Recipe: jfryk Renovate v0.1 (ScriptV2)

created by jfryk

Profile

• Name: jfryk Renovate v0.1 (ScriptV2)
• ID: 33914
• Shared with: Public
• Parent: jfryk Renovate v0.1
• Children: None
• Created on: October 16, 2011 at 21:25 PM UTC
• Updated on: October 16, 2011 at 21:25 PM UTC
• Description:

  Attempts to predict the structure of each segment based on Amino Acid type after converting to all loops. WARNING: Results are very average at the moment. Don't expect much.

Code

--Renovate sets secondary structures to most common structure for AA
--I am not a programmer, advice is appreciated!


numSegs = structure.GetCount()

freeze.UnfreezeAll()
selection.SelectAll()
structure.SetSecondaryStructureSelected("l") -- Convert to loops

print("Starting Renovate...")  --Checks Amino Acid  type and converts to most common structure, leave frist and last as Loops
for seg = 2, numSegs - 1 do
        selection.DeselectAll()
        ca= structure.GetAminoAcid(seg)
       if ca == "a" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("h")
        elseif ca == "c" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l") -- trying Loop instead of Sheet
        elseif ca == "d" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l")
        elseif ca == "e" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("h")
        elseif ca == "f" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "g" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l")
        elseif ca == "h" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "i" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "k" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("h")
        elseif ca == "l" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "m" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("h")
        elseif ca == "n" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l")
        elseif ca == "p" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l")
        elseif ca == "q" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l") --Any structure is OK so try loop
        elseif ca == "r" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "s" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("l")
        elseif ca == "t" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e") 
        elseif ca == "v" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "w" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        elseif ca == "y" then 
                selection.Select(seg)
                structure.SetSecondaryStructureSelected("e")
        else
        end
end


-- Look for "sandwiched" structures and convert them to be the same type
for segHome  = 2, numSegs  -1 do
        cs = structure.GetSecondaryStructure(segHome)
        ps = structure.GetSecondaryStructure(segHome-1)
        ns = structure.GetSecondaryStructure(segHome+1)
        print(ps, cs, ns)
        if ps == ns then
                if ps ~= cs then
                        if freeze.IsFrozen(segHome) ~= 1 then
                                print("Found Sandwich!")
                                selection.Select(segHome)
                                structure.SetSecondaryStructureSelected(ps)
                                selection.Select(segHome)
                                freeze.FreezeSelected(1, 0)
                        else
                        end
                else
                end
        else
        end
end

freeze.UnfreezeAll()


-- Find Helicies that are alone and convert to loop
for seg = 2, numSegs - 1 do
        cs = structure.GetSecondaryStructure(seg)
        ps = structure.GetSecondaryStructure(seg-1)
        ns = structure.GetSecondaryStructure(seg+1)
        print(ps, cs, ns)
        if cs == "H" then
                if cs ~= ps then
                        if cs ~= ns then
                                print("Lonely Helix!")
                                selection.Select(seg)
                                structure.SetSecondaryStructureSelected("l")
                        else
                        end
                else
                end
        else
        end
end

print("Done!")

Comments

[jfryk]

I Learned LUA yesterday and I am not a programmer. This is a ScriptV2 recipe so it only works on the Beta right now.

Like the description says, this recipe is supposed to predict the structures of your segments based on amino acid type.

I plan on using it on De-novo puzzles to help me guess where the structures should be. Do NOT expect it to build complete structures. At least not at this time.

This recipe will NOT gain points, if you didn't already assume that.