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
]]--
--
-- globals section
--
Recipe = "print protein"
Version = "2.0"
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
print ( "sequence with single-letter amino acid codes for searching PDB" )
print ( seqstring )
print ( "sequence with i if hydrophobic" )
print ( hydrostring )
print ( "sequence of structure" )
print ( strucstring )
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
