Recipe: eke3

created by jeff101

Profile

• Name: eke3
• ID: 44419
• Shared with: Public
• Parent: None
• Children: None
• Created on: October 27, 2012 at 03:48 AM UTC
• Updated on: October 27, 2012 at 03:48 AM UTC
• Description:

  copied 743pm 10/25/12 from eke3dx.txt

Code

function Main()
-- eke by jeff101 9/30/12 3pm
-- goal is to randomly do shake and wiggle to improve the score
--
-- adapted 10/17/12 from eke0d3.txt(=eke0d2.txt=eke0d.txt) to eke1.txt
-- adapted 10/22/12 from eke1d.txt to eke2.txt
-- adapted 10/25/12 from eke2d.txt to eke3.txt
--
-- last updated 1030pm 10/25/12
--
rtot=structure.GetCount()
btot=band.GetCount()
ostime=os.time()
math.randomseed(ostime)
print('Running eke on puzzle '..puzzle.GetName()..'\n   with Puzzle ID '..puzzle.GetPuzzleID()..', '..rtot..' residues, and '..btot..' bands:')
print(' ')
print('ntries is how many loops since last score improvement.')
print('length of each loop generally rises as ntries rises.')
print('eke will run until you force it to quit.')
print(' ')
mutok=0
mutstr=' '
canmut={}
for num=1,rtot do
   if structure.IsMutable(num) then
      if mutok>0 and mutok==10*math.floor(mutok/10) then
         mutstr=(mutstr..'\n         ')
      end -- if mutok
      mutok=mutok+1
      canmut[num]=1
      mutstr=(mutstr..num..' ')
   else -- not mutable
      canmut[num]=0
   end -- if IsMutable
end -- for num
if mutok>0 then
   print('Residues'..mutstr..'('..mutok..' in all) can be mutated.\n ')
end -- if mutok
qflag=0
steps={5, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 1, 1}
ways=#steps -- set ways to length of steps
newscore=current.GetScore() -- get current score
recentbest.Save() -- save current score's pose
indx=0
ntries=1
while qflag==0 do
   way=round(1+(ways-1)*math.random()) -- random number from 1 to ways
   if (mutok>0 and way~=11) or (mutok==0 and way~=11 and way~=12) then -- mutation is allowed
      -- 1 step of way 11 takes too long for 30 residues 10/25/12
      if mutok==0 and (way==11 or way==12) then
          print('ERROR: way='..way..' (mutation) is not allowed when mutok='..mutok..'.')
      end -- if mutok   
      osdate=os.date()
      indx=indx+1
      ciold=behavior.GetClashImportance()
      if way==4 or way==9 then
         ci=math.random() -- random number from 0 to 1
         behavior.SetClashImportance(ci)
      else
         ci=ciold
      end -- if way==4 or way==9
      print('Loop '..indx..': score='..round3(newscore)..' ci='..round3(ci)..' ntries='..ntries..' ('..osdate..'):')
      stp=round(1+(math.ceil(steps[way]*ntries*5/ways)-1)*math.random()) -- random number from 1 to math.ceil(steps[way]*ntries*5/ways)
      if way==1 then
         print('   (1) WiggleAll '..stp..' steps.')
         structure.WiggleAll(stp)
      elseif way==2 then
         print('   (2) WiggleAll Backbone '..stp..' steps.')
         structure.WiggleAll(stp,true,false)
      elseif way==3 or way==4 then
         print('   ('..way..') WiggleAll Sidechains '..stp..' steps.')
         structure.WiggleAll(stp,false,true)
         if way==4 then
            behavior.SetClashImportance(ciold) -- reset to old clashing importance
         end -- if way==4
      elseif way==5 or way==10 then
         print('   ('..way..') ShakeSidechainsAll '..stp..' steps.')
         structure.ShakeSidechainsAll(stp)
      elseif way==6 then
         print('   (6) LocalWiggleAll '..stp..' steps.')
         structure.LocalWiggleAll(stp)
      elseif way==7 then
         print('   (7) LocalWiggleAll Backbone '..stp..' steps.')
         structure.LocalWiggleAll(stp,true,false)
      elseif way==8 or way==9 then
         print('   ('..way..') LocalWiggleAll Sidechains '..stp..' steps.')
         structure.LocalWiggleAll(stp,false,true)
         if way==9 then
            behavior.SetClashImportance(ciold) -- reset to old clashing importance
         end -- if way==9
      elseif way==11 then
         print('   (11) MutateSidechainsAll '..stp..' steps.')
         oldseq=getseq(1,rtot)
         structure.MutateSidechainsAll(stp)
         checkseq(oldseq,1,rtot)
      elseif way==12 or way==13 then
         indok=0
         while indok==0 do
            indok=1
            indx2=round(1+(5-1)*math.random()) -- random number from 1 to 5
            indx1=round(1+(rtot-indx2)*math.random()) -- random number from 1 to rtot-indx2
            indx2=indx1+indx2
            if way==12 then
               for num=indx1,indx2 do
                  indok=indok*canmut[num] -- any zeros in canmut will make indok be 0
               end -- for num
            end -- if way
         end -- while indok
         -- all indices must be mutable to use way 12
         oldsel=getsel(rtot) -- find & print original selection
         selection.DeselectAll() -- select none
         selection.SelectRange(indx1,indx2) -- select just from indx1 to indx2
         newsel=getsel(rtot) -- find & print new selection
         if way==12 then
            print('   (12) MutateSidechainsSelected '..indx1..'-'..indx2..' for '..stp..' steps.')
            oldseq=getseq(indx1,indx2)
            structure.MutateSidechainsSelected(stp)
            checkseq(oldseq,indx1,indx2)
         elseif way==13 then
            print('   (13) RebuildSelected '..indx1..'-'..indx2..' for '..stp..' steps.')
            structure.RebuildSelected(stp)
         end -- if way
         setsel(oldsel,rtot) -- restore & print original selection
      end -- if way
      oldscore=newscore
      newscore1=current.GetScore() -- get current score
      recentbest.Restore() -- restore best since last recentbest.Save()
      newscore=current.GetScore() -- get current score
      recentbest.Save() -- save best again
      if newscore>oldscore then
         str=('   Score rose from '..round3(oldscore)..' to '..round3(newscore))
      elseif newscore==oldscore then
         str=('   Score did not rise above '..round3(oldscore))
      else 
         str=('   Score fell from '..round3(oldscore)..' to '..round3(newscore))
      end
      if newscore1<newscore then
         str1='but'
         str2='restoring'
      elseif newscore1==newscore then
         str1='and'
         str2='keeping'
      else
         str1='and'
         str2='mistakenly restoring'
      end
      print(str..' '..str1..' ended with '..round3(newscore1)..', so '..str2..' '..round3(newscore)..'.')
      if newscore1>newscore then
         print('   ERROR: '..round3(newscore1)..' > '..round3(newscore)..' should not occur.')
      end 
      if oldscore>=newscore then
         ntries=ntries+1
      else
         ntries=1
      end -- if oldscore>=newscore  
   end -- if mutok
end -- while qflag
end -- Main()

-- below rounds val to the nearest thousandth to get res
function round3(val)
local res=round(val*1000)/1000
return res
end -- round3()

-- below rounds val to the nearest integer to get res
function round(val)
local res=math.floor(val)
if val-res>=0.5 then
   res=res+1
end
return res
end -- round()

function getsel(rtot)
local sel={}
local num
local seltot=0
local selstr=' '
for num=1,rtot do
   sel[num]=selection.IsSelected(num)
   if sel[num] then
      selstr=(selstr..num..' ')
      seltot=seltot+1
   end -- if sel
end -- for num
print('        '..seltot..' residues'..selstr..'are selected.')
return sel
end -- getsel()

function setsel(sel,rtot)
selection.DeselectAll()
local num
local seltot=0
local selstr=' '
for num=1,rtot do
   if sel[num] then
      selection.Select(num)
      selstr=(selstr..num..' ')
      seltot=seltot+1
   end -- if sel
end -- for num
print('        '..seltot..' residues'..selstr..'just got re-selected.')
end -- setsel()

function getseq(indx1,indx2)
local seq={}
local num
for num=indx1,indx2 do
   seq[num]=structure.GetAminoAcid(num)
end -- for num
return seq
end -- getseq()

function checkseq(seq,indx1,indx2)
local num
local tot=0
local str=' '
for num=indx1,indx2 do
   aa=structure.GetAminoAcid(num)
   if aa~=seq[num] then
      tot=tot+1
      str=(str..seq[num]..num..'->'..aa..num..' ')
   end -- if aa
end -- for num
if tot>0 then
   print('   Mutated residues'..str..' ('..tot..' in all).')
else
   print('   No mutations succeeded.')
end -- if tot
end -- checkseq()

Main()

Comments

[jeff101]

eke3 does rebuild, mutate, shake, or wiggle all, backbone, or sidechains at random to improve the score. Sometimes changes clashing importance randomly before wiggling sidechains. Does not tolerate loss. Spends longer with each method if stuck. If score rises and then falls during a particular stage, it keeps the highest score found during the stage. eke3 runs until you force it to quit.