Recipe: nicm25.dei.TestBaseScoring V0

created by Nicm25

Profile

• Name: nicm25.dei.TestBaseScoring V0
• ID: 105164
• Shared with: Public
• Parent: None
• Children: None
• Created on: August 30, 2021 at 12:14 PM UTC
• Updated on: August 30, 2021 at 12:14 PM UTC
• Description:

  *demo script, test base scoring! (segment select, number seed, number setcount, boolean fixrandom)

Code

-- created by Nicm25;
function pldc()
 local retd=dialog.CreateDialog("TestBaseScoring V0 - message")
 retd.la=dialog.AddLabel("can choose any value you like for random seed")
 retd.sr=dialog.AddSlider("seed",0.5,0.0,1.0,3)
 retd.si=dialog.AddSlider("set count",1,1,50,0)
 retd.ck=dialog.AddCheckbox("fix random",false)
 retd.bt=dialog.AddButton("Check",1)
 retd.bs=dialog.AddButton("Test",2)
 return retd
end

function plfa(avx,avy,avz,avt)
 local lc=0
 local retv=0.0
 local lfx=0
 for lc=avx+5,avy-5 do
  retv=current.GetSegmentEnergyScore(lc)-
   current.GetSegmentEnergySubscore(lc,"clashing")-
   current.GetSegmentEnergySubscore(lc,"bonding")-
   current.GetSegmentEnergySubscore(lc,"ideality")
  lfx=avz[lc+3]
  avt[lfx+20]=avt[lfx+20]+retv
  avt[lfx+40]=avt[lfx+40]+1
 end
 return retv
end

function plfb(avx,avy,avz,avd,avt)
 local lc=0
 local lfx=0.1415926535897932
 local lfy=avz
 lfx=(lfx*lfx*127+lfy)%1.0
 lfy=(lfx+lfy)%1.0
 lfx=(lfx*101.23457+0.53)%1.0
 lfy=(lfx+lfy)%1.0
 for lc=avx,avy do
  lfx=(lfx*101.23457+0.53)%1.0
  lfy=(lfx+lfy)%1.0
  avd[lc+3]=math.floor(lfy*19.1+1.0)
  structure.SetAminoAcid(lc,avt[avd[lc+3]])
 end
end

function plfc(avx,avy,avz)
 local lc=0
 local lfx=0.1415926535897932
 local lfy=avz
 local lfz=0
 lfx=(lfx*lfx*127+lfy)%1.0
 lfy=(lfx+lfy)%1.0
 lfx=(lfx*101.23457+0.53)%1.0
 lfy=(lfx+lfy)%1.0
 lfz=math.floor((avy-avx+1.25)*0.5)+avx
 lfz=band.Add(lfz,lfz+1,lfz+2,0.001,0.01,0.01,2,2,2)
 band.Disable(lfz)
 selection.DeselectAll()
 selection.SelectRange(avx+1,avy-1)
 structure.IdealSSSelected()
 selection.DeselectAll()
 selection.SelectRange(avx,avx+1)
 structure.IdealizeSelected()
 selection.DeselectAll()
 band.SetStrength(band.Add(avx,avx+1,avx+2,0.001,0.01,0.01,2,2,2),0.2)
 band.SetStrength(band.Add(avy,avy-1,avy-2,0.001,0.01,0.01,2,2,2),0.2)
 recentbest.Save()
 behavior.SetClashImportance(0.05)
 structure.ShakeSidechainsAll(1)
 behavior.SetClashImportance(0.25)
 structure.WiggleAll(3)
 for lc=1,6 do
  behavior.SetClashImportance(0.1-lc*0.01)
  structure.ShakeSidechainsAll(1)
  if (lc-0.5)%3.0>2.0 then
   behavior.SetClashImportance(0.25)
   structure.WiggleAll(3)
   behavior.SetClashImportance(0.5)
   structure.ShakeSidechainsAll(1)
  end
  behavior.SetClashImportance(1.0)
  structure.WiggleAll(3)
 end
 recentbest.Restore()
 band.Delete(lfz+2)
 band.Delete(lfz+1)
 lfz=math.floor((avy-avx+1.25)*0.5)+avx
 for lc=1,6 do
  lfx=(lfx*101.23457+0.53)%1.0
  lfy=(lfx+lfy)%1.0
  lfz=math.floor(lfy*(avy-avx+1))+avx
  lfx=(lfx*101.23457+0.53)%1.0
  lfy=(lfx+lfy)%1.0
  lfx=(lfx*101.23457+0.53)%1.0
  band.Add(lfz,lfz+(avy-lfz<1.5 and -1 or 1),lfz+(avy-lfz<1.5 and -2 or 2),
   1.6-lc*0.1,(lfx+lfy)%1.0*3.14159,lfy*6.28318,2,2,2)
  lfy=(lfx+lfy)%1.0
  structure.WiggleAll(5)
  band.Delete(2)
 end
 recentbest.Restore()
 if band.GetCount(false)>1.5 then
  band.Delete(2)
 end
 if band.GetCount(false)>0.5 then
  band.Enable(1)
  structure.WiggleAll(5)
  band.DeleteAll()
 end
end

function plss()
 local lc=1
 local retd={}
 for lc=1,structure.GetCount() do
  retd[lc]=selection.IsSelected(lc) and 1 or 0
 end
 return retd
end

function run(avs,avx,avy,avz)
local lc=0
local stcd={}
local stcs={}
local setsd=0.0
stcs[1]=structure.GetCount()
stcs[2]=band.GetCount(false)
stcd[1]="A"
stcd[2]="C"
stcd[3]="D"
stcd[4]="E"
stcd[5]="F"
stcd[6]="G"
stcd[7]="H"
stcd[8]="I"
stcd[9]="K"
stcd[10]="L"
stcd[11]="M"
stcd[12]="N"
stcd[13]="Q"
stcd[14]="R"
stcd[15]="S"
stcd[16]="T"
stcd[17]="V"
stcd[18]="W"
stcd[19]="Y"
stcd[20]="P"
stcs[3]=1
if avy<0.5 then
 stcs[4]=0
 if selection.GetCount()>1.5 then
  for lc=stcs[4]+1,stcs[1] do
   if avs[lc]>0.5 then
    if stcs[4]<0.5 then
     stcs[4]=lc
    else
     stcs[1]=lc
    end
   end
  end
 end
 if stcs[4]<0.5 then
  stcs[4]=1
 end
 stcs[3]=0.0
 for lc=stcs[4],stcs[1] do
  stcs[3]=stcs[3]+current.GetSegmentEnergyScore(lc)
 end
 print("energy score :"..stcs[3])
 stcs[3]=0.0
 for lc=stcs[4],stcs[1] do
  stcs[3]=stcs[3]+current.GetSegmentEnergyScore(lc)-
   current.GetSegmentEnergySubscore(lc,"clashing")-
   current.GetSegmentEnergySubscore(lc,"bonding")-
   current.GetSegmentEnergySubscore(lc,"ideality")
 end
 print("offset score :"..stcs[3])
 return 0
end
for lc=1,40 do
 stcd[lc+20]=0.0
end
setsd=avz and avx or ((os.time()%1000.0*101000.0+avx*1000000.0+
 (((os.time()%500000.0)*101.0+0.5)%500000.0-0.5)+0.5)%1000000.0-0.5)*0.000001
if not("Protein Design Sandbox"==puzzle.GetName()) then
 print("this not Protein Design Sandbox")
 print("please try open that puzzle.")
 return 1
end
if stcs[1]<10.5 then
 print("sorry not support too few residues.")
 return 1
end
print("seed: "..(setsd*1000000.0)..",test begin")
behavior.SetWigglePower("h")
band.DeleteAll()
undo.SetUndo(false)
while avy*20-stcs[3]>-0.5 do
 plfb(1,stcs[1],(0.1271*(stcs[3]-1)+setsd)%1.0,stcs,stcd)
 plfc(1,stcs[1],(0.1271*stcs[3]+setsd+0.1)%1.0)
 plfa(1,stcs[1],stcs,stcd)
 if (stcs[3]-0.5)%20.0>19.0 and avy*20-stcs[3]>0.5 then
  undo.SetUndo(true)
  band.DeleteAll()
  undo.SetUndo(false)
  print("middle result:"..stcs[3])
  for lc=1,40 do
   print(stcd[(lc-0.5)%20.0+0.5]..":"..stcd[lc+20])
  end
 end
 stcs[3]=stcs[3]+1
end
print("Last result:")
for lc=1,40 do
 print(stcd[(lc-0.5)%20.0+0.5]..":"..stcd[lc+20])
end
for lc=1,20 do
 print(stcd[lc]..":"..(stcd[lc+40]<0.5 and "none" or stcd[lc+20]/stcd[lc+40]))
end
undo.SetUndo(true)
band.DeleteAll()
return 0
end

local lfi=0
local tdr=pldc()
lfi=dialog.Show(tdr)
if lfi>0.5 then
 lfi=run(plss(),tdr.sr.value,lfi>1.5 and tdr.si.value or -1,tdr.ck.value)
 if lfi>0.5 then
  print("terminated by exception error")
 end
end

Comments

[Nicm25]

*note: this is demo script.
This recipe just repeats the random mutation and quick relax to find out the base energy required for folding,
and recipe has been adjusted to run in the 'Protein Design Sandbox'.
before running you should give secondary structure to you protein, examine it using idealSS as initial structure by this recipe.
4 arguments
select: currently selected segment will be this argument.(check mode only)
seed: choose any value you like to generate random AA's by random seed.
range: 0.0-1.0, default: 0.5, function: 1.0 is plus value, 0.0 is none value
setcount: run 20 times as one set, only 0 is check mode for scoring only.
range: 0-50 (ext0-1000), default: 1, function: 1 is one set 20 counts, 0 is check mode
fixrandom: set whether to fixed random seed.
default: false, function: false is always random seed, true is fixed random seed

[Nicm25]

Hi, this is an explanation of how this recipe was created….

I was trying to investigate in this recipe was true(valid) energy required for folding.
If we could pick arbitrary AA's and have our folding trends known, we would be able to design more stable energy landscape.
It is known that we have tendency to spontaneously fold from single strand(beta) into helix(alpha) where hydrogen bonds exist.
In order fold to helix, we must find another energy landscape that is more stable from helix.
to bend the helix, we have to find another energy landscape that makes helix more stable,
such as AA's sequence that is more stable when attached to each other's side chains by hydrophobic interactions.
How do we do this? using that result table, we can deduce from delta score the energy required to go from helix to strand.
and to bend the helix, we as loop 2-3 segments, some of which are untied from helix, and re fold them as strand.
this means that we need hydrophobic sidechain that gives high score in the regular case, least about 100 points(10 kcal/mol).
and when conformation can be altered by surface hydrogen bonding etc…, it may be re folded for more stable, lower energy.
*however, since that result table does not include hydrogen bonds, there is offset of about 10 points per segment in delta score.

*attached data
the results of helix and strand(sheet) data for each sidechains.

results tabulated using this recipe are as follows.

AAIndex,samples,helixscore,sheetscore,deltascore
A,3758,10.262,-61.200,71.462
C,3759,-61.791,-107.314,45.523
D,3832,24.937,3.691,21.246
E,3782,27.563,10.892,16.671
F,3754,-21.907,-18.889,-3.018
G,3759,5.880,-48.695,54.575
H,3865,14.048,-0.313,14.361
I,3683,-25.382,-50.216,24.834
K,3776,26.419,8.902,17.517
L,3748,-21.663,-63.682,42.019
M,3762,-23.315,-50.707,27.392
N,3772,22.178,-1.865,24.043
P,376,4.343,42.710,-38.367
Q,3746,21.790,2.002,19.788
R,3714,17.443,-2.977,20.420
S,3697,21.226,-16.516,37.742
T,3805,20.256,-35.937,56.193
V,3856,-22.929,-74.463,51.534
W,3824,-31.079,-46.403,15.324
Y,3732,-10.375,-2.023,-8.352
*sigma=0.18

[Nicm25]

New recipes are available here
https://fold.it/portal/recipe/105209

that difference is added arguments, and testing score in shape at start of this recipe using Quick save and load(1).