Recipe: gentle_compress_V1

created by robgee

Profile

• Name: gentle_compress_V1
• ID: 47673
• Shared with: Public
• Parent: None
• Children: None
• Created on: January 04, 2014 at 19:36 PM UTC
• Updated on: January 04, 2014 at 19:36 PM UTC
• Description:

  Gentle compress.

Code

--Gentle compress LuaV2 code by robgee.
--seems to work best on structures that have symmetry.
--Options at end.

print("Gentle compressor")

SegCount=structure.GetCount()
print("Protein length ",SegCount)

local score=current.GetScore()
print("Start score: ",score)



function compress(num,stren)
    local loop=1
    repeat
        print("Loop: ",loop)
        for i=1,(SegCount-1),2 do 
           j=(SegCount-i)
           qid=band.AddBetweenSegments(i,j)
           if qid>=1 then
               band.SetStrength(qid,stren)
           end
        end

        for l=2,(SegCount-2),2 do
           k=(SegCount-l)
           qed=band.AddBetweenSegments(l,k)
           if qed>=1 then
               band.SetStrength(qed,stren)
           end
        end

        --###########################################################################
        -- You can add or comment out any of these lines, or change the wiggle iters

        structure.WiggleAll(1 , true, true)--wiggle for compress
        band.DeleteAll()
        behavior.SetClashImportance(0.09)
        structure.ShakeSidechainsAll(1)

        --##############################################################
        behavior.SetClashImportance(0.24)
        structure.ShakeSidechainsAll(1)
        behavior.SetClashImportance(0.49)
        structure.ShakeSidechainsAll(1)
        structure.WiggleAll(1 , false, true)--wiggle sidechains
    
        --###############################################################
        behavior.SetClashImportance(0.73)   --Hmmm?
        structure.WiggleAll(1 , true, true) --penultimate wiggle
        --structure.ShakeSidechainsAll(1)   --Hmmm?
        --###############################################################
        behavior.SetClashImportance(1)
        structure.ShakeSidechainsAll(1)
        structure.WiggleAll(1 , true, true)--final full wiggle
        structure.ShakeSidechainsAll(1)

        local score=current.GetScore()
        print(score)
        loop=loop+1
    until loop>num
end
--###############################################################
--Options
cycles=3 --how many times compressor will run ( a cycle takes about 5 mins)

StrengthofBands=0.04 --Band strength, it's this low because 1 iter of wiggle is a long time[works best around 0.03-0.08].
                     --If you set it higher you can always watch it work and stop the wiggle by pressing spacebar.

compress(cycles,StrengthofBands)

Comments

[robgee]

This is a very simple compressor recipe.
It bands the stucture symmetricaly then does a wiggle at low band strength,
followed by shake and wiggle at 3 different CI.
-
It has the options (in the code):
To change amount of cycles(a single run of recipe).[default is 3.]
To change band strength.[default is 0.04]
-
Recipe seems to work best on structures that have some symmetry.
Tried and tested on Puzzle:826.
Suggestions or feedback would be welcome.
[This is beginners code, it works, but not very well]
N.B on small proteins, best to do another wiggle after its finished.