Recipe: Band All Contacts Adaptive v2.2

created by Susume

Profile

• Name: Band All Contacts Adaptive v2.2
• ID: 101238
• Shared with: Public
• Parent: Band All Contacts Adaptive v2.1
• Children:
  • Band Pruner v0.1
  • Band All Contacts Adaptive v2.2m
  • Band All Contacts Adaptive v2.3
• Created on: July 17, 2015 at 03:28 AM UTC
• Updated on: July 17, 2015 at 03:28 AM 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.

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.

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

MinWeight = 0
MaxWeight = 4
MadeWeight = 0
UnmadeWeight = 0
MadeMult = .9
UnmadeMult = .75
MinMult = .1
MaxMult = 3
MadeStrength = 0.5
UnmadeStrength = 1.5
MinStrength = .1
MaxStrength = 5
MadeBeta = false
UnmadeBeta = false
------------------------

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

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.MadeBeta = dialog.AddCheckbox("Band beta carbons instead of center",MadeBeta)
    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.UnmadeBeta = dialog.AddCheckbox("Band beta carbons instead of center",UnmadeBeta)
    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
        MadeBeta = dlg.MadeBeta.value
        UnmadeWeight = dlg.UnmadeWeight.value
        UnmadeMult = dlg.UnmadeMult.value
        UnmadeStrength = dlg.UnmadeStrength.value
        UnmadeBeta = dlg.UnmadeBeta.value

        print("Made Contacts:")
        print("   band if weight > "..MadeWeight)
        print("   current distance * "..MadeMult)
        print("   strength "..MadeStrength)
        if 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)
        print("   strength "..UnmadeStrength)
        if 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
                else
                    UseBeta = UnmadeBeta
                end
                if UseBeta==false or structure.GetAminoAcid(i)==GLYCINE then
                    Atom1 = CENTER_CARBON
                elseif i==EndSegment then
                    Atom1 = TERMINAL_BETA
                else
                    Atom1 = BETA_CARBON
                end
                if UseBeta==false or structure.GetAminoAcid(j)==GLYCINE then
                    Atom2 = CENTER_CARBON
                elseif j==EndSegment then
                    Atom2 = TERMINAL_BETA
                else
                    Atom2 = BETA_CARBON
                end
                b = band.AddBetweenSegments(i,j,Atom1,Atom2)
                bcount = bcount + 1
                if ContactMade then
                    band.SetGoalLength(b, MadeMult * band.GetLength(b))
                    band.SetStrength(b, MadeStrength)
                else
                    band.SetGoalLength(b, UnmadeMult * band.GetLength(b))
                    band.SetStrength(b, UnmadeStrength)
                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)