Recipe: HNetwork Probe 2.1

created by spvincent

Profile

• Name: HNetwork Probe 2.1
• ID: 104038
• Shared with: Public
• Parent: None
• Children:
  • HNetwork Probe 2.3
• Created on: October 08, 2020 at 16:36 PM UTC
• Updated on: October 08, 2020 at 16:36 PM UTC
• Description:

  Bug fix: 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 ) 
        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 )
        end
    end

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

 end

function PrintParameters ()

    print  ( "HNetworkProbe 2.1" )
    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 2.1" )

    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]

From 2.0 : fixed bug at that could cause a crash during Initialization.

Otherwise see the comments here from the original script:

https://fold.it/portal/recipe/103779