Recipe: print protein 2.1

created by LociOiling

Profile

• Name: print protein 2.1
• ID: 101963
• Shared with: Public
• Parent: print protein 2.0
• Children:
  • print protein 2.2
• Created on: March 25, 2016 at 01:57 AM UTC
• Updated on: March 25, 2016 at 01:57 AM UTC
• Description:

  Updated version of "print protein lua2 V0" by marie_s. Version 2.1 includes rulers.

Code

--[[
    print protein
    
    info on the protein - 

    Concatenation of recipes, part of recipes or functions by:
        Tlaloc, spvincent, seagate, John McLeod, Crashguard303,
        Gary Forbis and authors on wiki

    Now with code from Timo van der Laan and and more code from
    spvincent.

    Borrowed HerobrinesArmy's idea for copy-and-paste on the 
    segment score table, plus option for including atom and
    rotamer counts.

    Intended use:
    1. Run
    2. Open the script log (scriptlog.default.xml) in a text editor.
    3. Strip off the start and end lines and save it as a text file with another name.
    4. Import that into Excel as a comma-delimited text file.

    Alternately:

    3. Select and copy the lines containing the score detail.
    4. Paste into a spreadsheet or other program that accepts
       CSV (comma-separated values) format.

    Yet another alternative:

    3.  Select and copy the "score report" from the new "copy-and-paste" dialog.
    4.  Paste into the spreadsheet of your choice.

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

    print protein lua v0 - 2011/08/15 - marie_s (Marie Suchard)

    print protein 2.0 - 2015/05/13 - LociOiling
        + add dialog
        + use active subscores
        + restrict scope of most variables
        + convert amino acid table to keyed format
        + added kludges specific to puzzle 879 (hope they are never needed)
        + add adjustable rounding, eliminate existing "no trunc" logic
        + made tab the default delimiter, with comma or semicolon as alternates
        + add detailed scoring information
        + add "modifiable sections" report, make original "mutable" report optional
        + make "mini contact table" optional
        + in subscores report, add option for atom and rotamer counts, make
          hydropathy index optional
        + add warnings for unknown amino acid or secondary structure codes, 
          subtotal mismatches, suspect ligands
        + and copy-and-paste dialog for subscores, primary and secondary structure

    print protein 2.1 - 2016/03/23 - LociOiling
        + add ruler
]]--
--
--  globals section
--
Recipe = "print protein"
Version = "2.1"
ReVersion = Recipe .. " " .. Version

segCnt = structure.GetCount()
segCnt2 = segCnt
isLigand = false

subScores = {}  -- subscore table
gTotal = 0      -- grand total all subscores

BoxScore = {
    tSubScores = 0,     -- total of active subscores, all segments
    tSegScores = 0,     -- total of segment scores
    tScoreFilt = 0,     -- total score, filters on
    tScoreFOff = 0,     -- total score, filters off
    tScoreNrgy = 0,     -- total energy score
    tScoreBonus = 0,    -- total filter bonus
    tScoreForm = 0,     -- subscores + filter bonus + 8000
    tScoreDark = 0,     -- total "dark" score
}

kHydro = false      -- include hydropathy index
kAtom = false       -- include atom count
kRotamer = false    -- include rotamer count

kRound = 3          -- number of digits for rounding
kFax = 10 ^ -kRound -- initial rounding factor

dtab = true
delim = "\t"    -- default delimiter is tab character
dcomma = false  -- allow user to select comma
dsemic = false  -- allow user to select semicolon

kMutDet = false -- detailed mutable report
kContact = false -- contact table
--
--  indexes for helixList, sheetList, structList
--
STRCTTYP = 1            --structure type
STRCTSTR = 2            --starting segment
STRCTEND = 3            --ending segment
STRCTUSE = 4            --use flag (boolean)
STRCTSCR = 5            --score
--
--  end of globals section
--

--
--  function print score by spvincent
--
function round ( x )
    if x == nil then 
        return "nil" 
    end
    return x - x % kFax
end

--
--  Segment set and list module
--  Notice that most functions assume that the sets are well formed
--  (=ordered and no overlaps)
--  02-05-2012 TvdL Free to use for non commercial purposes
--

function SegmentListToSet ( list ) -- retirer doublons
    local result = {}
    local f = 0
    local l = -1
    table.sort ( list )
    for ii = 1, #list do
        if list [ ii ] ~= l + 1 and list [ ii ] ~= l then
            -- note: duplicates are removed
            if l > 0 then result [ #result + 1 ] = { f, l } end
            f = list [ ii ]
        end
        l = list [ ii ]
    end
    if l > 0 then result [ #result + 1 ] = { f, l } end
    return result
end

function SegmentSetToList ( set ) -- faire une liste a partir d'une zone
    local result = {}
    for ii = 1, #set do
        for k = set [ ii ] [ 1 ], set [ ii ]  [ 2 ] do
            result [ #result + 1 ] = k
        end
    end
    return result
end

function SegmentCleanSet ( set )
-- Makes it well formed
    return SegmentListToSet ( SegmentSetToList ( set ) )
end

function SegmentInvertSet ( set, maxseg )
-- Gives back all segments not in the set
-- maxseg is added for ligand
    local result={}
    if maxseg == nil then 
        maxseg = structure.GetCount () 
    end
    if #set == 0 then return { { 1, maxseg } } end
    if set [ 1 ] [ 1 ] ~= 1 then 
        result [ 1 ] = { 1, set [ 1 ]  [ 1 ] - 1 } 
    end
    for i = 2, #set do
        result [ #result + 1 ] = { set [ i - 1 ] [ 2 ] + 1, set [ i ] [ 1 ] - 1}
    end
    if set [ #set ] [ 2 ] ~= maxseg then 
        result [ #result + 1 ] = { set [ #set ] [ 2 ] + 1, maxseg } 
    end
    return result
end

function SegmentInList ( s, list ) -- verifier si segment est dans la liste
    table.sort ( list )
    for ii = 1, #list do
        if list [ ii ] == s then 
            return true
        elseif list [ ii ] > s then 
            return false
        end
    end
    return false
end

function SegmentInSet ( set, s ) --verifie si segment est dans la zone
    for ii = 1, #set do
        if s >= set [ ii ] [ 1 ] and s <= set [ ii ] [ 2 ] then 
            return true
        elseif s < set [ ii ] [ 1 ] then 
            return false
        end
    end
    return false
end

function SegmentJoinList ( list1, list2 ) -- fusionner 2 listes de segments
    local result = list1
    if result == nil then 
        return list2 
    end
    for ii = 1, #list2 do 
        result [ #result + 1 ] = list2 [ ii ] 
    end
    table.sort ( result )
    return result
end

function SegmentJoinSet ( set1, set2 ) --fusionner (ajouter) 2 zones
    return SegmentListToSet ( SegmentJoinList ( SegmentSetToList ( set1 ), SegmentSetToList ( set2 ) ) )
end

function SegmentCommList ( list1, list2 ) -- chercher intersection de 2 listes
    local result = {}
    table.sort ( list1 )
    table.sort ( list2 )
    if #list2 == 0 then return result end
    local j = 1
    for ii = 1, #list1 do
        while list2 [ j ] < list1 [ ii ] do
            j = j + 1
            if j > #list2 then return result end
        end
        if list1 [ ii ] == list2 [ j ] then result [ #result + 1 ] = list1 [ ii ] end
    end
    return result
end

function SegmentCommSet ( set1, set2 ) -- intersection de 2 zones
    return SegmentListToSet ( SegmentCommList ( SegmentSetToList ( set1 ), SegmentSetToList ( set2 ) ) )
end

function SegmentSetMinus ( set1, set2 )
    return SegmentCommSet ( set1, SegmentInvertSet ( set2 ) )
end

function SegmentPrintSet ( set )
    print ( SegmentSetToString ( set ) )
end

function SegmentSetToString ( set ) -- pour pouvoir imprimer
    local line = ""
    for ii = 1, #set do
        if ii ~= 1 then line = line .. ", " end
        line = line .. set [ ii ] [ 1 ] .. "-" .. set [ ii ] [ 2 ]
    end
    return line
end

function SegmentSetInSet ( set, sub )
    if sub == nil then 
        return true 
    end
    -- Checks if sub is a proper subset of set
    for ii = 1, #sub do
        if not SegmentRangeInSet ( set, sub [ ii ] ) then return false end
    end
    return true
end

function SegmentRangeInSet ( set, range ) --verifier si zone est dans suite
    if range == nil or #range == 0 then return true end
    local bb = range [ 1 ]
    local ee = range [ 2 ]
    for ii = 1, #set do
        if bb >= set [ ii ] [ 1 ] and bb <= set [ ii ] [ 2 ] then
            return ( ee <= set [ ii ] [ 2 ] )
        elseif ee <= set [ ii ] [ 1 ] then 
            return false 
        end
    end
    return false
end

function SegmentSetToBool ( set ) --vrai ou faux pour chaque segment utilisable ou non
    local result = {}
    for ii = 1, structure.GetCount () do
        result [ ii ] = SegmentInSet ( set, ii )
    end
    return result
end
--- End of Segment Set module

-- Module Find Segment Types
function FindMutablesList ()
    local result = {}
    for ii = 1, segCnt2 do 
        if structure.IsMutable ( ii ) then 
            result [ #result + 1 ] = ii 
        end 
    end
    return result
end
function FindMutables()
    return SegmentListToSet ( FindMutablesList () )
end

function FindFrozenList ()
    local result = {}
    for ii = 1, segCnt2 do 
        if freeze.IsFrozen ( ii ) then 
            result [ #result + 1 ] = ii 
        end 
    end
    return result
end
function FindFrozen ()
    return SegmentListToSet ( FindFrozenList () )
end

function FindLockedList ()
    local result = {}
    for ii = 1, segCnt2 do 
        if structure.IsLocked ( ii ) then 
            result [ #result + 1 ] = ii 
        end 
    end
    return result
end
function FindLocked ()
    return SegmentListToSet ( FindLockedList () )
end

function FindZeroScoreList ()
    local result = {}
    for ii = 1, segCnt do 
        local sub = 0
        for jj = 1, #subScores do
            sub = sub + current.GetSegmentEnergySubscore ( ii, subScores [ jj ] [ 1 ] )
        end
        if sub == 0 then 
            result [ #result + 1 ] = ii 
        end 
    end
    return result
end

function FindZeroScore ()
    return SegmentListToSet ( FindZeroScoreList () )
end

function FindSelectedList ()
    local result = {}
    for ii = 1, segCnt do 
        if selection.IsSelected ( ii ) then 
            result [ #result + 1 ] = ii 
        end 
    end
    return result
end

function FindSelected()
    return SegmentListToSet ( FindSelectedList () )
end

function FindAAtypeList ( aa )
    local result = {}
    for ii = 1, segCnt2 do
        if structure.GetSecondaryStructure ( ii ) == aa then 
            result [ #result + 1 ] = ii 
        end
    end
    return result
end
function FindAAtype ( aa )
    return SegmentListToSet ( FindAAtypeList ( aa ) )
end

function FindAminotype ( at ) --NOTE: only this one gives a list not a set
    local result={}
    for ii = 1, segCnt2 do
        if structure.GetAminoAcid ( ii ) == at then 
            result [ #result + 1 ] = ii 
        end
    end
    return result
end
--
-- end Module Find Segment Types
--

--
--  count segments, check for ligand 
--
function GetSeCount ()
    segCnt = structure.GetCount()

--
--  ultra-paranoid method for detecting ligands
--
    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, segment " 
                            .. segCnt .. 
                        ", score = "
                            .. round ( ligandList [ 1 ] [ STRCTSCR ] ) 
                      )
                segCnt2 = segCnt - 1
                if ligandList [ 1 ] [ STRUCTSCR ] ~= 0 then
                    print ( "WARNING: normal ligand with non-zero score" )
                end
            elseif ligandList [ 1 ] [ STRCTEND ] == segCnt then
                print ( "normal ligand, segments " 
                            .. ligandList [ 1 ] [ STRCTSTR ] ..
                        "-"
                            .. ligandList [ 1 ] [ STRCTEND ] ..
                        ", score = "
                            .. round ( ligandList [ jj ] [ STRCTSCR ] ) 
                      )
                if ligandList [ 1 ] [ STRUCTSCR ] ~= 0 then
                    print ( "WARNING: suspect multi-segment ligand with non-zero score, segment count not adjusted" )
                else
                    segCnt2 = ligandList [ 1 ] [ STRCTSTR ] - 1
                end
            else
                print ( "WARNING: non-standard ligand, ligand not at end" )
                print ( "most ligand-aware recipes will not work correctly" )
                print ( "ligand # 1, start = " 
                            .. ligandList [ jj ] [ STRCTSTR ] ..
                        ", end = "
                            .. ligandList [ jj ] [ STRCTEND ] ..
                        ", score = "
                            .. round ( ligandList [ jj ] [ STRCTSCR ] )
                      )
                print ( "WARNING: suspect ligand, segment count not adjusted" )
            end
        else
            print ( "WARNING: non-standard ligands, " .. #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
            print ( "WARNING: suspect ligands, segment count not adjusted" )
        end
    end

    if segCnt2 == segCnt then
        print ( "segment count = " .. segCnt )
    else
        print ( "original segment count = " .. segCnt )
        print ( "adjusted segment count = " .. segCnt2 )
    end
    return ligandList
end 

--
--  build segments table, without any ligand segments
--
function tablesegment ()
--
--  indexes for amino acid table
--
AASHORT = 1         -- three-letter code
AALONG = 2          -- full name
AAPOLARITY = 3      -- polarity (text)
AAACIDITY = 4       -- acidity (text)
AAHYDROPATHY = 5    -- hydropathy index
--
--  residues with -- in front (commented) are not in Foldit (as of Nov 15, 2010)
--  one-letter amino acid code is the table key
--
local AminoAcids = {
           a = { "Ala", "Alanine",        "nonpolar", "neutral",   1.8 },
        -- b = { "Asx", "Asparagine or Aspartic acid" }, 
           c = { "Cys", "Cysteine",       "nonpolar", "neutral",   2.5 },
           d = { "Asp", "Aspartate",      "polar",    "negative", -3.5 },
           e = { "Glu", "Glutamate",      "polar",    "negative", -3.5 },
           f = { "Phe", "Phenylalanine",  "nonpolar", "neutral",   2.8 },
           g = { "Gly", "Glycine",        "nonpolar", "neutral",  -0.4 },
           h = { "His", "Histidine",       "polar",   "neutral",  -3.2 },
           i = { "Ile", "Isoleucine",     "nonpolar", "neutral",   4.5 },
        -- j = { "Xle", "Leucine or Isoleucine" },  
           k = { "Lys", "Lysine",          "polar",   "positive", -3.9 },
           l = { "Leu", "Leucine",        "nonpolar", "neutral",   3.8 },
           m = { "Met", "Methionine ",    "nonpolar", "neutral",   1.9 },
           n = { "Asn", "Asparagine",     "polar",    "neutral",  -3.5 },
        -- o = { "Pyl", "Pyrrolysine" }, 
           p = { "Pro", "Proline",        "nonpolar", "neutral",  -1.6 },
           q = { "Gln", "Glutamine",      "polar",    "neutral",  -3.5 },
           r = { "Arg", "Arginine",       "polar",    "positive", -4.5 },
           s = { "Ser", "Serine",         "polar",    "neutral",  -0.8 },
           t = { "Thr", "Threonine",      "polar",    "neutral",  -0.7 },
        -- u = { "Sec", "Selenocysteine" },
           v = { "Val", "Valine",         "nonpolar", "neutral",   4.2 },
           w = { "Trp", "Tryptophan",     "nonpolar", "neutral",  -0.9 },
           x = { "Xaa", "Unspecified/unknown", "", "", 0 }, -- kludge for puzzle 879
           y = { "Tyr", "Tyrosine",       "polar",    "neutral",  -1.3 },
        -- z = { "Glx", "Glutamine or glutamic acid" } ,
    }
    local table = { {} }
    for ii = 1, segCnt2 do
        table [ ii ] = {}
        local aac = structure.GetAminoAcid ( ii )
        if AminoAcids [ aac ] == nil then -- bizarro kludge code "unk" used 
                                          -- for segment 134, puzzle 879
            print ( "WARNING: unknown amino acid \'" 
                        .. aac .. 
                    "\' at segment " 
                        .. ii .. 
                    ", code \'x\' substituted" 
                  )
            aac = "x"
        end
        table [ ii ] [ 1 ] = aac
        table [ ii ] [ 2 ] = AminoAcids [ aac ] [ AASHORT ]
        table [ ii ] [ 3 ] = AminoAcids [ aac ] [ AALONG ]
        table [ ii ] [ 4 ] = AminoAcids [ aac ] [ AAHYDROPATHY ]
        table [ ii ] [ 5 ] = structure.GetSecondaryStructure ( ii )
        if  table [ ii ] [ 5 ] ~= "H"
        and table [ ii ] [ 5 ] ~= "E"
        and table [ ii ] [ 5 ] ~= "L" 
        and table [ ii ] [ 5 ] ~= "M" then
            print ( "WARNING: unknown secondary structure code \'"
                        .. table [ ii ] [ 5 ] ..
                    "\' at segment " 
                        .. ii
                  )
        end
    end
    return table
end

--
--  tlaloc functions to print sequence of letter 
--
function BuildSequence ( table )
    local seqstring = ""
    local hydrostring = ""
    local strucstring = ""
    for ii = 1, segCnt2 do
        seqstring = seqstring .. table [ ii ] [ 1 ]
        if structure.IsHydrophobic ( ii ) then
            hydrostring = hydrostring .. "i"
        else
            hydrostring = hydrostring .. "e" 
        end 
        strucstring = strucstring .. table [ ii ] [ 5 ] 
    end 
    local onez = ""
    local tenz = ""
    local hunz = ""
    local numz = 1
    for ii = 1, segCnt2 do
        onez = onez .. numz % 10
        if ii % 10 == 0 then
            local ff = ii
            if ff >= 100 then
                ff = ff % 100
            end
            tenz = tenz .. ( ff - ( ff % 10 ) ) / 10
            if ii >= 100 then
                local ff = ii
                if ff >= 1000 then
                   ff = ff % 1000
                end
                hunz = hunz .. ( ff - ( ff % 100 ) ) / 100
            else
                hunz = hunz .. " "
            end
        else
            tenz = tenz .. " "
            hunz = hunz .. " "
        end
        numz = numz + 1
        if numz > 10 then
            numz = 1
        end
    end

    print ( "sequence with single-letter amino acid codes for searching PDB" )
    if segCnt2 >= 100 then
        print ( hunz )
    end
    print ( tenz )
    print ( onez )
    print ( seqstring )
    print ( "" )
    print ( "sequence with i if hydrophobic" )
    if segCnt2 >= 100 then
        print ( hunz )
    end
    print ( tenz )
    print ( onez )
    print ( hydrostring )
    print ( "" )
    print ( "sequence of structure" )
    if segCnt2 >= 100 then
        print ( hunz )
    end
    print ( tenz )
    print ( onez )
    print ( strucstring )
    print ( "" )
    print ( "--" )
    return seqstring, hydrostring, strucstring 
end 

--
--  find modifiable sections
--
function FindModifiable ()
--
    local flocked = FindLocked ()
    --print ( #flocked .. " locked sections" )
    for kk = 1, #flocked do
        print ( "locked section " 
                    .. kk .. 
                ": " 
                    .. flocked [ kk ] [ 1 ] ..
                "-" 
                    .. flocked [ kk ] [ 2 ] )
    end
--
    local funlocked = SegmentInvertSet ( flocked )
    --print ( #funlocked .. " unlocked sections" )
    for kk = 1, #funlocked do
        print ( "unlocked section " 
                    .. kk .. 
                ": " 
                    .. funlocked [ kk ] [ 1 ] ..
                "-" 
                    .. funlocked [ kk ] [ 2 ] )
    end
--
    local zeroScore = FindZeroScore ()
    --print ( #zeroScore .. " zero score sections" )
    for kk = 1, #zeroScore do
        print ( "zero score section " 
                    .. kk .. 
                ": " 
                    .. zeroScore [ kk ] [ 1 ] ..
                "-" 
                    .. zeroScore [ kk ] [ 2 ] )
    end
--
    if #flocked == 1 and #zeroScore > 0 then
        local LockedNZ = SegmentInvertSet ( zeroScore, flocked [ 1 ] [ 2 ] )
        for kk = 1, #LockedNZ do
            print ( "locked, non-zero score section " 
                        .. kk .. 
                    ": " 
                        .. LockedNZ [ kk ] [ 1 ] ..
                    "-" 
                        .. LockedNZ [ kk ] [ 2 ] )
        end
        if flocked [ 1 ] [ 1 ] == 1 then
            segStart = math.min ( flocked [ 1 ] [ 2 ] + 1, segCnt2 )
        end
    end
--
    local mutables = FindMutables ()
    --print ( #mutables .. " mutable sections" )
    for kk = 1, #mutables do
        print ( "mutable section " 
                    .. kk .. 
                ": " 
                    .. mutables [ kk ] [ 1 ] ..
                "-" 
                    .. mutables [ kk ] [ 2 ] )
    end
--
    local lockmut = SegmentCommSet ( flocked, mutables )
    --print ( #lockmut .. " locked, mutable sections" )
    for kk = 1, #lockmut do
        print ( "locked, mutable section " 
                    .. kk .. 
                ": " 
                    .. lockmut [ kk ] [ 1 ] ..
                "-" 
                    .. lockmut [ kk ] [ 2 ] )
    end
end

--
--  find mutable segments
--
function FindMutable ( table ) 
    local mutable = {}
    local mutablestring = ''
    for ii = 1, segCnt2 do
        if structure.IsMutable ( ii ) == true then        
            mutable [ #mutable + 1 ] = ii
        end 
    end 
    print ( #mutable .. " mutables found" )
    if #mutable > 0 then
        print ( "n" 
                    .. delim .. 
                "segment" 
                    .. delim ..
                "aacode"
                    .. delim ..
                "aaname"
              )
    end
    for ii = 1, #mutable do
        print ( ii
                    .. delim ..
                mutable[ii]
                    .. delim ..
                table [ mutable [ ii ] ] [ 1 ]
                    .. delim ..
                table [ mutable [ ii ] ] [ 3 ]
              )
        mutablestring = mutablestring
                            .. "'" ..
                        table [ mutable [ ii ] ] [ 1 ]
                            .. "',"
    end 
    print ( mutablestring )  --- for copy paste on other recipe
    return mutable
end 

--
--  function FindActiveSubscores adapted from EDRW by Timo van der Laan
--
function FindActiveSubscores ( show )

    local result = {}
    local gTotal = 0 -- grand total all subscores
    local gTotalS = 0 -- grand total all segment subscores
    local Subs = puzzle.GetPuzzleSubscoreNames ()
    for ii = 1, #Subs do
        local total = 0
        local abstotal = 0
        local part
        for jj = 1, segCnt2 do
            part = current.GetSegmentEnergySubscore ( jj, Subs [ ii ] ) 
            total = total + part
            abstotal = abstotal + math.abs ( part )
        end
        if abstotal > 10 then
            result [ #result + 1 ] = { Subs [ ii ], total }
            gTotal = gTotal + total
            if show then 
                print ( "active subscore "
                            .. #result ..
                        ": " 
                            .. Subs [ ii ] .. 
                        ", total = " 
                            .. round ( total ) 
                      ) 
            end
        end
    end
    for ii = 1, segCnt2 do
        gTotalS = gTotalS + current.GetSegmentEnergyScore ( ii )
    end
    if show then print ( #result .. " active subscores" ) end
    if show then print ( "total of all subscores: " .. round ( gTotal ) ) end
    if show then print ( "total of all segment scores: " .. round ( gTotalS ) ) end
    if ( round ( gTotal ) ~= round ( gTotalS ) ) then
        print ( "WARNING: total subscores "
                    .. round ( gTotal ) ..
                " not equal total segment scores "
                    .. round ( gTotalS ) 
              )
    end
    return result, gTotal, gTotalS
end

--
--  print segment scores in spreadsheet format
--
function SegScores ( table, subScores )
    local tReport = ""
    local headStr =
            "n" 
                .. delim ..
            "ID"
                .. delim ..
            "SS"
                .. delim 
    if kHydro then
        headStr = headStr .. "Hyd" .. delim
    end
    if kAtom then
        headStr = headStr .. "atoms" .. delim
    end
    if kRotamer then
        headStr = headStr .. "rotamers" .. delim
    end
    headStr = headStr .. "score" .. delim 
          
    for ii = 1, #subScores do
        headStr = headStr .. subScores [ ii ] [ 1 ] .. delim
    end
    print ( "--" )
    print ( "\"segment scores\"" )
    print ( headStr )
    tReport = tReport .. "\"segment scores\"\n" .. headStr .. "\n"

    local tSegEnergy = 0
    for ii = 1, segCnt2 do
        local segEnergy = current.GetSegmentEnergyScore ( ii )
        tSegEnergy = tSegEnergy + segEnergy
        local segScore = 
                ii 
                    .. delim ..
                table [ ii ] [ 1 ]
                    .. delim ..
                table [ ii ] [ 5 ]
                    .. delim
        if kHydro then
            segScore = segScore .. round ( table [ ii ] [ 4 ] ) .. delim
        end
        if kAtom then
            segScore = segScore .. structure.GetAtomCount ( ii ) .. delim
        end
        if kRotamer then
            segScore = segScore .. rotamer.GetCount ( ii ) .. delim
        end
        segScore = segScore .. round ( segEnergy ) .. delim 

        for jj = 1, #subScores do
            segScore = segScore ..
                    round ( current.GetSegmentEnergySubscore ( ii, subScores [ jj ] [ 1 ] ) ) ..
                    delim
        end
        print ( segScore )
        tReport = tReport .. segScore .. "\n"
    end 
    local footstr =
            "totals" 
                .. delim ..
            ""
                .. delim ..
            ""
                .. delim
    if kHydro then
        footstr = footstr .. delim -- no totals for hydropathy
    end
    if kAtom then
        footstr = footstr .. delim -- no totals for atoms
    end
    if kRotamer then
        footstr = footstr .. delim -- no totals for rotamers
    end
    footstr = footstr .. round ( tSegEnergy ) .. delim 
    for ii = 1, #subScores do
        footstr = footstr .. round ( subScores [ ii ] [ 2 ] ) .. delim
    end
    print ( footstr )
    tReport = tReport .. footstr .. "\n"
    return tReport
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 structScr = 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
                structScr = 0
           end
           structLast = ii
           structScr = structScr + current.GetSegmentEnergyScore ( ii ) 
        elseif ( within_struct == true ) then

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

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

    return structList
end

--
--  function to print a little contact table
--
function contact ( structs )
    local head = delim .. delim
    local first = true
    for s = 1, #structs do
        if structs [ s ] [ STRCTTYP ] == "H" 
        or structs [ s ] [ STRCTTYP ] == "E" then
            local string = structs [ s ] [ STRCTTYP ]
                        .. delim .. 
                     structs [ s ] [ STRCTSTR ]
                        ..  delim   ..  
                     structs [ s ] [ STRCTEND ] 
            for s2 = 1, #structs do
                if structs [ s2 ] [ STRCTTYP ] == "H" 
                or structs [ s2 ] [ STRCTTYP ] == "E" then
                    if first then 
                        head = head .. delim .. structs [ s2 ] [ STRCTTYP ] 
                    end
                    local mean = 0
                    local nb = 0
                    for i = structs [ s ] [ STRCTSTR ], structs [ s ] [ STRCTEND ] do
                        local min = 999999
                        for j = structs [ s2 ] [ STRCTSTR ], structs [ s2 ] [ STRCTEND ] do
                            dist = structure.GetDistance ( i, j )
                            if dist < min then 
                                min = dist 
                            end
                        end
                        mean = mean + min
                        nb = nb + 1
                    end 
                    mean = mean / nb
                    local c = " "
                    if structure.GetDistance ( structs [ s ] [ STRCTSTR ], structs [ s2 ] [ STRCTEND ] ) < 
                       structure.GetDistance ( structs [ s ] [ STRCTSTR ], structs [ s2 ] [ STRCTSTR ] ) then
                        if mean < 5 then  
                            c = 'X' 
                        elseif mean < 10 then 
                            c = 'x' 
                        end 
                    else
                        if mean < 5 then 
                            c = 'O' 
                        elseif mean < 10 then 
                            c = 'o' 
                        end 
                    end
                    string = string .. delim .. c
                end
            end
            if first then 
                print ( "--" )
                print ( "\"mini contact table\"" ) 
                print ( head ) 
                first = false 
            end
            print ( string )
        end
    end
end

function ShowReport ( tReport, seq, struc )
    local ask = dialog.CreateDialog ( ReVersion .. " copy-and-paste" )

    ask.l15    = dialog.AddLabel ( "Click inside the one of the text boxes, then" )
    ask.l16    = dialog.AddLabel ( "use ctrl+a (command+a on Mac) to select all," )
    ask.l20    = dialog.AddLabel ( "and control+c or command+c to copy, then" )
    ask.l30    = dialog.AddLabel ( "paste into spreadsheet" )
    ask.l10    = dialog.AddLabel ( "---- segment subscores report ----" )
    ask.rep   = dialog.AddTextbox ( "subscores:", tReport )
    ask.SEQN = dialog.AddLabel ( "---- primary (sequence) and secondary structure detail ----" )
    ask.seq   = dialog.AddTextbox ( "AA sequence:", seq )
    ask.struc = dialog.AddTextbox ( "secondary:", struc )
    ask.OK = dialog.AddButton ( "OK", 1 )  
    dialog.Show ( ask ) 
end

function GetParms ( scrParts, ligands )
    local selParts = {}

    local ask = dialog.CreateDialog ( ReVersion )

    if segcnt == segcnt2 then
        ask.segcnt = dialog.AddLabel ( segCnt2 .. " segments" )
    else
        ask.segcnt = dialog.AddLabel ( segCnt .. " segments" )
        ask.segcnt2 = dialog.AddLabel ( segCnt2 .. " segments, adjusted for ligands" )
    end

    if #ligands > 0 then
        ask.ligands = dialog.AddLabel ( #ligands .. 
                                        " ligand section(s), see scriptlog for details" )
    end

    ask.NRGE = dialog.AddLabel ( "---- score information ----" )
--[[
BoxScore = {
    tSubScores = 0,     -- total of active subscores, all segments
    tSegScores = 0,     -- total of segment scores
    tScoreFilt = 0,     -- total score, filters on
    tScoreFOff = 0,     -- total score, filters off
    tScoreNrgy = 0,     -- total energy score
    tScoreBonus = 0,    -- total filter bonus
    tScoreForm = 0,     -- subscores + filter bonus + 8000
    tScoreDark = 0,     -- total "dark" score
}
]]--
    ask.active = dialog.AddLabel ( #scrParts .. " active subscores" )
    ask.tSubScores = dialog.AddLabel  ( "total of all subscores = " 
                                        .. round ( BoxScore.tSubScores ) )
    ask.tScoreFilt = dialog.AddLabel  ( "current score = " 
                                        .. round ( BoxScore.tScoreFilt ) ) 
    if BoxScore.tScoreBonus ~= 0 then
        ask.tScoreBonus = dialog.AddLabel ( "filter bonus = " 
                                            .. round ( BoxScore.tScoreBonus ) ) 
    else
        ask.tScoreBonus = dialog.AddLabel ( "no filter bonus" )
    end
    ask.tScoreForm = dialog.AddLabel  ( "subscores + filter bonus + 8000 = " 
                                        .. round ( BoxScore.tScoreForm ) ) 
    ask.tScoreDark = dialog.AddLabel  ( "\"dark\" points = " 
                                        .. round ( BoxScore.tScoreDark ) ) 

    ask.DETAIL = dialog.AddLabel ( "---- subscore reporting options ----" )
    for ii = 1,#scrParts do
        ask [ scrParts [ ii ] [ 1 ] ] = dialog.AddCheckbox ( scrParts [ ii ] [ 1 ] .. ":  " .. round ( scrParts [ ii ] [ 2 ] ), true )
    end

    ask.kHydro = dialog.AddCheckbox ( "hydropathy index", kHydro )
    ask.kAtom = dialog.AddCheckbox ( "atom count", kAtom )
    ask.kRotamer = dialog.AddCheckbox ( "rotamer count", kRotamer )
    ask.kRound = dialog.AddSlider ( "decimal places:", kRound, 1, 8, 0 )
    ask.ddlm = dialog.AddLabel ( "delimiters (last selected wins)" )
    ask.dtab = dialog.AddCheckbox ( "tab", dtab )
    ask.dcomma = dialog.AddCheckbox ( "comma", dcomma )
    ask.dsemic = dialog.AddCheckbox ( "semicolon", dsemic )

    ask.SECT = dialog.AddLabel ( "---- report sections ----" )
    ask.kContact = dialog.AddCheckbox ( "mini contact table", kContact )
    ask.kMutDet = dialog.AddCheckbox ( "mutable details", kMutDet )

    ask.OK = dialog.AddButton ( "OK", 1 )  
    ask.Cancel = dialog.AddButton ( "Cancel", 0 )
    local kRet = dialog.Show ( ask ) 
    if kRet > 0 then
        for ii = 1, #scrParts do
            if ask [ scrParts [ ii ] [ 1 ] ].value then selParts [ #selParts + 1 ] = scrParts [ ii ] end
        end
    --
    --  select all if nothing selected
    --
        if #selParts == 0 then
            for ii = 1, #scrParts do
                selParts [ #selParts + 1 ] = scrParts [ ii ]
            end
        end
        kHydro = ask.kHydro.value
        kAtom = ask.kAtom.value
        kRotamer = ask.kRotamer.value
        kRound = ask.kRound.value
        kFax = 10 ^ -kRound
        dtab = ask.dtab.value
        if dtab then
            delim = "\t"
        end
        dcomma = ask.dcomma.value
        if dcomma then
            delim = ","
        end
        dsemic = ask.dsemic.value
        if dsemic then
            delim = ";"
        end

        kContact = ask.kContact.value
        kMutDet = ask.kMutDet.value
        return true, selParts
    end
    return false, scrParts
end

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

--
-- count segments and search for ligand 
--
    local ligands = GetSeCount ()
--
--  determine which subscores are active
--
    print ( "--" )
    print ( "score information" )
--[[
BoxScore = {
    tSubScores = 0,     -- total of active subscores, all segments
    tSegScores = 0,     -- total of segment scores
    tScoreFilt = 0,     -- total score, filters on
    tScoreFOff = 0,     -- total score, filters off
    tScoreNrgy = 0,     -- total energy score
    tScoreBonus = 0,    -- total filter bonus
    tScoreForm = 0,     -- subscores + filter bonus + 8000
    tScoreDark = 0,     -- total "dark" score
}
]]--
    subScores, BoxScore.tSubScores, BoxScore.tSegScores = FindActiveSubscores ( true )
    behavior.SetFiltersDisabled ( false )
    BoxScore.tScoreFilt = current.GetEnergyScore () 
    behavior.SetFiltersDisabled ( true )
    BoxScore.tScoreFOff = current.GetEnergyScore () 
    BoxScore.tScoreBonus = BoxScore.tScoreFilt - BoxScore.tScoreFOff
    if fBonus ~= 0 then
        print ( "current filter bonus = " .. round ( BoxScore.tScoreBonus ) )
    end
    behavior.SetFiltersDisabled ( false )
    BoxScore.tScoreForm = BoxScore.tSubScores + BoxScore.tScoreBonus + 8000
    print ( "subscores + filter bonus + 8000 = " .. round ( BoxScore.tScoreForm ) )
    BoxScore.tScoreDark = BoxScore.tScoreFilt - BoxScore.tScoreForm
    print ( "current score = " .. round ( BoxScore.tScoreFilt ) )
    print ( "\"dark\" points = " .. round ( BoxScore.tScoreDark ) )
    
    print ( "--" )
    print ( "sequence information" )
--
--  build table of non-ligand segments
--
    local segTable = tablesegment ()
--
--  sequence of letters, hydrophobes, structures
--
    local seq, hydro, struc = BuildSequence ( segTable )
--
--  find modifiable sections
--
    print ( "--" )
    print ( "modifiable sections" )
    FindModifiable ()
--
--  get details for subscore report
--
    local go, selScores = GetParms ( subScores, ligands )
    if go then
    --
    --  print segment scores
    --
        local tReport = SegScores ( segTable, selScores )
    --
    --  detect structures
    --
        local helixList = GetStruct ( "H" )
        local sheetList = GetStruct ( "E" )
        local structList = {}
        for ii = 1, #helixList do
            structList [ #structList + 1 ] = helixList [ ii ]
        end
        for ii = 1, #sheetList do
            structList [ #structList + 1 ] = sheetList [ ii ]
        end
     
        if kContact then
        --
        --  mini contact table
        --
            contact ( structList )
        end
    --
    --  find mutable segments and print them 
    --
        if kMutDet then
            print ( "--" )
            print ( "mutable segments" )
            FindMutable ( segTable ) 
        end
    --
    --  show report for copy and paste
    --
        ShowReport ( tReport, seq, struc )
    end
--
--  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]

The sequence information now includes rulers to show the position of each segment.

[Bruno Kestemont]

The only problem I see is that the dialog is too big to be showed on a small laptop screen (cannot click on "ok")