Recipe: The Disulfides v1.1.17

created by isaksson

Profile

• Name: The Disulfides v1.1.17
• ID: 102657
• Shared with: Public
• Parent: None
• Children:
  • Disulfides v1.1.17
• Created on: March 31, 2018 at 19:39 PM UTC
• Updated on: March 31, 2018 at 19:39 PM UTC
• Description:

  Lennart Isaksson

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


]]--

version = "V2 v1.1.17"


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 = ""


-- 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(),0.1)
	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)

	selection = dialog.Show(ask)

	value_connection = ask.c3.value
	
	if ((selection >= 0) and (selection <= 3))then
		exe_flag = 1
		main2()
	end
	if (selection == 9) then
		exe_flag = 0
		cleanup() 
	end
end

function main()
	print("The Disulfides, version: ".." "..version..", "..get_time())
	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

Comments

[toshiue]

Nice! Very clean and straightforward.

[Bruno Kestemont]

Identifies the cysteins and let you decide which pairs you want to link.
You can choose to do it automatically, choosing the closest ones or Rnd (?).
Then you choose to band or not, and that's it. Further recipes are needed.