Recipe: Lig Detector 1.0

created by LociOiling

Profile

• Name: Lig Detector 1.0
• ID: 101024
• Shared with: Public
• Parent: None
• Children:
  • Lig Detector 1.1
• Created on: May 19, 2015 at 19:21 PM UTC
• Updated on: May 19, 2015 at 19:21 PM UTC
• Description:

  Detects ligands and flags suspicious ligands. In puzzles such as 1088, the last segment sometimes incorrectly appears to be a ligand. The segment's non-zero score may be one clue that this is a bug, not the intended design.

Code

--[[
    Lig Detector -- detect presence of possibly spurious "ligands"

    Some foldit puzzles include a "ligand", a non-protein attachment.
    
    The foldit convention is that ligands are attached as the last segment 
    of the puzzle, with a structure code "M".

    On a couple of recent puzzles, a puzzle will sometimes have a ligand 
    in the last position, and sometimes not. This seems to be a defect.

    The problem is that some recipes detect the ligand and avoid working on
    it. This is an issue when the segment has a large negative score. 

    For example, on puzzle 1088, segment 141 is sometimes marked as a 
    ligand, and has a starting score of -345.6. Skipping this segment is 
    enough to guarantee a poor finish on the puzzle.

    This recipe is based in part on "print protein lua v0" by marie_s

    Thanks to spvincent for the structure detection logic.

    Lig Detector looks for all possible ligand sections, and reports 
    the position and total score of each one found. The recipes flags 
    multiple ligands or a ligand that is not at the end. 

    Even a "normal" ligand puzzle may note be a bug, not a true ligand.
    Ligands with a non-zero score are suspect.

    version history
    ---------------

    Lig Detector 1.0 - 2015/05/19 - LociOiling

]]--
--
--  globals section
--
Recipe = "Lig Detector"
Version = "1.0"
ReVersion = Recipe .. " " .. Version

--
--  indexes for structure list
--
STRCTTYP = 1            --structure type
STRCTSTR = 2            --starting segment
STRCTEND = 3            --ending segment
STRCTSCR = 4            --total score
--
--  end of globals section
--

local function round ( x )
    if x == nil then 
        return "nil" 
    end
    return x - x % 0.001
end

--
--  LigDetector: ultra-paranoid method for detecting ligands
--
function LigDetector ()
    local segCnt = structure.GetCount()

    local ligandList = GetStruct ( "M" )
    print ( #ligandList .. " ligands" )
    if #ligandList > 0 then
        if #ligandList == 1 then
            if  ligandList [ 1 ] [ STRCTSTR ] == segCnt
            and ligandList [ 1 ] [ STRCTEND ] == segCnt then
                print ( "normal ligand puzzle, segment " 
                            .. segCnt .. 
                        " represents ligand, score = "
                            .. round ( ligandList [ 1 ] [ STRCTSCR ] )
                      )
                if ligandList [ 1 ] [ STRCTSCR ] ~= 0 then
                    print ( "Caution! Non-zero score may indicate spurious ligand." )
                end
            elseif ligandList [ 1 ] [ STRCTEND ] == segCnt then
                print ( "normal ligand puzzle, segments " 
                            .. ligandList [ 1 ] [ STRCTSTR ] ..
                        "-"
                            .. ligandList [ 1 ] [ STRCTEND ] ..
                        " represent ligand, score = "
                            .. round ( ligandList [ 1 ] [ STRCTSCR ] )
                      )
                if ligandList [ 1 ] [ STRCTSCR ] ~= 0 then
                    print ( "Caution! Non-zero score may indicate spurious ligand." )
                end
            else
                print ( "non-standard ligand puzzle, ligand section not at end" )
                print ( "most ligand-aware recipes will not work correctly" )
                print ( "ligand # 1, start = " 
                            .. ligandList [ 1 ] [ STRCTSTR ] ..
                        ", end = "
                            .. ligandList [ 1 ] [ STRCTEND ] ..
                        ", score = "
                            .. round ( ligandList [ 1 ] [ STRCTSCR ] )
                      )
            end
        else
            print ( "non-standard ligand puzzle, " .. #ligandList .. " ligand sections" )
            print ( "most ligand-aware recipes will not work correctly" )
            for jj = 1, #ligandList do
                print ( "ligand # " 
                            .. jj .. 
                        ", start = " 
                            .. ligandList [ jj ] [ STRCTSTR ] ..
                        ", end = "
                            .. ligandList [ jj ] [ STRCTEND ] ..
                        ", score = "
                            .. round ( ligandList [ jj ] [ STRCTSCR ] )
                      )
            end
        end
    end

    return ligandList
end 

--
--  GetStruct -- return a list of structures of a specified type
--
--  adapted from spvincent's Helix Rebuild
--
function GetStruct ( structT )

    local within_struct = false
  
    local structList = {}
    local structStart = 0
    local structLast = 0
    local structScore = 0

    local segCnt = structure.GetCount() -- do our own count, lets us check for ligands
    for ii = 1, segCnt do
        if ( structure.GetSecondaryStructure ( ii ) == structT ) then
           if ( within_struct == false ) then

                -- start of a new struct

                within_struct = true

                structStart = ii
                structScore = 0
           end
           structLast = ii
           structScore = structScore + current.GetSegmentEnergyScore ( ii )
        elseif ( within_struct == true ) then

            -- end of a struct
           
            within_struct = false
            structList [ #structList + 1 ] = { structT, structStart, structLast, structScore }
        end
    end    

    if ( within_struct == true ) then
        structList [ #structList + 1 ] = { structT, structStart, structLast, structScore }
    end

    return structList
end

function ShowReport ( ligandList )
    local ask = dialog.CreateDialog ( ReVersion )

    if #ligandList == 0 then
        ask.l10 = dialog.AddLabel ( "No ligands detected" )
    else
        local segCnt = structure.GetCount()
        ask.l05 = dialog.AddLabel ( segCnt .. " segments" )
        ask.l10 = dialog.AddLabel ( #ligandList .. " ligand sections found" )
        local asterisk = " "
        local marked = false
        local suspect = false
        for jj = 1, #ligandList do
            if ligandList [ jj ] [ STRCTEND ] ~= segCnt then
                asterisk = "*"
                marked = true
            elseif ligandList [ jj ] [ STRCTSCR ] ~= 0 then
                asterisk = "!"
                suspect = true
            end
            ask [ "lig" .. jj ] = dialog.AddLabel ( 
                                                    "ligand # " 
                                                        .. jj .. 
                                                    ", start = " 
                                                        .. ligandList [ jj ] [ STRCTSTR ] ..
                                                    ", end = "
                                                        .. ligandList [ jj ] [ STRCTEND ] ..
                                                    ", score = "
                                                        .. round ( ligandList [ jj ] [ STRCTSCR ] ) ..
                                                    " " 
                                                        .. asterisk
                                                  )
            asterisk = " "
        end
        if marked then
            ask.l50 = dialog.AddLabel ( "*   non-standard ligand, breaks many recipes" )
        end
        if suspect then
            ask.l60 = dialog.AddLabel ( "!   ligand with non-zero score, may be bug" )
        end
    end
    ask.OK  = dialog.AddButton ( "OK", 1 )  
    dialog.Show ( ask ) 
end


function main ()
    print (  ReVersion )
    print ( "Puzzle: " .. puzzle.GetName () )
    print ( "Track: " .. ui.GetTrackName () )

--
--  search for ligand 
--
    local ligs = LigDetector ()
    ShowReport ( ligs )
--
--  exit via the cleanup function
--
    cleanup ()
end

function cleanup ( error )
    print ( "---" )
--
--  model 100 - print recipe name, puzzle, track, time, score, and gain
--
    local reason
    local start, stop, line, msg
    if error == nil then
        reason = "complete"
    else
    --
    --  model 120 - civilized error reporting,
    --              thanks to Bruno K. and Jean-Bob
    --
        start, stop, line, msg = error:find ( ":(%d+):%s()" )
        if msg ~= nil then
            error = error:sub ( msg, #error )
        end
        if error:find ( "Cancelled" ) ~= nil then
            reason = "cancelled"
        else
            reason = "error"
        end
    end

    print (  ReVersion .. " " .. reason )
    print ( "Puzzle: " .. puzzle.GetName () )
    print ( "Track: " .. ui.GetTrackName () )

    if reason == "error" then
        print ( "Unexpected error detected" )
        print ( "Error line: " .. line )
        print ( "Error: \"" .. error .. "\"" )
    end

end

xpcall ( main, cleanup )
--- end of recipe

Comments

[LociOiling]

On puzzle 1088, and previously on puzzle 1073, some clients show the last segment as a ligand…but some clients don't. This is apparently a bug. In puzzle 1088, one clue is that the "ligand" segment has a non-zero score.

Lig Detector identifies all possible ligands in a puzzle. The convention has been that a ligand appears as the last segment or segments of a puzzle, and has a structure code "M". Lig Detector finds all sections with structure code "M", and reports them in a dialog box and the scriptlog. Multiple ligands, ligands not at the end of the protein, and ligands with non-zero scores are noted as being suspect.

See http://fold.it/portal/node/2000613

[LociOiling]

Another way to find a ligand to use the "EnzDes" coloring under view options. Segments marked as a ligand will show in white.

When you select the "ligand", you find that you won't be able to change its secondary structure, for example to helix. In a design puzzle, however, you'll probably be able to mutate the "ligand".

[LociOiling]

Just observed a new wrinkle on puzzle 1091. Initially, the puzzle showed no ligands with "EnzDes" coloring. Then after "select all" and "auto structures", segment 139 turned white, and the Lig Detector recipe shows it as a ligand.

In this case, "undo" was enough to un-ligandize segment 139.