Recipe: Fast Relax 1.0

created by LociOiling

Profile

• Name: Fast Relax 1.0
• ID: 107977
• Shared with: Public
• Parent: None
• Children:
  • Fast Relax 2.0
• Created on: September 18, 2022 at 01:16 AM UTC
• Updated on: September 18, 2022 at 01:16 AM UTC
• Description:

  V2 port of the classic shared by Frankie_says in 2011

  https://old.fold.it/portal/recipe/34893

Code

--[[ 
        FastRelax

        Based on a recipe used in Rosetta,
        as described in a Foldit publication in PNAS:

            Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon,
            Zoran Popovic, David Baker and Foldit Players. 

            Algorithm discovery by protein folding game players. 

            Proceedings of the National Academy of Sciences of the United States of America (2011)

            http://www.pnas.org/content/108/47/18949.abstract

        Converted from v1 Lua by Rav3n_pl's v1 to v2 converter, FolditLuaConverter.
    
        Fast Relax 1.0 - LociOiling -- 2022/09/17
        + converted using FolditLuaConverter
        + fixed #NEED EDIT! lines (only two in this case)
        + minimal testing
]]--


-- options at end

p=print
CI=behavior.SetClashImportance
S=structure.ShakeSidechainsSelected
WA=structure.WiggleAll

function Score()
    if energy==true then
        return current.GetEnergyScore() -- #NEED EDIT! remove(true) if you have it#()
    else
        return current.GetScore()       -- #NEED EDIT! remove(true) if you have it#()
    end
end
function round(x)--cut all afer 3-rd place
    return x-x%0.001
end

function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        bestScore=Score()
        save.Quicksave(3)
    else
        save.Quickload(3)
    end
end

function FastRelax()
    bestScore=Score()    
    save.Quicksave(3)
    p("Starting FastRelax, Score: ",round(bestScore))
    selection.SelectAll()
    recentbest.Save()
    repeat
        local ss=Score()
        CI(0.02)
        S(shakes)
        WA(wiggles)
        CI(0.25)
        S(shakes)
        WA(wiggles)
        CI(0.55)
        S(shakes)
        WA(wiggles)
        CI(1)
        S(shakes)
        WA(wiggles)
        recentbest.Restore()
        SaveBest()
        local g=Score()-ss
        p("Loop gain: ",round(g))
    until g<minPpi
    p("End score: ",round(Score()))
end

-- options below VVVV

energy=false --set true to seek energy in exploration puzzles
minPpi=2 --minimum points gain per loop
shakes=2 --number of shakes
wiggles=5 --number of wiggles

-- main call
FastRelax()

--end of script

Comments

[Artoria2e5]

On the rosetta side they've change the script up a bit, at https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/relax#description-of-algorithm. Changes are:

• CI order.
• Now they have a new coord_cst_weight, which seems to be some sort of band-in-space to discourage super huge movements.

The documentation also mentions a whole family of relax scripts. The different CI schedule can be found in PMC8299543 supplementary info table SI1, https://europepmc.org/articles/PMC8299543/bin/NIHMS1650092-supplement-supinfo.pdf. PMC8299543 / PMID 33249652 can be treated as the primary citation for this new family of relax functions with different shake and wiggle CI.

I think I can find enough time to get a new version out, minus the BiS part.

Another discrepancy is minimization tolerance. I have no idea how to even approximate that one. Perhaps with "Rosetta energy" calculation and cycle-by-cycle score change tracking?