Recipe: Complex_Remix v0.9

created by Serca

Profile

• Name: Complex_Remix v0.9
• ID: 103304
• Shared with: Public
• Parent: None
• Children:
  • Fix Cysteine Disulfide Bonds
  • Complex Remix v1.0
• Created on: March 15, 2020 at 22:27 PM UTC
• Updated on: March 15, 2020 at 22:27 PM UTC
• Description:

  Remixes 2 large selections simultaneously.

  Before starting script 2 selections should be made by user manually! ; Script Remixes both selections together, iterating every possible combination between the Remix solutions for these 2 selections. Scores and fuzes all the solutions and chooses the best one. ; If the selection length is 1 (one residue is selected for any of two selections), script adds neighborhood to selection making selection length 5 residues. If no selections found it increases selection length.

  This script is usefull for building local mojo, packing 2 close loops very good. ; It's perfect for searching optimal solution of the 2 cysteines. Just select 2 close cysteines (ctrl+click) and run this script. Better band the cysteine sidechain endings with the strong short band (length 0.9 strength 4) to make good cysteine bridge on fuze.

Code

--[[ 
Remixes 2 large selections simultaneously.

Before starting script 2 selections should be made by user manually!
Script Remixes both selections together, iterating every possible combination between the Remix solutions for these 2 selections. Scores and fuzes all the solutions and chooses the best one.
If the selection length is 1 (one residue is selected for any of two selections), script adds neighborhood to selection making selection length 5 residues. If no selections found it increases selection length.

This script is usefull for building local mojo, packing 2 close loops very good.
It's perfect for searching optimal solution of the 2 cysteines. Just select 2 close cysteines (ctrl+click) and run this script. Better band the cysteine sidechain endings with the strong short band (length 0.9 strength 4) to make good cysteine bridge on fuze.
]]--




function FastFuze()
	behavior.SetClashImportance(0.05)
	structure.ShakeSidechainsAll(1)
	structure.WiggleAll(10)
	behavior.SetClashImportance(1)
	structure.WiggleAll(10)
end

function Fuze()
	behavior.SetClashImportance(0.05)
	structure.ShakeSidechainsAll(1)
	structure.WiggleAll(2)

	behavior.SetClashImportance(0.2)
	structure.ShakeSidechainsAll(1)
	structure.WiggleAll(1)

	behavior.SetClashImportance(1)
	structure.WiggleAll(1)

	behavior.SetClashImportance(0.3)
	structure.ShakeSidechainsAll(1)

	behavior.SetClashImportance(1)
	structure.WiggleAll(20)
end

function ScoreReturn()
	x = current.GetEnergyScore()
	return x-x%0.01
end 

--Return both selections back
function RestoreSelection()
	selection.DeselectAll()
	for j=1, proteinLength do
		if j+1>sel1 and j<sel1+sel1Length then
			selection.Select (j)
		end
		if j+1>sel2 and j<sel2+sel2Length then
			selection.Select (j)
		end
	end
end

--main
bestScore=-999999
bestSlot=0
proteinLength=structure.GetCount ()
wideSelection=2 --number of segments to wide (up and down) the short 1 segment length selection
wideSelection1=wideSelection
selectionLength=0
sel1=0
sel2=0
remixNum=0
remix2Num=0
incSwitch=0

recentbest.Save()
save.Quicksave(1)

--check for selections
for i=1, proteinLength do
	if selection.IsSelected(i) then 
		if selectionLength==0 then 
			if sel1==0 then sel1=i 
				--print ("sel1",i)
			elseif selectionLength == 0 then 
				sel2=i 
				--print ("sel2",i)
			end
		end
		selectionLength=selectionLength+1
		--print ("selectionLength", selectionLength)
	else
		if selectionLength > 0 then 
			if sel2 == 0 then 
				sel1Length=i-sel1
				--print ("sel1Length", sel1Length)
			else sel2Length=i-sel2 end
		end
		selectionLength=0
	end
end

-- Wide the selection1 and selection2 if they are too short
if sel1Length==1 then
	sel1=sel1-wideSelection
	sel1Length=wideSelection*2+1
	print ("Selection1 is too short. Setting length to", sel1Length)
end
if sel2Length==1 then
	sel2=sel2-wideSelection
	sel2Length=wideSelection*2+1
	print ("Selection2 is too short. Setting length to", sel2Length)
end

RestoreSelection()

print ("Sel1 starts at", sel1, "length", sel1Length, " / sel2 starts at", sel2, "length", sel2Length)

-- Remixing selection1 until get some solutions
while remixNum==0 do
	if sel1Length>12 then return end
	--select first selection
	selection.DeselectAll()
	for j=1, proteinLength do
		if j+1>sel1 and j<sel1+sel1Length then
			selection.Select (j)
		end
	end

	remixNum = structure.RemixSelected(2, 95)
	if remixNum==0 then -- make selection wider if no solutions founds
		if incSwitch==0 then -- switch is used to increase selection by 1 seg every round (not by 2)
			sel1=sel1-1    
			sel1Length=sel1Length+1
			incSwitch=1
		else 
			sel1Length=sel1Length+1
			incSwitch=0
		end
		print ("No solutions for selection1. Setting length to", sel1Length)
		
	end
	RestoreSelection()
end

print ("Got", remixNum, "solutions for 1st selection")
wideSelection1=wideSelection -- reset the wide selection counter

for i=2, remixNum+1 do
	save.Quickload(i)

	-- Remixing selection2 until get some solutions
	while remix2Num==0 do
		if sel2Length>12 then return end
		--select second selection
		selection.DeselectAll()
		for j=1, proteinLength do
			if j+1>sel2 and j<sel2+sel2Length then
				selection.Select (j)
			end
		end

		remix2Num = structure.RemixSelected(remixNum+2, 95-remixNum)
		if remix2Num==0 then -- make selection wider if no solutions founds
			if incSwitch==0 then -- switch is used to increase selection by 1 seg every round (not by 2)
				sel2=sel2-1    
				sel2Length=sel2Length+1
				incSwitch=1
			else 
				sel2Length=sel2Length+1
				incSwitch=0
			print ("No solutions for selection2. Setting length to", sel2Length)
			end
		end
		if i==2 then print ("Got", remix2Num, "solutions for 2nd selection") end

		RestoreSelection()
	end
	print ("Have", remixNum-i+2, "*", remix2Num, "=", remix2Num*(remixNum-i+2), " fuzes to go")

	--fuze slot after remix for 2nd selection
	for j=remixNum+2, remix2Num+remixNum+1 do
		save.Quickload(j)
		FastFuze(0.3)
		save.Quicksave(j)
		crntScore = ScoreReturn() 
		best=""
		if crntScore > bestScore then 
			bestScore=crntScore
			bestSlot=j
			save.Quicksave(99)
			--save.Quickload(98)
			--save.Quicksave(97)
			recentbest.Save()
			best="*best"
		end
		print ("Remix", i-1, "-", j-1-remixNum, ":  slot", j, "score", crntScore, " "..best)
	end
end


recentbest.Restore()
save.Quickload(1)
save.Quickload(99)
print ("Max score", bestScore, "from slot", bestSlot)
if remixNum*remix2Num > 1 then
	print ("Fuzing best position")
	Fuze()
end
save.Quicksave(99)
save.Quickload(1) --starting solution
save.Quickload(99)

Comments

[Serca]

Selection1 is too short. Setting length to 5 Selection2 is too short. Setting length to 5 Sel1 starts at 11 length 5 / sel2 starts at 35 length 5 No solutions for selection1. Setting length to 6 Got 3 solutions for 1st selection Got 19 solutions for 2nd selection Have 3 * 19 = 57 fuzes to go Remix 1 - 1 : slot 5 score 9425.38 *best Remix 1 - 2 : slot 6 score 9424.75 Remix 1 - 3 : slot 7 score 9397.59 Remix 1 - 4 : slot 8 score 9367.81 Remix 1 - 5 : slot 9 score 9429.13 *best Remix 1 - 6 : slot 10 score 9485.06 *best Remix 1 - 7 : slot 11 score 9458.42 Remix 1 - 8 : slot 12 score 9332.23 Remix 1 - 9 : slot 13 score 9411.58 Remix 1 - 10 : slot 14 score 8875.3 Remix 1 - 11 : slot 15 score 9484.84 Remix 1 - 12 : slot 16 score 9455.54 Remix 1 - 13 : slot 17 score 9503.47 *best Remix 1 - 14 : slot 18 score 9464.91 Remix 1 - 15 : slot 19 score 9407.39 Remix 1 - 16 : slot 20 score 9404.75 Remix 1 - 17 : slot 21 score 9508.16 *best Remix 1 - 18 : slot 22 score 9365.01 Remix 1 - 19 : slot 23 score 9500.32 Have 2 * 19 = 38 fuzes to go Remix 2 - 1 : slot 5 score 9482.53 Remix 2 - 2 : slot 6 score 9444.31 Remix 2 - 3 : slot 7 score 9448.99 Remix 2 - 4 : slot 8 score 9422.24 Remix 2 - 5 : slot 9 score 9462.3 Remix 2 - 6 : slot 10 score 9453.6 Remix 2 - 7 : slot 11 score 9483.11 Remix 2 - 8 : slot 12 score 9287.09 Remix 2 - 9 : slot 13 score 9417.29 Remix 2 - 10 : slot 14 score 8973.66 Remix 2 - 11 : slot 15 score 9440.95 Remix 2 - 12 : slot 16 score 9470.8 Remix 2 - 13 : slot 17 score 9511.33 *best Remix 2 - 14 : slot 18 score 9467.12 Remix 2 - 15 : slot 19 score 9445.43 Remix 2 - 16 : slot 20 score 9451.98 Remix 2 - 17 : slot 21 score 9516.46 *best Remix 2 - 18 : slot 22 score 9380.64 Remix 2 - 19 : slot 23 score 9464.28 Have 1 * 19 = 19 fuzes to go Remix 3 - 1 : slot 5 score 9481.42 Remix 3 - 2 : slot 6 score 9446.22 Remix 3 - 3 : slot 7 score 9487 Remix 3 - 4 : slot 8 score 9375.82 Remix 3 - 5 : slot 9 score 9507.69 Remix 3 - 6 : slot 10 score 9457.63 Remix 3 - 7 : slot 11 score 9482.97 Remix 3 - 8 : slot 12 score 9330.81 Remix 3 - 9 : slot 13 score 9419.65 Remix 3 - 10 : slot 14 score 8928.37 Remix 3 - 11 : slot 15 score 9454.53 Remix 3 - 12 : slot 16 score 9471.83 Remix 3 - 13 : slot 17 score 9465.82 Remix 3 - 14 : slot 18 score 9470.14 Remix 3 - 15 : slot 19 score 9444.45 Remix 3 - 16 : slot 20 score 9463.66 Remix 3 - 17 : slot 21 score 9475.67 Remix 3 - 18 : slot 22 score 9426.66 Remix 3 - 19 : slot 23 score 9469.54 Max score 9516.46 from slot 21 Fuzing best position

[Formula350]

Request: Instead of having us enter Interface Mode to make the selection (since annoyingly, there's no hotkey to quickly toggle that mode), could you also have it look for two Frozen segments to treat as selections and have it translate it into a selection through the API?
I don't remember which recipe it is that I have, but that's how it worked by being able to use Selection or "Freeze-Proxy" (for lack of better word lol). As I recall, it also have a lead-up dialog box to confirm with the user to use Frozen Segments as "Selected" points. So you could even offer that as well in case someone wants to use this while still having frozen points.

Alternatively… Since pressing Tab (for Segment Information) works even with a recipe running, you could offer input boxes in the configuration dialog window that asks for Segment Number in lieu of u using Frozen ones entirely.

Thanks! :)
-Form

[Perimus]

I cant figure out how to make the initial selection.

[Serca]

I cant figure out how to make the initial selection.

You need to switch to Selection Interface in Menu for that and make selection with ctrl+click or shift+click

Formula350, thank you for your opinion. I understand that Original Interface is not good to run this script. Will be updated soon.

[bravosk8erboy]

looks like quick save slot 1 is starting shape. it uses 2 through 99 for best scores. you can use the following recipe to load all quick save slots into the undo bar. https://fold.it/recipes/108871

[Serca]

New version published here:
https://fold.it/recipes/109182