Code
components = { "Backbone" ,
"Clashing" ,
"Ideality" ,
"Bonding" ,
"Packing" ,
"Hiding" ,
"Sidechain" ,
"Disulfides" ,
"Density" ,
"Reference" }
use_components = {}
scores = {}
ids = {}
residue = true
show_best = false
show_select = false -- added in 2.4 : if set then the worst residues are selected in game
show_n = 6
-- 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 ) )
if ( show_select == true ) then
selection.Select ( id )
end
end
function BestWorstString ()
if ( show_best == false ) then
return "Worst "
else
return "Best "
end
end
function sigma ()
total = 0
for i = 1 , n_residues do
total = total + scores [ i ]
end
return total
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 2.4" )
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 , n_residues , 0 )
dlog.show_select = dialog.AddCheckbox ( "Select" , show_select )
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
show_select = dlog.show_select.value
return true
else
return false
end
end
function main ()
n_residues = structure.GetCount ()
if ( GetParameters () == false ) then
return -- graceful exit
end
mid_pt = math.ceil ( n_residues / 2 )
if ( residue == true ) then
for j = 1 , n_residues do
scores [ j ] = current.GetSegmentEnergyScore ( j )
ids [ j ] = j
end
ShellSort ()
print ( BestWorstString () .. " residues ( Total = " .. r3 ( sigma () ) .. " : Median = " .. r3 ( scores [ mid_pt ] ) .. " )" )
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 ()
print ( BestWorstString () .. components [ i ] .. " ( Total = " .. r3 ( sigma () ) .. " : Median = " .. r3 ( scores [ mid_pt ] ) .. " )" )
print_dataset ()
end
end
end
function cleanup ()
end
main ()
--xpcall ( main , cleanup )
