Recipe: Band All Contacts Adaptive v2.2m

created by Madde

Profile

• Name: Band All Contacts Adaptive v2.2m
• ID: 101303
• Shared with: Public
• Parent: Band All Contacts Adaptive v2.2
• Children: None
• Created on: August 11, 2015 at 18:00 PM UTC
• Updated on: August 11, 2015 at 18:00 PM UTC
• Description:

  Places a band wherever there is a green dot on the contact map with weight greater than a chosen minimum; min weight of 0 bands all contacts. Dialog lets you set band length and strength based on whether the contact is currently made or not. Option to band beta carbons: contact distance in foldit is between beta carbons (the first joint in the sidechain); this can help rotate the segments to make more contacts. ---------------------------------------------- Original script by Susume, v2.2m by Madde ; Added option to set band strengths according to contact weights. Added option to band only hydrophobics to beta carbons.

Code

-- Places a band wherever there is a green dot on the contact map.
-- Dialog allows you to set different minimum contact weight, band length and strength for
-- unmade vs. made contacts.
-- Use length multiplier greater than 1.0 for "push" bands.
-- v2.1 Added option to band to beta carbons instead of the default central carbons
--   Beta carbons are the first joint in the sidechains and can help twist the
--   backbone where needed to make more contacts.
-- v2.2 Added sliders to choose minimum contact weights to be banded.
--   Default minimum weight of 0 means all predicted contacts will be banded.
-- Original script by Susume, v2.2m by Madde
-- v2.2m Added option to set band strengths according to contact weights.
--       (if checked then Strength slider will function as multiplier)
--   Added option to band only hydrophobics to beta carbons.

------------------------
--defaults for dialog box

MinWeight = 0
MaxWeight = 4
MadeWeight = 0
UnmadeWeight = 0
MadeMult = .9
UnmadeMult = .75
MinMult = .1
MaxMult = 3
MadeStrength = 1.0
UnmadeStrength = 1.0
MinStrength = .1
MaxStrength = 5
MadeBeta = false
UnmadeBeta = false
MadeWrength = false
UnmadeWrength = false
MadePhobicsBeta = false
UnmadePhobicsBeta = false
------------------------

BETA_CARBON = 5
TERMINAL_BETA = 6
CENTER_CARBON = 2 --this is the default atom for bands to attach to
GLYCINE = "g"
AA = "z"
SCRIPT = "Band All Contacts Adaptive"
VERSION = "2.2m"

bcount = 0
EndSegment = structure.GetCount()


function GetParams()
	dlg = dialog.CreateDialog(SCRIPT.." "..VERSION)
	dlg.l1a = dialog.AddLabel("--------  Bands on Made Contacts  --------")
	dlg.l1b = dialog.AddLabel("Band if contact weight greater than")
	dlg.MadeWeight = dialog.AddSlider("Min Weight:",MadeWeight,MinWeight,MaxWeight,1)
	dlg.l1c = dialog.AddLabel("Multiply current distance by")
	dlg.MadeMult = dialog.AddSlider("Multiplier:",MadeMult,MinMult,MaxMult,2)
	dlg.MadeStrength = dialog.AddSlider("Strength:",MadeStrength,MinStrength,MaxStrength,1)
	dlg.MadeWrength = dialog.AddCheckbox("Set strengths according to weights",MadeWrength)
	dlg.l1d = dialog.AddLabel("(if checked then Strength slider will act as multiplier)")
	dlg.MadeBeta = dialog.AddCheckbox("Band beta carbons instead of center (all AAs)",MadeBeta)
	dlg.MadePhobicsBeta = dialog.AddCheckbox("Band beta carbons instead of center (phobics only)",MadePhobicsBeta)
	dlg.l2a = dialog.AddLabel("--------  Bands on Unmade Contacts  --------")
	dlg.l2b = dialog.AddLabel("Band if contact weight greater than")
	dlg.UnmadeWeight = dialog.AddSlider("Min Weight:",UnmadeWeight,MinWeight,MaxWeight,1)
	dlg.l2c = dialog.AddLabel("Multiply current distance by")
	dlg.UnmadeMult = dialog.AddSlider("Multiplier:",UnmadeMult,MinMult,MaxMult,2)
	dlg.UnmadeStrength = dialog.AddSlider("Strength:",UnmadeStrength,MinStrength,MaxStrength,1)
	dlg.UnmadeWrength = dialog.AddCheckbox("Set strengths according to weights",UnmadeWrength)
	dlg.l2d = dialog.AddLabel("(if checked then Strength slider will act as multiplier)")
	dlg.UnmadeBeta = dialog.AddCheckbox("Band beta carbons instead of center (all AAs)",UnmadeBeta)
	dlg.UnmadePhobicsBeta = dialog.AddCheckbox("Band beta carbons instead of center (phobics only)",UnmadePhobicsBeta)
	dlg.ok = dialog.AddButton("OK", 1)
	dlg.cancel = dialog.AddButton("Cancel", 0)

	if dialog.Show(dlg) > 0 then
		MadeWeight = dlg.MadeWeight.value
		MadeMult = dlg.MadeMult.value
		MadeStrength = dlg.MadeStrength.value
		MadeWrength = dlg.MadeWrength.value
		MadeBeta = dlg.MadeBeta.value
		MadePhobicsBeta = dlg.MadePhobicsBeta.value
		UnmadeWeight = dlg.UnmadeWeight.value
		UnmadeMult = dlg.UnmadeMult.value
		UnmadeStrength = dlg.UnmadeStrength.value
		UnmadeWrength = dlg.UnmadeWrength.value
		UnmadeBeta = dlg.UnmadeBeta.value
		UnmadePhobicsBeta = dlg.UnmadePhobicsBeta.value

		print("Made Contacts:")
		print("   band if weight > "..MadeWeight)
		print("   current distance * "..MadeMult)
		if MadeWrength then
			print("   strength according to weight * "..MadeStrength)
		else print("   strength "..MadeStrength)
		end
		if MadePhobicsBeta then
			print("   band to beta carbons (hydrophobics only)")
		elseif MadeBeta then
			print("   band to beta carbons")
		else print("   normal band position")
		end

		print("Unmade Contacts:")
		print("   band if weight > "..UnmadeWeight)
		print("   current distance * "..UnmadeMult)
		if UnmadeWrength then
			print("   strength according to weight * "..UnmadeStrength)
		else print("   strength "..UnmadeStrength)
		end
		if UnmadePhobicsBeta then
			print("   band to beta carbons (hydrophobics only)")
		elseif UnmadeBeta then
			print("   band to beta carbons")
		else print("   normal band position")
		end
		return true
	else
		print("Dialog cancelled")
		return false
	end
end

function MakeBands()
	for i = 1, EndSegment-2 do
		for j = i+2, EndSegment do
			Weight = contactmap.GetHeat(i, j)
			ContactMade = contactmap.IsContact(i,j)
			if (ContactMade and Weight>MadeWeight) or (ContactMade==false and Weight>UnmadeWeight) then
				if ContactMade then
					UseBeta = MadeBeta
					UsePhobicsBeta = MadePhobicsBeta
				else
					UseBeta = UnmadeBeta
					UsePhobicsBeta = UnmadePhobicsBeta
				end
				if UsePhobicsBeta then
					AA = structure.GetAminoAcid(i)
					if i==EndSegment then
						Atom1 = TERMINAL_BETA
					elseif AA=="a" or AA=="c" or AA=="f" or AA=="i" or AA=="l" or AA=="m" or AA=="p" or AA=="v" or AA=="w" or AA=="y" then 
						Atom1 = BETA_CARBON
					else
						Atom1 = CENTER_CARBON
					end
				else				
					if UseBeta==false or structure.GetAminoAcid(i)==GLYCINE then
						Atom1 = CENTER_CARBON
					elseif i==EndSegment then
						Atom1 = TERMINAL_BETA
					else
						Atom1 = BETA_CARBON
					end
				end
				if UsePhobicsBeta then
					AA = structure.GetAminoAcid(j)
					if j==EndSegment then
						Atom2 = TERMINAL_BETA
					elseif AA=="a" or AA=="c" or AA=="f" or AA=="i" or AA=="l" or AA=="m" or AA=="p" or AA=="v" or AA=="w" or AA=="y" then 
						Atom2 = BETA_CARBON
					else
						Atom2 = CENTER_CARBON
					end
				else
					if UseBeta==false or structure.GetAminoAcid(j)==GLYCINE then
						Atom2 = CENTER_CARBON
					elseif j==EndSegment then
						Atom2 = TERMINAL_BETA
					else
						Atom2 = BETA_CARBON
					end
				end
				b = band.AddBetweenSegments(i,j,Atom1,Atom2)
				bcount = bcount + 1
				if ContactMade then
					band.SetGoalLength(b, MadeMult * band.GetLength(b))
					if MadeWrength then
						band.SetStrength(b, MadeStrength * Weight)
					else band.SetStrength(b, MadeStrength)
					end
				else
					band.SetGoalLength(b, UnmadeMult * band.GetLength(b))
					if UnmadeWrength then
						band.SetStrength(b, UnmadeStrength * Weight)
					else band.SetStrength(b, UnmadeStrength)
					end
				end
			end
		end
	end
end

-------------------

function Cleanup()
	print(bcount.." contact bands placed")
	print(band.GetCount().." total bands")
end

function Main()
	if GetParams() then
		MakeBands()
	end
	Cleanup()
end

xpcall(Main, Cleanup)

Comments

[Madde]

If you check "Set strengths according to weighs" then the "Strength" slider will function as a multiplier. So when it's on its default 1.0 a band for a contact with weight 0.522 will be set to strength 0.52, on 0.5 the strength would be 0.26, on 0.1 it'd be 0.05 etc.

[Madde]

Added option to band only hydrophobics to beta carbons.

[Skippysk8s]

great to be able to match bands and contact strength! was very tedious by hand

[Vredeman]

It would probably outdo the current version