

-- Precise LWS 2.0.1, Total LWS 1.0.4, Blue Fuze v1.1

-- Globals



loop_starts = {}
loop_ends  = {}

n_loops = 0

n_residues = 0


function Lockedresidues ()

    selection.SelectAll()

    structure.SetSecondaryStructureSelected("H")

    

    for i=1, structure.GetCount() do



        if structure.GetAminoAcid(i) == "unk" then

        structure.SetSecondaryStructure(i, "H")

        end



        if structure.IsLocked(i) == false then

        

        structure.SetSecondaryStructure(i, "L")

        

    end

    end

end

function GetLoops ()

    within_loop = false
  
    for i = 1, n_residues do

        if ( structure.GetSecondaryStructure ( i ) == "L" and structure.IsLocked(i) == false ) then
    
           if ( within_loop == false ) then

                -- start of a new loop

                within_loop = true

                n_loops = n_loops + 1
                loop_starts [ n_loops ] = i

           end
        elseif ( within_loop == true ) then

            -- end of a loop
           
            within_loop = false
            loop_ends [ n_loops ] = i -1
        end
    end    -- for i
  
    if ( within_loop == true ) then
      loop_ends [ n_loops ] = n_residues
    end

end

-- ================ Precise LWS v2.0.1 ================



--Precise LWS by rav3n_pl

--searches and wiggles worst segments

--options at end of script






function score() --score of puzzle

    return current.GetScore()

end



function getPartScore(segments)--using partial scoring

    local attr = {'packing','backbone','other','bonding','sidechain','clashing'}--,'hiding','reference','disulfides'}

    local score = 0

    for i=1,#attr do

        score =  score + current.GetSegmentEnergySubscore(segments, attr[i])

    end

    return score

end





function getworst() --fill score table

    worst={}

for f=1, #loop_starts do
    for i=loop_starts [ f ], loop_ends [ f ] do
        sc=getPartScore(i)

        worst[i]=sc
    end

end
    return worst

end


function wig(mingain)    --score conditioned wiggle,

    repeat                    --wiggles selected segments

        ss=score()

        structure.LocalWiggleSelected(2)

        se=score()

        wg=se-ss

        if wg<0 then

            recentbest.Restore()

        end

    until wg<mingain 

    selection.DeselectAll()

    freeze.UnfreezeAll()

end



function wiggle2(s, mingain, buddies)

    print("Wigglin segment "..s)

    selection.DeselectAll()

    freeze.UnfreezeAll()

    sgs=score()

    maxi=structure.GetCount()

    if s+1<=maxi then selection.Select(s+1)end

    if s-1>=1 then selection.Select(s-1)end 

    freeze.FreezeSelected(true, true)

    selection.DeselectAll()

    selection.Select(s)

    wig(mingain)

    

    if buddies > 0 then --select buddies

        for b=1, buddies do

        

            if s+b+1<=maxi then selection.Select(s+b+1)end

            if s-1>=1 then selection.Select(s-1)end 

            freeze.FreezeSelected(true, true)

            selection.DeselectAll()

            if s+b>maxi then selection.SelectRange(s,maxi)

            else selection.SelectRange(s,s+b)end

            wig(mingain)



            if s+1<=maxi then selection.Select(s+1)end

            if s-b-1>=1 then selection.Select(s-b-1)end 

            freeze.FreezeSelected(true, true)

            selection.DeselectAll()

            if s-b<1 then selection.SelectRange(1,s)

            else selection.SelectRange(s-b,s)end

            wig(mingain)



            if s+b+1<=maxi then selection.Select(s+b+1)end

            if s-b-1>=1 then selection.Select(s-b-1)end 

            freeze.FreezeSelected(true, true)

            selection.DeselectAll()

            if s+b>maxi then selection.SelectRange(s,maxi)

            else selection.SelectRange(s,s+b)end

            if s-b<1 then selection.SelectRange(1,s)

            else selection.SelectRange(s-b,s)end

            wig(mingain)

        end

    end

    sge=score()

    print("Segment gain: "..sge-sgs)

end

function wiggleworst(howmany, mingain, buddies)

    behavior.SetClashImportance(1)

    freeze.UnfreezeAll()

    selection.DeselectAll()

recentbest.Save()
    sscore=score()

    worst=getworst()

for f=1, #loop_starts do
for i=loop_starts [ f ],loop_ends [ f ] do
print(i.." "..worst[ i ])
end
end
 for i=1, howmany do

    print(((howmany*#loop_starts)+#loop_starts)-i*#loop_starts.." segments left to do.")

for a=1, #loop_starts do
        min=loop_starts [ a ]

        seg=1

        for f=loop_starts [ a ],loop_ends [ a ] do

            if min>worst[f] then 

                min=worst[f]

                seg=f

            end

        end

        wiggle2(seg, mingain, buddies)

        worst[seg]=9999--never again same one

    end

end
    escore=score()

    print("Total gain: "..escore-sscore.." pts")

    


end


-- ================ Total LWS 1.0.4 ================






local function score1() --score of puzzle

    return current.GetScore()

end



function AllLoop()

        selection.SelectAll()

        structure.SetSecondaryStructureSelected("L")

end



function freeze1(start, len)

        freeze.UnfreezeAll()

        selection.DeselectAll()

        for i = 1, n_loops do

        for f=loop_starts [ i ] -1 + start, loop_ends [ i ], len+1 do

                if f<= loop_ends [ i ] then selection.Select(f) end

        end

        freeze.FreezeSelected(true, false)

        end
end


function lw(minppi)

        local gain=true

        while gain do

                local ss=score1()

                structure.LocalWiggleSelected(2)

                local g=score()-ss

                if g<minppi then gain=false end

                if g<0 then recentbest.Restore() end

        end

end



function wiggle3(start, len,minppi)

        for i = 1, n_loops do
                if loop_starts [ i ] -1 + start > loop_starts [ i ] then

                selection.DeselectAll()

                selection.SelectRange(loop_starts [ i ],loop_starts [ i ] - 1 + start - 1)

                lw(minppi)
                
        end
        for f=loop_starts [ i ] -1 + start, loop_ends [ i ], len+1 do

                selection.DeselectAll()

                local ss = f+1

                local es=f+len

                if ss >= loop_ends [ i ] then ss=loop_ends [ i ] end

                if es >= loop_ends [ i ] then es=loop_ends [ i ] end

                selection.SelectRange(ss,es)

                lw(minppi)
        end

        end
end



function totalLws(minlen,maxlen, minppi)

        freeze.UnfreezeAll()

        selection.DeselectAll()

        behavior.SetClashImportance(1)

        local ssc=score1()

        print("Starting Total LWS: "..ssc)

        print("Lenght: "..minlen.." to "..maxlen.." ;minimum ppi: "..minppi)

        for l=minlen, maxlen do

                for s=1, l+1 do

                        print("Len: "..l.." start point: "..s)

                        local sp=score1()

                        freeze1(s,l)

                        recentbest.Save()

                        wiggle3(s,l,minppi)
                        print("Gained: "..score1()-sp)

                        save.Quicksave(3)

                end

        end

        print("Finished! Total gain: "..score1()-ssc)

        freeze.UnfreezeAll()

end






-- ================ Blue Fuze v1.1 ================


function BlueFuze ()
print("=============== Blue Fuze v1.1 ===============")





freeze.UnfreezeAll()
selection.DeselectAll()
behavior.SetClashImportance(1)
recentbest.Save()
for i= 1 , #loop_starts do
selection.SelectRange(loop_starts[ i ],loop_ends[ i ])
end
behavior.SetClashImportance(.05)

structure.ShakeSidechainsSelected(1)

behavior.SetClashImportance(1)

structure.WiggleSelected(8)

behavior.SetClashImportance(.07)

structure.ShakeSidechainsSelected(1)

behavior.SetClashImportance(1)

structure.WiggleSelected(8)

recentbest.Restore()

behavior.SetClashImportance(.3)

structure.WiggleSelected(1)

behavior.SetClashImportance(1)

structure.WiggleSelected(8)

recentbest.Restore()
score2=current.GetScore()

print("Blue Fuze score: "..score2-score2%0.001)
end



function main ()

    print (  "ZeroLeak7 Multiwalker for locked ones v0.9" )

    band.DisableAll ()
    save.SaveSecondaryStructure()

    n_residues = structure.GetCount ()

    behavior.SetClashImportance ( 1 )

    Lockedresidues ()


    GetLoops ()

    n_loops = #loop_starts

    print ( n_loops .. " loops" )

   

    n_loops = #loop_starts


    for i = 1 , n_loops  do 
         print ( "Loop " .. i .. " : (" .. loop_starts [ i ] .. "-" .. loop_ends [ i ] .. ")" )
    end
    AllLoop()

while (true) do
--wiggleworst(howmany, mingain, buddies)
--howmany = 3      -how many worst segments to process mutiplied by loop count example(if you have 2 loops (howmany = 3) * 2 loops = 6

--mingain = 0.3 -minimum gain per wiggle iterations (if more per 2 wiggle wiggles again)

--buddies = 3   -how many segments aside should be wiggled too

                              --ie worst segment is no 44 and buddies set to 1 then

                              -- willging seg 44 then 43+44; later seg 44+45 and finally 43+44+45

print("=============== Precise LWS v2.0.1 ===============")
wiggleworst(3,0.3,3)


--totalLws(minlen, maxlen, minppi)

--minlen - minimum lenggh of sgmnts - if you have done lws by 1 and 2 you may want set it to 3

--maxlen - maximum lenght of sgments - more than 7 looks useless

--minppi - minimum gain per local wiggle iter

print("=============== Total LWS 1.0.4 ===============")
totalLws(1,7,0.001)
 

BlueFuze ()
        
        
end
end


function cleanup ()
   
    print ( "Cleaning up" )
    behavior.SetClashImportance ( 1.0 )
    band.EnableAll ()
    freeze.UnfreezeAll()
    save.LoadSecondaryStructure()

end
xpcall(main , cleanup)