Code
min_residue = 1
max_residue = 999
n_residues = 0
delta_residue = 5
kMaxDelta = 20
best_score = 0
clash_importance_during_modify = 0.1
kWiggleIterations = 15
modify_radius = 14
modifier_type = 2
original_slow_filters_setting = 0
score_type = 2
loss_from_modify = {}
-- Amino acids. Hydrophobics first.
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"}
-- Use of quicksave slots
kOriginalStructureOrNewBest = 10
function r3 ( x )
-- Round to 3 decimal places
t = 10 ^ 3
return math.floor ( x*t + 0.5 ) / t
end
function GetScore ()
if ( score_type == 1 ) then
score = current.GetScore ()
elseif ( score_type == 2 ) then
behavior.SetFiltersDisabled ( false )
score = current.GetScore ()
behavior.SetFiltersDisabled ( true )
end
return score
end
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 PostModify ()
behavior.SetClashImportance ( 1.0 )
selection.SelectAll ()
structure.WiggleSelected ( 1 , false , true ) -- sidechains
structure.WiggleSelected ( kWiggleIterations )
end
function MutateResidue ( i )
save.Quickload ( kOriginalStructureOrNewBest )
selection.DeselectAll ()
for j = 1 , n_residues do
if ( structure.GetDistance ( i , j ) < modify_radius ) then
selection.Select ( j )
end
end
behavior.SetClashImportance ( clash_importance_during_modify )
if ( modifier_type == 1 ) then
structure.WiggleSelected ( 1 )
structure.ShakeSidechainsSelected ( 1 )
elseif ( modifier_type == 2 ) then
structure.MutateSidechainsSelected ( 1 )
end
score = GetScore ()
table.insert ( loss_from_modify , best_score - score )
if ( math.abs ( score - best_score ) > 0.5 ) then
PostModify()
score = GetScore ()
if ( score > best_score ) then
save.Quicksave ( kOriginalStructureOrNewBest )
best_score = score
print ( "Improvement to " .. r3 ( best_score ) )
end
end
end
function MutateAll ()
n = 1
for start_idx = 1 , delta_residue do
i = min_residue - 1 + start_idx
while ( i < max_residue ) do
print ( get_aa3 (i) .. " " .. i .. " (" .. n .. "/" .. max_residue - min_residue + 1 .. ")" )
MutateResidue ( i )
i = i + delta_residue
n = n + 1
end
end
end
function GetParameters ()
local dlog = dialog.CreateDialog ( "Local Mutate 2.0" )
dlog.min_residue = dialog.AddSlider ( "Min residue" , 1 , 1 , n_residues , 0 )
dlog.max_residue = dialog.AddSlider ( "Max residue" , n_residues , 1 , n_residues , 0 )
dlog.delta_residue = dialog.AddSlider ( "Delta residue" , delta_residue , 1 , kMaxDelta , 0 )
dlog.cidm = dialog.AddSlider ( "Clash importance" , clash_importance_during_modify , 0 , 1.0 , 2 )
dlog.modifier = dialog.AddSlider ( "Modifier" , modifier_type , 1 , 2 , 0 )
dlog.tp = dialog.AddLabel ( "1 = W/S : 2 = Mutate" )
dlog.modify_radius = dialog.AddSlider ( "Sphere radius" , modify_radius , 1 , 30 , 1 )
dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )
dlog.tp2 = dialog.AddLabel ( "1 = Normal : 2 = Normal for Filters" )
dlog.ok = dialog.AddButton ( "OK" , 1 )
dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
if ( dialog.Show ( dlog ) > 0 ) then
min_residue = dlog.min_residue.value
max_residue = dlog.max_residue.value
delta_residue = dlog.delta_residue.value
clash_importance_during_modify = dlog.cidm.value
modifier_type = dlog.modifier.value
modify_radius = dlog.modify_radius.value
score_type = dlog.score_type.value
return true
else
return false
end
end
function main ()
band.DisableAll ()
n_residues = structure.GetCount ()
save.Quicksave ( kOriginalStructureOrNewBest )
original_slow_filters_setting = behavior.GetSlowFiltersDisabled ()
if ( GetParameters () == false ) then
return -- graceful exit
end
print ( "Local Mutate 2.0" )
max_residue = math.min ( n_residues , max_residue )
min_residue = math.max ( 1 , min_residue )
print ( "Rebuild range " .. min_residue .. " to " .. max_residue )
if ( max_residue < min_residue ) then
print ( "Rebuild range error." )
return
end
print ( "Delta " .. delta_residue )
print ( "Modifier " .. modifier_type )
print ( "CI on modify " .. r3 ( clash_importance_during_modify ) )
print ( "Selection radius " .. r3 ( modify_radius ) )
print ( "Score type " .. score_type )
print ( "" )
best_score = GetScore ()
print ( "Start score : " .. r3 ( best_score ) )
MutateAll ()
cleanup ()
end
function cleanup ()
print ( "Cleaning up" )
behavior.SetClashImportance ( 1.0 )
save.Quickload ( kOriginalStructureOrNewBest )
selection.SelectAll ()
band.EnableAll ()
behavior.SetSlowFiltersDisabled ( original_slow_filters_setting )
if ( #loss_from_modify > 1 ) then
table.sort ( loss_from_modify )
mid_pt = math.ceil ( #loss_from_modify / 2 )
print ( "Median loss from modify " .. r3 ( loss_from_modify [ mid_pt ] ) )
end
end
--main ()
xpcall ( main , cleanup )
