Recipe: bandsome2

created by Wipf

Profile

• Name: bandsome2
• ID: 103181
• Shared with: Public
• Parent: bandsome
• Children:
  • L
• Created on: November 21, 2019 at 13:12 PM UTC
• Updated on: November 21, 2019 at 13:12 PM UTC
• Description:

  Interactively place bands between specific atoms in protein. ; Version 2 handles the atom numbers more robustly.

Code

--
-- bandsome: interactively place bands between specific atoms in protein
--
-- by jeff101 8/11/12
-- edited by Wipf
--
function Main()
    -- recipe information in global variables
    RecipeName    = "bandsome"
    RecipeVersion = "2"
    Recipe        = RecipeName .. "" .. RecipeVersion
    -- set logger variable
    wipf.logger = print

    local residue_count = structure.GetCount()
    local band_count = band.GetCount()
    print(string.format( '%s begins at %s on\n   puzzle %s\n   with puzzle ID %d, %d residues, %d bands,\n   and score %.3f.', Recipe, os.date(), puzzle.GetName(), puzzle.GetPuzzleID(), residue_count, band_count, current.GetScore() ))

    local symmetry_copy_count
    if nil ~= structure.GetSymCount then
        symmetry_copy_count = structure.GetSymCount()
    else
        -- Foldit version older than devprev 2019-Okt-29
        -- For testing purposes the count can be set to any number here, it won't crash the recipe.
        symmetry_copy_count = 0
    end

    ---- create dialog with default values ----
    local from_residue = 36
    local to_residue   = 72
    if from_residue > residue_count then
       from_residue = 1
    end
    if to_residue > residue_count then
       to_residue = residue_count
    end
    local ask=dialog.CreateDialog( Recipe .. " - add band" )
    ask.message        = dialog.AddLabel("")
    --ask.top_separator  = dialog.AddLabel("")
    -- display this text if and only if the monomer slider is available
    if symmetry_copy_count > 0 then
        ask.label_w1   = dialog.AddLabel("The first residue is always on the main monomer.")
    end
    ask.from_residue   = dialog.AddSlider("from residue",from_residue,1,residue_count,0)
    ask.from_atom      = dialog.AddLabel("from atom")
    ask.separator1     = dialog.AddLabel("")
    -- If there are no symmetric copies, the slider would have a value range from 0 to 0,
    -- which foldit's sliders don't like. Thus this will only be there on symmetry puzzles.
    ---- Wipf, 2019-Nov-09
    if symmetry_copy_count > 0 then
        ask.to_monomer = dialog.AddSlider( "to monomer", 0, 0,symmetry_copy_count, 0 )
        ask.label_w2   = dialog.AddLabel( "monomer 0 is the main monomer,\nthe others are its symmetric copies" )
    end
    ask.to_residue     = dialog.AddSlider("to residue",to_residue,1,residue_count,0)
    ask.to_atom        = dialog.AddLabel("to atom")
    ask.separator2     = dialog.AddLabel("")
    ask.length         = dialog.AddSlider( "goal length", 2, 0,10, 1 )
    ask.strength       = dialog.AddSlider( "strength",   10, 0,10, 1 )
    ask.bottom_separator = dialog.AddLabel("")
    ask.keeplast=dialog.AddSlider( "keep last: ", 0, -1,2,0 )
    ask.Label7a=dialog.AddLabel("-1: remove all existing bands\n 0: replace previous band")
    --ask.Label7a=dialog.AddLabel("-1: remove all existing bands")
    --ask.Label7b=dialog.AddLabel(" 0: replace previous band")
    ask.Label7c=dialog.AddLabel(" 1: keep previous band")
    ask.Label7d=dialog.AddLabel(" 2: quit now without adding a new band\n ") -- the space in the second line prevents the second line from being ignored, making sure the first line is raised up a little bit
    --ask.Label7e=dialog.AddLabel("")
    ask.label_w2a      = dialog.AddLabel("Different residues have different numbers of atoms.")
    ask.label_w2b      = dialog.AddLabel("Use the 'update' button after selecting the residues\nto update the atom slider ranges.")
    ask.update = dialog.AddButton("update", 2)
    ask.OK = dialog.AddButton("OK", 1)

    function log_to_dialog( message )
        print(message)
        ask.message.label = message
    end
    wipf.logger = log_to_dialog

    -- 0 is always the alpha-carbon
    local   to_monomer
    local from_atom = 0
    local   to_atom = 0
    local band_number = 0
    local band_length
    local band_strength

    ---- get input values ----
    while true do
        -- make sure atom numbers are in range
        local from_atom_count=structure.GetAtomCount(from_residue)
        local to_atom_count=structure.GetAtomCount(    to_residue)
        if from_atom > from_atom_count then
            from_atom = from_atom_count
        end
        if to_atom > to_atom_count then
            to_atom = to_atom_count
        end

        ---- update dialog ----
        ask.from_atom = dialog.AddSlider( "from atom", from_atom, 0, from_atom_count, 0 )
        ask.to_atom   = dialog.AddSlider(   "to atom",   to_atom, 0,   to_atom_count, 0 )
        ---- display dialog and read the new values ----
        local answer = dialog.Show(ask)
        ask.message.label = ""
        if 0 == answer then
            -- user closed the dialog using the red cross at the top corner
            break
        end

        if symmetry_copy_count > 0 then
            to_monomer = ask.to_monomer.value
        end
        from_residue  = ask.from_residue.value
          to_residue  = ask.to_residue.value
        from_atom     = ask.from_atom.value
          to_atom     = ask.to_atom.value
        band_length   = ask.length.value
        band_strength = ask.strength.value
        local keeplast = ask.keeplast.value

        -- update button: skip band deletion and creation
        if 2 ~= answer then
            ---- delete / add bands ----
            if keeplast== -1 then
                print('Deleting all '..band.GetCount()..' previous bands.')
                band.DeleteAll()
            elseif keeplast==0 then
                if band_number > 0 then
                    print('Deleting band '..band_number..'...')
                    band.Delete( band_number )
                    print(tostring(band.GetCount())..' bands remaining.')
                end
            elseif keeplast == 2 then
                break -- this will quit
            end

            local aa1=structure.GetAminoAcid(from_residue)
            local aa2=structure.GetAminoAcid(to_residue)
            local ss1=structure.GetSecondaryStructure(from_residue)
            local ss2=structure.GetSecondaryStructure(to_residue)
            print('Adding band between atom '..from_atom..' on '..aa1..from_residue..' ('..ss1..')\n   and atom '..to_atom..' on '..aa2..to_residue..' ('..ss2..') with strength '..band_strength..',\n   goal length '..band_length..'.')
            band_number = wipf.AddBandBetweenSegments( from_residue, to_residue, from_atom, to_atom, to_monomer )
            if band_number > 0 then
                band.SetGoalLength(band_number,band_length) -- 3.5 is default band length
                band.SetStrength(band_number,band_strength) -- 10 is max, 1 is default
                print(string.format( 'Band %d added, its present length is %.2f.', band_number, band.GetLength(band_number) ))
            else 
                print('Failed to add new band. Still have '..band.GetCount()..' bands.')
            end

        end -- if (update button)
    end -- while
    Cleanup()
end -- Main()


-- table for Wipf's functions and variables
wipf={}

--
-- safety wrapper around band.AddBetweenSegments to prevent
-- the game from hanging up
--
function wipf.AddBandBetweenSegments( from_segment, to_segment, from_atom, to_atom, to_symmetric_copy )
    -- check atom indices
    if nil ~= from_atom then
        if from_atom < 0 or from_atom > structure.GetAtomCount(from_segment) then
            if nil ~= wipf.logger then
                wipf.logger(string.format( "Invalid atom index %d for residue %d (it has %d atoms)!", from_atom, from_segment, structure.GetAtomCount(from_segment) ))
            end
            return 0
        end
    end
    if nil ~= to_atom then
        if to_atom < 0 or to_atom > structure.GetAtomCount(to_segment) then
            if nil ~= wipf.logger then
                wipf.logger(string.format( "Invalid atom index %d for residue %d (it has %d atoms)!", to_atom, to_segment, structure.GetAtomCount(to_segment) ))
            end
            return 0
        end
    end
    -- add band
    if nil ~= structure.GetSymCount then
        -- devprev only currently (2019-Nov-10)
        return band.AddBetweenSegments( from_segment, to_segment, from_atom, to_atom, to_symmetric_copy )
    else
        return band.AddBetweenSegments( from_segment, to_segment, from_atom, to_atom )
    end
end


--
-- rounds to nearest integer
--
function round(val)
    local res=math.floor(val)
    if val-res>=0.5 then
        res=res+1
    end
    return res
end

--
-- cleanup routine to be called whenever the recipe terminates,
-- optionally with an error message
--
function Cleanup( error )
    -- Model 120: error reporting
    local reason, start, stop, line, msg
    if nil == error then
        reason = "complete"
    else
        start, stop, line, msg = error:find( ":(%d+):%s()" )
        if msg ~= nil then
            error = error:sub( msg )
        end
        if error:find( "Cancelled" ) ~= nil then
            reason = "cancelled"
        else
            reason = "error"
            print( "---- recipe error ----" )
            print( "Line number: " .. line )
            print( "Error message: " .. error )
        end
    end
    -- Model 100: report recipe, termination reason, puzzle and track
    print( "---- terminated: " .. reason .. " ----" )
    print('Ending with '..band.GetCount()..' bands for '..structure.GetCount()..' residues.')
    print( "Puzzle: " .. puzzle.GetName() )
    print( "Track: " .. ui.GetTrackName() )
    print( "Recipe: " .. Recipe )
    print('All done at '..os.date()..'.')
    print( "==== END ====" )
end

-- start main script and catch if it crashes
-- according to rule 'Model 000'
xpcall(Main,Cleanup)

Comments

[Wipf]

I just updated the recipe to enable support for banding to the symmetric copies.