Code
--[[
The Disulfides
LUA V2
by Lennart Isaksson
Description:
Finds those disulfides by creating bands between them.
Option:
Rnd: Random selection of two disulfides and create a band between them.
Closest: finds the closest distance between two disulfides and create a band between them.
Text Box: Create bands according the text box
Options added for band goal length and strength. --JMP
]]--
version = "V2 v1.1.18"
math.randomseed(os.time())
math.random() -- Has to be use once, otherwise the random number doesn't produce any correct random number
segCnt = structure.GetCount()
count_disulfides = 0
disulfides = {}
distance = {}
disulfides_vector = {}
disulfides_pair = ""
pair_str = ""
bStrength = 9.0
bGoal = 2.0
-- Search for the Disulfides
disulfides_tmp = {}
for i=1,segCnt,1 do
if structure.GetAminoAcid(i) == "c" then
disulfides_tmp[#disulfides_tmp+1] = {i}
end
end
--print("total: "..#disulfides_tmp)
-- put each Disulfide into a string
str = ""
for i = 1,#disulfides_tmp,1 do
str = str..disulfides_tmp[i][1].." "
end
disulfides_connection = str
--########################################
pair = {}
function check_segment(a,b)
for i = 1,#pair,1 do
--print(pair[i][1]..":"..a..","..pair[i][2]..":"..b..","..pair[i][1]..":"..b..","..pair[i][2]..":"..a)
if (((pair[i][1] == a) or (pair[i][2] == b)) or ((pair[i][1] == b) or (pair[i][2] == a))) then
return 1
end
end
return 0
end
function get_time()
return os.date("%X",os.time())
end
function Sort_Ascending(vector,idx)
--print("Sorting Ascending ...")
for x = 1,#vector-1 do
for y = x+1,#vector do
if vector[x][idx]>vector[y][idx] then
vector[x],vector[y]=vector[y],vector[x]
end
end
end
return vector
end
function get_colon_pairs(v)
local d = {}
local p1
local p2
for p1 in string.gmatch(v,'([%d]+[:][%d]+)') do
--print("p1:"..p1)
d = {}
for p2 in string.gmatch(p1,'([%d]+)') do
--print("p2:"..p2)
d[#d+1] = {p2}
end
band.AddBetweenSegments(d[1][1],d[2][1],6,6)
band.SetGoalLength(band.GetCount(),bGoal)
band.SetStrength(band.GetCount(),bStrength)
end
end
function showMainConfigDialog()
local ask = dialog.CreateDialog("The Disulfides ".." "..version)
ask.b0 = dialog.AddButton("Rnd",0)
ask.b1 = dialog.AddButton("Closest",1)
ask.b2 = dialog.AddButton("Add band",2)
ask.b9 = dialog.AddButton("Cancel",9)
ask.b3 = dialog.AddButton("Help",3)
--options
ask.c2 = dialog.AddTextbox("Disulfide(s): ",disulfides_connection)
ask.c3 = dialog.AddTextbox("Pair(s): ",disulfides_pair)
ask.note = dialog.AddLabel("Band Characteristics:")
ask.bGoal = dialog.AddSlider("Goal Length: ", bGoal, 0.0, 5.0, 2)
ask.bStrength = dialog.AddSlider("Band Strength: ", bStrength, 0.0, 10.0, 1)
selection = dialog.Show(ask)
value_connection = ask.c3.value
if ((selection >= 0) and (selection <= 3))then
bGoal = ask.bGoal.value
bStrength = ask.bStrength.value
exe_flag = 1
main2()
end
if (selection == 9) then
exe_flag = 0
cleanup()
end
end
function main()
print("The Disulfides, version: ".." "..version..", "..get_time())
print("Band Goal: " .. bGoal)
print("Band Strength: " .. bStrength)
showMainConfigDialog()
end
function main2()
disulfides = {}
pair_str = ""
pair = {}
if exe_flag == 1 then
-- Create a list of disulfides with random values
for i = 1,segCnt,1 do
if structure.GetAminoAcid(i) == "c" then
disulfides[#disulfides+1] = {i,math.random(1000)}
end
end
--print("Rnd")
if (selection == 0) then
disulfides_pair = ""
Sorted_Disulfides_vector = Sort_Ascending(disulfides,2)
a = disulfides_tmp[math.random(1,#disulfides_tmp)][1]
b = disulfides_tmp[math.random(1,#disulfides_tmp)][1]
while (b == a) do
b = disulfides_tmp[math.random(1,#disulfides_tmp)][1]
end
pair_str = a..":"..b
--print("Segment Index:"..pair_str)
band.AddBetweenSegments(a,b,6,6)
band.SetGoalLength(band.GetCount(),0.1)
band.Delete(band.GetCount())
disulfides_pair = pair_str
end
--print("Closest")
if (selection == 1) then
disulfides_pair = ""
for i = 1,#disulfides-1,1 do
for j = i+1,#disulfides,1 do
band.AddBetweenSegments(disulfides[i][1],disulfides[j][1],6,6)
--print(band.GetCount())
k = band.GetLength(band.GetCount())
band.Delete(band.GetCount())
distance[#distance+1] = {disulfides[i][1],disulfides[j][1],k}
--print(disulfides[i][1]..":"..disulfides[j][1]..", "..k)
end
end
print("")
--print("Sorted")
Sorted_Distance_vector = Sort_Ascending(distance,3)
for i = 1,#Sorted_Distance_vector,1 do
--print(Sorted_Distance_vector[i][1].." "..Sorted_Distance_vector[i][2].." "..Sorted_Distance_vector[i][3])
--print("check_segment: "..(check_segment(Sorted_Distance_vector[i][1],Sorted_Distance_vector[i][2])))
if (check_segment(Sorted_Distance_vector[i][1],Sorted_Distance_vector[i][2]) == 0) then
pair[#pair+1] = {Sorted_Distance_vector[i][1],Sorted_Distance_vector[i][2]}
a = Sorted_Distance_vector[i][1]
b = Sorted_Distance_vector[i][2]
pair_str = a..":"..b
--print("Segment Index:"..pair_str)
band.AddBetweenSegments(a,b,6,6)
band.Delete(band.GetCount())
--band.SetGoalLength(band.GetCount(),0.1)
disulfides_pair = disulfides_pair .. pair_str .. " "
end
end
end
--print("Text Box")
if (selection == 2) then
if string.len(value_connection) > 0 then
get_colon_pairs(value_connection)
disulfides_pair = value_connection
else
print("Text Box is Empty!")
print("Run Rnd or Closest first.")
end
end
--print("Help")
if (selection == 3) then
print("Rnd: will select a pair randomly")
print("Closest: will select all closest pair(s)")
print("Add band: will create band(s) defined in the Pair(s) text box")
end
end
exe_flag = 0
showMainConfigDialog()
end
function cleanup(err)
end
-- main call
xpcall ( main, cleanup )
--end of script
