Recipe: ShowWorst

created by spvincent

Profile

• Name: ShowWorst
• ID: 48284
• Shared with: Public
• Parent: None
• Children: None
• Created on: February 19, 2014 at 20:35 PM UTC
• Updated on: February 19, 2014 at 20:35 PM UTC
• Description:

  See first comment

Code

components = { "Backbone" ,
		          "Clashing" ,
			"Ideality" ,
			"Bonding" ,
			"Packing" ,
                             "Hiding" ,
                             "Sidechain" ,
                             "Disulfides" ,
                             "Reference" }

use_components = {}

scores = {}
ids = {}

residue = true
show_best = false

show_n = 5

--    Amino acids.

single_letter_codes = { "g","a","v","l","i","m","f","w","p","s","t","c","y","n","q","d","e","k","r","h"}
three_letter_codes  = { "Gly","Ala","Val","Leu","Ile","Met","Phe","Trp","Pro","Ser","Thr","Cys","Tyr","Asn","Gln","Asp","Glu","Lys","Arg","His"}

function get_aa3 ( i )

    k = structure.GetAminoAcid (  i )

    for  j = 1, 20 do
        if ( k == single_letter_codes [  j ] ) then
            return three_letter_codes [  j  ]
        end
    end

    return "Unk"

end

function r3 ( i )

-- printing convenience

   return i - i % 0.001

end

function print_line ( id , v )

    print ( get_aa3 ( id ) .. " " .. id .. "  " .. r3 ( v ) )
 
end

function print_dataset ()

    print ( " " )

    if ( show_best == false ) then
        for j = 1, math.min ( show_n , n_residues ) do
            print_line ( ids [ j ] , scores [ j ] )
        end
     else
        for j = n_residues , math.max ( n_residues - show_n + 1 , 1 ) , -1 do
            print_line ( ids [ j ] , scores [ j ] )
        end
    end

    print ( " " )

end


function ShellSort ()

-- Adapted from Numerical Recipes in C

    inc =  1
    
    repeat 
        inc = inc * 3 + 1
    until  inc > n_residues

    repeat

        inc = inc  / 3 
        inc = inc - inc % 1

        for i = inc + 1 ,  n_residues do

            v =  scores [  i  ]
            w = ids [ i ]

            j = i

            flag = false 

            while (  flag == false and scores [  j - inc ] > v ) do
                scores [  j  ] = scores [  j  - inc ]
                ids [ j ] = ids [ j - inc ]

                j = j - inc
                
                if ( j <= inc ) then
                    flag = true
                end

            end

            scores [ j ]  = v
             ids [ j ] = w
        end

    until  inc  <= 1

end

function GetParameters ()


    local dlog = dialog.CreateDialog ( "Show Worst" )

    dlog.residue = dialog.AddCheckbox ( "Residue" , residue  )  

    dlog.div_1 = dialog.AddLabel ( "__________________________"  )

    for i = 1 , #components do
      dlog [ "comp_" .. i ] = dialog.AddCheckbox ( components [ i ]  , false )  
    end

    dlog.div_2 = dialog.AddLabel ( "__________________________"  )

    dlog.show_best = dialog.AddCheckbox ( "Show best" , show_best )  
    dlog.show_n = dialog.AddSlider ( "Show" , show_n , 2 , 20 , 0 )  

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

    if ( dialog.Show ( dlog ) > 0 ) then
    
        residue = dlog. residue.value

        for i = 1 , #components do
           use_components [ i ] = dlog [ "comp_" .. i ].value
        end
    
        show_best = dlog.show_best.value
        show_n = dlog.show_n.value

        return true
     else
        return false
    end

end

function main ()

    n_residues = structure.GetCount ()

    if ( GetParameters () == false ) then
      return                -- graceful exit
    end

    if ( residue == true ) then

        for  j = 1 , n_residues do
            scores [ j ] = current.GetSegmentEnergyScore ( j  )
            ids [ j ] = j
        end 

        ShellSort ()

        if ( show_best == false ) then
            print ( "Worst residues" )
          else
            print ( "Best residues"  )
        end

        print_dataset ()

   end

    for i = 1 , #components do

        if ( use_components [ i ] == true ) then

            for  j = 1 , n_residues do
                scores [ j ] = current.GetSegmentEnergySubscore ( j , components [ i ] )
                ids [ j ] = j
            end 

            ShellSort ()

            if ( show_best == false ) then
                print ( "Worst " .. components [ i ]  )
              else
                print ( "Best " .. components [ i ]  )
            end

            print_dataset ()

       end
    end

end

function cleanup ()
   
end

main ()
--xpcall ( main , cleanup )

Comments

[spvincent]

A utility script that prints out the worst (or best if that option is chosen) scoring amino acids; either by total score or component score. Not going to bother descring the dialog settings: they should be self-explanatory