Recipe: HNetwork Probe 2.0

created by spvincent

Profile

• Name: HNetwork Probe 2.0
• ID: 103779
• Shared with: Public
• Parent: None
• Children:
  • Enable all filters
• Created on: August 06, 2020 at 14:46 PM UTC
• Updated on: August 06, 2020 at 14:46 PM UTC
• Description:

  See first comment

Code

polar_aas = "stnqdehyw"
n_polar_aas = 0

n_residues = 0
first_qs_slot = 13
last_qs_slot = 35

next_qs_slot = 0
start_slot = 1

select_unfrozen = true

sidechain_minimum = -70

n_it = 0

mutate_list_ui = {}  -- will be a list of 1's & 0's for each residue. 1 means can mutate.  0 means don't mutate.

mutable_list = {}

filter_list = {}
init_filter_score = 0

function r3 ( x )

-- Round to 3 decimal places

  t  = 10 ^ 3

  return math.floor ( x*t + 0.5 ) /  t 

end

function GetFilterScore ()


     filter_bonus = filter.GetBonus ( "Hydrogen Bond Network" )
   
     return filter_bonus

end

function GetListOfMutablesUnfrozen ()

    for i = 1 , n_residues do

       seg_backbone_frozen, seg_sidechain_frozen = freeze.IsFrozen ( i )

        if ( ( seg_sidechain_frozen == false ) and
 --            ( seg_backbone_frozen == false )  and
             ( structure.IsMutable ( i ) == true ) ) then
             table.insert ( mutable_list , i )
        end
    end

end

function  GetListOfMutablesSelected ()

    for i = 1 , n_residues do

        seg_backbone_frozen, seg_sidechain_frozen = freeze.IsFrozen ( i )

        if ( ( seg_sidechain_frozen == false ) and
             ( mutate_list_ui [ i ] == 1  )  and
             ( structure.IsMutable ( i ) == true ) ) then
             table.insert ( mutable_list , i )
        end
    end

end


-- getlist pinched from Loop Rebuild 9.0
-- http://www.lua.org/manual/5.2/manual.html#6.4 
-- helped make this function 11/16/17
function getlist(liststr)
   local newlist={}
   local i,ilo,ihi,idir,substr
   for i=1,n_residues do
      newlist[i]=0
   end -- for i

-- below reads from liststr a series of substr's
-- where each substr contains an integer
-- followed by one or more '-' signs
-- followed by an integer
   for substr in string.gmatch(liststr,"(%d+%-+%d+)") do
      -- substr includes one or more '-' characters in a row 
      
      -- below gets ilo & ihi from substr
      ilo=string.gsub(substr,"(%d+)%-+(%d+)","%1")+0
      ihi=string.gsub(substr,"(%d+)%-+(%d+)","%2")+0
      -- above gets ilo & ihi from substr
      
      idir=1 -- the increment to use from ilo to ihi
      if ilo>ihi then
         idir= -1
      end -- if ilo
      for i=ilo,ihi,idir do -- for i=ilo to ihi step idir
         if i>=1 and i<=n_residues then
            newlist[i]=1
         end -- if i
      end -- for i
   end -- for substr

-- below reads from liststr a series of substr's
-- where each substr contains an integer
   for substr in string.gmatch(liststr,"(%d+)") do
      i=substr+0 -- converts substr into the number i
      if i>=1 and i<=n_residues then
         newlist[i]=1
      end -- if i
   end -- for substr

   return newlist
end

function Init ()

    save.Quickload ( start_slot )
 
    for i = 1 , #mutable_list do

        k = math.random ( n_polar_aas ) 
        structure.SetAminoAcid ( mutable_list [ i ] , string.sub ( polar_aas , k , k  ) )
    end

    selection.SelectAll ()
    structure.WiggleSelected ( 2 , false , true )    -- sidechains

 end

function PrintParameters ()

    print  ( "HNetworkProbe 2.0" )
    print ( " n mutables " .. #mutable_list )
    print ( "Amino acids to use : " .. polar_aas )

    print ( "Sidechain minimum " .. r3 ( sidechain_minimum ) )
    print ( "Using slots " .. first_qs_slot .. " to " .. last_qs_slot )

end

function GetParameters ()

    local dlog = dialog.CreateDialog ( "HNetworkProbe 2.0" )

    dlog.use_unfrozen = dialog.AddCheckbox ( "Select unfrozen" , select_unfrozen ) 

    dlog.mutate_list = dialog.AddTextbox ( "Mutate segments" , "" )
    dlog.mlabela = dialog.AddLabel('List segs to mutate like 1-3,6,19-30,45-62')
 
    dlog.aa_list = dialog.AddTextbox ( "Amino acids" , polar_aas )
    dlog.sidechain_minimum = dialog.AddSlider ( "Side chain minimum" , sidechain_minimum  , -200 , -20 , 0 )  

    dlog.start_qs_slot = dialog.AddSlider( "Start quick save" , first_qs_slot , 1 , 99 , 0 )
    dlog.end_qs_slot = dialog.AddSlider ( "End quick save" , last_qs_slot  ,1 , 99 , 0 )

    dlog.ok = dialog.AddButton ( "OK" , 1 )
    dlog.cancel = dialog.AddButton ( "Cancel" , 0 )

    if ( dialog.Show ( dlog ) > 0 ) then
    
        select_unfrozen = dlog.use_unfrozen.value  
        mutate_list_ui = getlist(dlog.mutate_list.value)
        polar_aas = dlog.aa_list.value
 
        sidechain_minimum = dlog.sidechain_minimum.value

        first_qs_slot = dlog.start_qs_slot.value
        last_qs_slot = dlog.end_qs_slot.value

        return true
      else
        return false
    end

end

function main ()

    n_residues = structure.GetCount ()

    save.Quicksave ( start_slot )
 
    if ( GetParameters () == false ) then
         return                -- graceful exit
    end

    n_polar_aas = string.len ( polar_aas )

    if ( select_unfrozen == true ) then
       GetListOfMutablesUnfrozen ()
     else
       GetListOfMutablesSelected ()
    end

    PrintParameters ()

    if ( #mutable_list  == 0 ) then
        print ( "No mutable residues found" )
        exit (0)
    end

    if ( first_qs_slot > last_qs_slot ) then
         print ( "Invalid quicksave slot values" )
        return
    end

    filter_list = filter.GetNames ()

    print ( "Filters" )
    print ( "" )

    for i = 1 , #filter_list do
      if ( filter_list [ i ] == "Hydrogen Bond Network" ) then
          filter.Enable ( filter_list [ i ] )
          print ( "Enabling " .. filter_list [ i ] )
       else
          filter.Disable ( filter_list [ i ] )
          print ( "Disabling " .. filter_list [ i ] )
      end

    end

    band.DisableAll ()
    undo.SetUndo ( false )

    init_filter_score = GetFilterScore ()
    print ( "Init HNet score " .. r3 ( init_filter_score ) )

    math.randomseed ( os.time () )
 
    next_qs_slot = first_qs_slot

    Init ()
 
    while ( next_qs_slot <= last_qs_slot ) do

        n_it = n_it + 1
        i = math.random ( #mutable_list )

        nn = 0
        valid_replacement_found = false
        
        -- a bit untidy this code
        
        repeat
            nn = nn + 1
            k = math.random ( n_polar_aas )
            replacement_aa = string.sub ( polar_aas , k , k  )
            if ( structure.CanMutate ( mutable_list [ i ] , replacement_aa ) == true ) then
               structure.SetAminoAcid ( mutable_list [ i ] , replacement_aa )
            
               sidechain_score = current.GetSegmentEnergySubscore ( mutable_list [ i ] , "Sidechain" )

               --print ( "nn " .. nn .. " " .. mutable_list [ i ] .. " " .. replacement_aa .. "  " .. r3 ( sidechain_score ) )
               if ( sidechain_score > sidechain_minimum ) then
                 valid_replacement_found = true
               end
           end
           
        until ( ( nn > 5 ) or ( valid_replacement_found == true ) )

        selection.SelectAll ()

        --structure.ShakeSidechainsSelected ( 1 )
        structure.WiggleSelected ( 2 , false , true )    -- sidechains

        filter_score = GetFilterScore ()
  
        if ( filter_score > init_filter_score ) then

             print ( "Found network ( gain " .. r3 ( filter_score - init_filter_score ) .. " ) storing in qs " .. next_qs_slot )
             save.Quicksave ( next_qs_slot )
             next_qs_slot = next_qs_slot + 1

             Init ()

        end
 
    end

    cleanup ()

end

function cleanup ()
   
    print ( "Cleaning up" )

    print ( "n_it " .. n_it )

    undo.SetUndo ( true )

    if ( next_qs_slot > first_qs_slot ) then

        print ( "Loading quick saves " .. first_qs_slot .. " to " .. next_qs_slot - 1  )
        for i = first_qs_slot , next_qs_slot - 1 do
            save.Quickload ( i )
        end
    end

    band.EnableAll ()

end

--main ()
xpcall ( main , cleanup )

Comments

[spvincent]

https://foldit.fandom.com/wiki/Making_Hydrogen_Bond_Networks

[Bruno Kestemont]

Thanks for the method explained in the Wiki. And for the recipe of course.

[LociOiling]

Here are a few things I've found out about how HNetwork Probe works.

The recipe has two ways to specify which segments to mutate:

1. If "select unfrozen" is checked, only segments with unfrozen sidechains are mutated.
2. Otherwise, the "mutate segments" box can be used to specify numeric ranges of segments, such as "1-3,6,19-30,45-62". The recipe will try to mutate the segments in these ranges, as long as they are mutable and have unfrozen sidechains. </ol> You must use one or the other of these methods. The "amino acids" box lists the amino acids the recipe will try when mutating. The recipe disables all filters except "Hydrogen Bond Network". (Call it HBN for short.) The recipe mainly checks the HBN score, and not the overall score. The recipe initially mutates each specified segment to a random amino acid from the list specified in the dialog. The recipe then does a minimal wiggle sidechains. This is the start of a "run". The recipe then picks one mutable from the ones specified, and tries up to five further mutations on it. The recipe does a minimal wiggle sidechains after each mutation. If the HBN score improves, the new pose is saved in a quick save slot, and a message is printed. Otherwise, the recipe just keeps going, again making random mutations to each specified segment, starting another "run". Each run includes the random mutate of all the specified segments, plus a new random pick of the segment to focus on for five more mutations. The recipe is quiet unless there's a gain, so the output window may not change for a long time. The recipe only does wiggle sidechains, there's no shake sidechains or wiggle backbone. The recipe stops when the specified range of quick save slots it exhausted. In many cases, this means the recipe runs until you cancel it. The recipe turns off undo processing at the start. At the end, it turns undo processing back on, and then loads each quick save slot it used, in sequence. In theory, this means you should see the best hydrogen bond network score when the recipe terminates. Undo or control-z gets you the next best HBN score, and so on. The recipe is focused on the best hydrogen bond network score. If there's a gain, you should see the pose with the best HBN score at the end. If there's no gain, the protein will just be left where it was when you cancelled the recipe. You'll need to restore credit best or load a previous save. The recipe does not re-enable any conditions at the end, so the final score will almost certainly be invalid, unless you're working on a test puzzle which includes only an HBN condition.