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
print protein 2.2 - 2016/04/18 - LociOiling
+ fix crash in normal ligand case
+ add mean score to subscore display
print protein 2.3 - 2016/10/27 - LociOiling
+ add density analysis for ED puzzles
* density by amino acid
* density by aromatic vs. non-aromatic
* density by aliphatic vs. non-aliphatic
* density by hydrophobic vs. hydrophilic
* density deviation, showing whether each segment is
above or below mean density for the segment's amino acid type
+ move less-used parms to second screen to avoid screen overflow
print protein 2.4 - 2016/11/15 - LociOiling
+ move ED items to separate dialog to avoid textbox bug
+ add "active" flag to active subscores table to fix
totally messed up selection logic; ripple change to GetScore
print protein 2.5 - 2017/05/19 - LociOiling
+ fix rulers, split long lines
print protein 2.6 - 2017/08/06 - LociOiling
+ save and restore to conserve moves
print protein 2.7 - 2017/11/02 - LociOiling
+ consolidate duplicated segment subscore calls
+ add info from scoreboard and user functions
print protein 2.8 - 2017/12/15 - LociOiling
+ handle RNA, make educated guess for DNA
+ include ligands in report, treat each ligand independently
+ add new type column, P for protein, R for RNA, D for DNA, M for molecule (ligand)
+ if locked segments found, include "locked" column
+ check for unlocked sidechains of locked segments
]]--
--
-- globals section
--
Recipe = "print protein"
Version = "2.8"
ReVersion = Recipe .. " " .. Version
WAYBACK = 99 -- save and restore
segCnt = structure.GetCount()
segCnt2 = segCnt
isLigand = false
subScores = {} -- subscore table
gTotal = 0 -- grand total all subscores
segScoreCache = {} -- current.GetSegmentEnergyScore results saved here by FindActiveSubscores
subScoreCache = {} -- current.GetSegmentEnergySubscore results saved here by FindActiveSubscores
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
kLongnm = false -- include full name of amino acid or nucleobase
kAbbrev = false -- include abbreviation
kRound = 3 -- number of digits for rounding
kFax = 10 ^ -kRound -- initial rounding factor
jMaxL = 100 -- max line length for strings
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
kDensity = false -- density report
jDensity = false -- true if density component present
--
-- 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
--
-- ligand list offsets
--
LLSEG = 1
LLATM = 2
LLROT = 3
LLSCR = 4
--
-- 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
--
-- indexes for segment table
--
TSAA = 1 -- amino acid - one letter for protein, two letters for RNA/DNA
TSAS = 2 -- amino acid short name
TSAL = 3 -- amino acid long name
TSHY = 4 -- hydropathy index
TSSS = 5 -- secondary structure
TSLO = 6 -- locked - true or false
TSSL = 7 -- sidechain locked - true or false
TSTY = 8 -- segment type - P for protein, R for RNA, D for DNA, M for molecule (ligand)
--
-- residues with -- in front (commented) are not in Foldit (as of Nov 15, 2010)
-- one-letter amino acid code is the table key
-- two-letter RNA and DNA nucleotides are also valid
--
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" } ,
--
-- bonus! RNA nucleotides
--
ra = { "a", "Adenine", "", "", 0, },
rc = { "c", "Cytosine", "", "", 0, },
rg = { "g", "Guanine", "", "", 0, },
ru = { "u", "Uracil", "", "", 0, },
--
-- bonus! DNA nucleotides (as seen in PDB, not confirmed for Foldit)
--
da = { "a", "Adenine", "", "", 0, },
dc = { "c", "Cytosine", "", "", 0, },
dg = { "g", "Guanine", "", "", 0, },
du = { "t", "Thymine", "", "", 0, },
}
--
-- separate tables for easy type check
--
RNAcodes = {
ra = { "adenine", },
rc = { "cytosine", },
rg = { "guanine", },
ru = { "uracil", },
}
DNAcodes = {
da = { "adenine", },
dc = { "cytosine", },
dg = { "guanine", },
dt = { "thymine", },
}
--
-- amino acid types
--
Aromatic = {
f = { "phenylalanine", },
h = { "histidine", },
w = { "tryptophan", },
y = { "tyrosine", },
}
Aliphatic = {
i = { "isoleucine", },
l = { "leucine", },
v = { "valine", },
}
Hydrophobic = {
a = { "alanine", },
c = { "cysteine", },
f = { "phenylalanine", },
i = { "isoleucine", },
l = { "leucine", },
m = { "methionine", },
p = { "proline", },
v = { "valine", },
w = { "tryptophan", },
y = { "tyrosine", },
}
--
-- amino acids which normally have one rotamer
-- if other AAs report one rotamer, it may
-- indicate a locked sidechain
--
OneRotamer = {
a = { "alanine", },
g = { "glycine", },
}
--
-- end of globals section
--
--
-- begin protNfo Beta package version 0.1
--
-- version 0.1 is packaged as a psuedo-class or psuedo-module
-- containing a mix of data fields and functions
--
-- all entries must be terminated with a comma to keep Lua happy
--
-- the commas aren't necessary if only function definitions are present
--
--
protNfo = {
aa = {}, -- amino acid codes
ss = {}, -- secondary structure codes
atom = {}, -- atom counts
rot = {}, -- rotamer counts
phobe = {}, -- hydro phobics
lock = {}, -- locked segments
slck = {}, -- locked sidechains
mute = {}, -- mutable segments
setNfo = function ()
for ii = 1, structure.GetCount () do
protNfo.aa [ #protNfo.aa + 1 ] = structure.GetAminoAcid ( ii )
protNfo.ss [ #protNfo.ss + 1 ] = structure.GetSecondaryStructure ( ii )
protNfo.atom [ #protNfo.atom + 1 ] = structure.GetAtomCount ( ii )
protNfo.rot [ #protNfo.rot + 1 ] = rotamer.GetCount ( ii )
protNfo.phobe [ #protNfo.phobe + 1 ] = structure.IsHydrophobic ( ii )
protNfo.lock [ #protNfo.lock + 1 ] = structure.IsLocked ( ii )
protNfo.mute [ #protNfo.mute + 1 ] = structure.IsMutable ( ii )
--
-- take a stab at those locked sidechains
--
local slk = false
if OneRotamer [ protNfo.aa [ ii ] ] == nil and protNfo.rot [ ii ] <= 1 then
slk = true
end
protNfo.slck [ #protNfo.slck + 1 ] = slk
end
end,
}
--
-- end protNfo Beta package version 0.1
--
--
-- 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, segCnt do
if protNfo.mute [ 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, segCnt do
if protNfo.lock [ ii ] then
result [ #result + 1 ] = ii
end
end
return result
end
function FindLocked ()
return SegmentListToSet ( FindLockedList () )
end
function FindSLockedList ()
local result = {}
for ii = 1, segCnt do
if protNfo.slck [ ii ] then
result [ #result + 1 ] = ii
end
end
return result
end
function FindSLocked ()
return SegmentListToSet ( FindSLockedList () )
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 ] )
--
-- special mod for print protein: use subScoreCache
--
sub = sub + subScoreCache [ subScores [ jj ] [ 1 ] ] [ ii ]
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, segCnt do
if protNfo.ss [ 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, segCnt do
if protNfo.aa [ 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()
--
-- standard ligand adjustment
--
segCnt2 = segCnt
while protNfo.ss [ segCnt2 ] == "M" do
segCnt2 = segCnt2 - 1
end
if segCnt2 == segCnt then
print ( "segment count = " .. segCnt )
else
print ( "original segment count = " .. segCnt )
print ( "adjusted segment count = " .. segCnt2 )
end
--
-- ultra-paranoid method for detecting ligands
--
-- each ligand segment is treated separately in this version
--
ligandList = {}
for ii = 1, segCnt do
if protNfo.ss [ ii ] == "M" then
local atoms = protNfo.atom [ ii ]
local rots = protNfo.rot [ ii ]
local sscor = current.GetSegmentEnergyScore ( ii )
ligandList [ #ligandList + 1 ] = { ii, atoms, rots, sscor }
end
end
print ( #ligandList .. " ligands" )
for jj = 1, #ligandList do
print ( "ligand # "
.. jj ..
", segment = "
.. ligandList [ jj ] [ LLSEG ] ..
", atoms = "
.. ligandList [ jj ] [ LLATM ] ..
", rotamers = "
.. ligandList [ jj ] [ LLROT ] ..
", score = "
.. round ( ligandList [ jj ] [ LLSCR ] )
)
if ligandList [ jj ] [ LLSEG ] < segCnt2 then
print ( "WARNING: non-standard ligand at segment "
.. ligandList [ jj ] [ LLSEG ] ..
", most ligand-aware recipes won't work properly" )
end
end
return ligandList
end
--
-- build segments table
--
function tablesegment ()
local table = { {} }
for ii = 1, segCnt do
table [ ii ] = {}
local aac = protNfo.aa [ ii ]
if AminoAcids [ aac ] == nil then
print ( "WARNING: unknown amino acid \'"
.. aac ..
"\' at segment "
.. ii ..
", code \'x\' substituted"
)
aac = "x"
end
table [ ii ] [ TSAA ] = aac
table [ ii ] [ TSAS ] = AminoAcids [ aac ] [ AASHORT ]
table [ ii ] [ TSAL ] = AminoAcids [ aac ] [ AALONG ]
table [ ii ] [ TSHY ] = AminoAcids [ aac ] [ AAHYDROPATHY ]
table [ ii ] [ TSSS ] = protNfo.ss [ ii ]
if table [ ii ] [ TSSS ] ~= "H"
and table [ ii ] [ TSSS ] ~= "E"
and table [ ii ] [ TSSS ] ~= "L"
and table [ ii ] [ TSSS ] ~= "M" then
print ( "WARNING: unknown secondary structure code \'"
.. table [ ii ] [ TSSS ] ..
"\' at segment "
.. ii
)
end
--
-- get locked status
--
table [ ii ] [ TSLO ] = protNfo.lock [ ii ]
--
-- get sidechain locked status
--
table [ ii ] [ TSSL ] = protNfo.slck [ ii ]
--
-- determine type of segment
--
local stype = "P" -- protein (default)
if RNAcodes [ aac ] ~= nil then
stype = "R" -- RNA
elseif DNAcodes [ aac ] ~= nil then
stype = "D" -- DNA
elseif table [ ii ] [ TSSS ] == "M" then
stype = "M" -- other molecule
end
table [ ii ] [ TSTY ] = stype
end
return table
end
function makeruler ( sBeg, sEnd )
local function tenpart ( ff )
if ff >= 100 then
ff = ff % 100
end
return ( ff - ( ff % 10 ) ) / 10
end
local function hunpart ( ff )
if ff >= 1000 then
ff = ff % 1000
end
return ( ff - ( ff % 100 ) ) / 100
end
local onez = ""
local tenz = ""
local hunz = ""
local numz = 1
for ii = sBeg, sEnd do
onez = onez .. numz % 10
if ii % 10 == 0 then
tenz = tenz .. tenpart ( ii )
if ii >= 100 then
hunz = hunz .. hunpart ( ii )
else
hunz = hunz .. " "
end
else
if ii == sBeg and ii > 1 then
tenz = tenz .. tenpart ( ii )
hunz = hunz .. hunpart ( ii )
else
tenz = tenz .. " "
hunz = hunz .. " "
end
end
if ii == segCnt2 then
tenz = tenz:sub ( 1, tenz:len () - 1 ) .. tenpart ( ii )
hunz = hunz:sub ( 1, hunz:len () - 1 ) .. hunpart ( ii )
end
numz = numz + 1
if numz > 10 then
numz = 1
end
end
local ruler = ""
if sEnd >= 100 then
ruler = hunz .. "\n"
end
if sEnd >= 10 then
ruler = ruler .. tenz .. "\n"
end
ruler = ruler .. onez
return ruler
end
function linotype ( line )
if line:len () > jMaxL then
print ( line )
print ( "" )
end
for ii = 1, segCnt, jMaxL do
local lastseg = math.min ( ii + jMaxL - 1, segCnt )
print ( makeruler ( ii, lastseg ) )
print ( line:sub ( ii, lastseg ) )
print ( "" )
end
end
--
-- tlaloc functions to print sequence of letter
--
function BuildSequence ( table )
local seqstring = ""
local hydrostring = ""
local strucstring = ""
local stypestring = ""
local lockstring = ""
local slockstring = ""
local nonp = 0
local locks = 0
local slocks = 0
for ii = 1, segCnt do
local aac = table [ ii ] [ TSAA ]
if aac:len () > 1 then
nonp = nonp + 1
aac = aac:sub ( aac:len () )
end
seqstring = seqstring .. aac
if protNfo.phobe [ ii ] then
hydrostring = hydrostring .. "i"
else
hydrostring = hydrostring .. "e"
end
strucstring = strucstring .. table [ ii ] [ TSSS ]
if table [ ii ] [ TSSS ] == "M" then
nonp = nonp + 1
end
stypestring = stypestring .. table [ ii ] [ TSTY ]
local locked = "U"
if table [ ii ] [ TSLO ] then
locked = "L"
locks = locks + 1
end
lockstring = lockstring .. locked
local slocked = "U"
if table [ ii ] [ TSSL ] then
slocked = "L"
slocks = slocks + 1
end
slockstring = slockstring .. slocked
end
print ( "primary structure sequence (single-letter amino acid codes for searching PDB)" )
linotype ( seqstring )
if nonp > 0 then
print ( "CAUTION: non-protein entries found, consult types below" )
print ( "" )
end
print ( "type of each segment (P = protein, R = RNA, D = DNA, M = molecule (ligand))" )
linotype ( stypestring )
print ( "sequence with i if hydrophobic" )
linotype ( hydrostring )
print ( "secondary structure sequence" )
linotype ( strucstring )
if locks > 0 then
print ( "locked backbone segments" )
linotype ( lockstring )
end
if slocks > 0 then
print ( "locked sidechain segments" )
linotype ( slockstring )
end
print ( "--" )
return seqstring, hydrostring, strucstring, stypestring, lockstring, slockstring, nonp, locks, slocks
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 fslocked = FindSLocked ()
--print ( #fslocked .. " locked sidechain sections" )
for kk = 1, #fslocked do
print ( "locked sidechain section "
.. kk ..
": "
.. fslocked [ kk ] [ 1 ] ..
"-"
.. fslocked [ kk ] [ 2 ] )
end
--
local fsunlocked = SegmentInvertSet ( fslocked )
--print ( #fsunlocked .. " unlocked sidechain sections" )
for kk = 1, #fsunlocked do
print ( "unlocked sidechain section "
.. kk ..
": "
.. fsunlocked [ kk ] [ 1 ] ..
"-"
.. fsunlocked [ kk ] [ 2 ] )
end
--
local ulckblcks = SegmentCommSet ( funlocked, fslocked )
--print ( #ulckblcks .. " unlocked backbone, locked sidechain" )
for kk = 1, #ulckblcks do
print ( "unlocked backbone, locked sidechain section "
.. kk ..
": "
.. ulckblcks [ kk ] [ 1 ] ..
"-"
.. ulckblcks [ 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 protNfo.mute [ 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
--
-- This function should be called first -- it saves segment scores and subscores
-- in segScoreCache and subScoreCache.
--
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
subScoreCache [ Subs [ ii ] ] = {} -- save for later
local total = 0
local abstotal = 0
local part
for jj = 1, segCnt do
part = current.GetSegmentEnergySubscore ( jj, Subs [ ii ] )
subScoreCache [ Subs [ ii ] ] [ jj ] = part
total = total + part
abstotal = abstotal + math.abs ( part )
end
if abstotal > 10 then
result [ #result + 1 ] = { Subs [ ii ], total, true }
gTotal = gTotal + total
if show then
print ( "active subscore "
.. #result ..
": "
.. Subs [ ii ] ..
", total = "
.. round ( total )
)
end
end
end
for ii = 1, segCnt do
segScoreCache [ #segScoreCache + 1 ] = current.GetSegmentEnergyScore ( ii )
gTotalS = gTotalS + segScoreCache [ 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
--
-- table - segment table
-- subScores - selected subscores
-- nonprot - number of non-protein segments
-- locked - number of locked segments
-- slocked - number of locked segments
--
function SegScores ( table, subScores, nonprot, locked, slocked )
local tReport = ""
local headStr =
"n"
.. delim ..
"ID"
.. delim ..
"SS"
.. delim
if nonprot > 0 then
headStr = headStr .. "type" .. delim
end
if kLongnm then
headStr = headStr .. "name" .. delim
end
if kAbbrev then
headStr = headStr .. "abbrev" .. delim
end
if locked > 0 or slocked > 0 then
headStr = headStr .. "lock" .. delim
end
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
if subScores [ ii ] [ 3 ] then
headStr = headStr .. subScores [ ii ] [ 1 ] .. delim
end
end
print ( "--" )
print ( "\"segment scores\"" )
print ( headStr )
tReport = tReport .. "\"segment scores\"\n" .. headStr .. "\n"
local tSegEnergy = 0
for ii = 1, segCnt do
local segEnergy = segScoreCache [ ii ]
tSegEnergy = tSegEnergy + segEnergy
local segScore =
ii
.. delim ..
table [ ii ] [ TSAA ]
.. delim ..
table [ ii ] [ TSSS ]
.. delim
if nonprot > 0 then
segScore = segScore .. table [ ii ] [ TSTY ] .. delim
end
if kLongnm then
segScore = segScore .. table [ ii ] [ TSAL ] .. delim
end
if kAbbrev then
segScore = segScore .. table [ ii ] [ TSAS ] .. delim
end
if locked > 0 or slocked > 0 then
local ll = "U"
if table [ ii ] [ TSLO ] then
ll = "L"
end
if table [ ii ] [ TSSL ] then
ll = ll .. " L"
else
ll = ll .. " U"
end
segScore = segScore .. ll .. delim
end
if kHydro then
segScore = segScore .. round ( table [ ii ] [ TSHY ] ) .. delim
end
if kAtom then
segScore = segScore .. protNfo.atom [ ii ] .. delim
end
if kRotamer then
segScore = segScore .. protNfo.rot [ ii ] .. delim
end
segScore = segScore .. round ( segEnergy ) .. delim
for jj = 1, #subScores do
if subScores [ jj ] [ 3 ] then
segScore = segScore ..
round ( subScoreCache [ subScores [ jj ] [ 1 ] ] [ ii ] ) ..
delim
end
end
print ( segScore )
tReport = tReport .. segScore .. "\n"
end
local footstr =
"totals"
.. delim ..
""
.. delim ..
""
.. delim
if nonprot > 0 then
footstr = footstr .. delim -- no totals for type
end
if kLongnm then
footstr = footstr .. delim -- no totals for long name
end
if kAbbrev then
footstr = footstr .. delim -- no totals for abbreviation
end
if locked > 0 or slocked > 0 then
footstr = footstr .. delim -- no totals for locked
end
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
if subScores [ ii ] [ 3 ] then
footstr = footstr .. round ( subScores [ ii ] [ 2 ] ) .. delim
end
end
print ( footstr )
tReport = tReport .. footstr .. "\n"
return tReport
end
--
-- print density analysis
--
function DensityRat ( table )
local tReport = ""
local headStr =
"\"AA code\""
.. delim ..
"\"AA name\""
.. delim ..
"\"segment count\""
.. delim ..
"\"total density\""
.. delim ..
"\"% total density\""
.. delim ..
"\"mean density\""
.. delim ..
"\"worst density\""
.. delim ..
"\"worst density seg\""
.. delim ..
"\"best density\""
.. delim ..
"\"best density seg\""
.. delim
--
-- AA density table - keyed by AA code
--
DENCOUNT = 1
DENTOTAL = 2
DENMEAN = 3
DENBEST = 4
DENBESTS = 5
DENWORST = 6
DENWORSTS = 7
--
-- density by amino acid
--
local tAA = {}
--
-- binary (true/false) tables for density by AA type
--
--
-- density of aromatics - true => aromatic
--
local tAromatic = {}
tAromatic [ true ] = { 0, 0, 0, -999, 0, 999, 0, }
tAromatic [ false ] = { 0, 0, 0, -999, 0, 999, 0, }
--
-- density of aliphatics - true => alphatic
--
local tAliphatic = {}
tAliphatic [ true ] = { 0, 0, 0, -999, 0, 999, 0, }
tAliphatic [ false ] = { 0, 0, 0, -999, 0, 999, 0, }
--
-- density of hydrophobics - true => hydrophobic
--
local tHydrophobic = {}
tHydrophobic [ true ] = { 0, 0, 0, -999, 0, 999, 0, }
tHydrophobic [ false ] = { 0, 0, 0, -999, 0, 999, 0, }
local function denUpdate ( tDen, segDensity, segindx )
tDen [ DENCOUNT ] = tDen [ DENCOUNT ] + 1
tDen [ DENTOTAL ] = tDen [ DENTOTAL ] + segDensity
if segDensity > tDen [ DENBEST ] then
tDen [ DENBEST ] = segDensity
tDen [ DENBESTS ] = segindx
end
if segDensity < tDen [ DENWORST ] then
tDen [ DENWORST ] = segDensity
tDen [ DENWORSTS ] = segindx
end
end
local tSegDensity = 0
for ii = 1, segCnt do
local aaCode = table [ ii ] [ 1 ]
if tAA [ aaCode ] == nil then
tAA [ aaCode ] = { 0, 0, 0, -999, 0, 999, 0, }
end
--
-- update table of density by amino acid
--
local segDensity = subScoreCache [ "Density" ] [ ii ]
tSegDensity = tSegDensity + segDensity
local aaDen = tAA [ aaCode ]
if aaDen ~= nil then
denUpdate ( aaDen, segDensity, ii )
else
print ( "ERROR: AA density table entry for " .. aaCode .. " is nil" )
end
--
-- update table of density by aromatic vs. non-aromatic
--
local aromDen = tAromatic [ Aromatic [ aaCode ] ~= nil ]
if aromDen ~= nil then
denUpdate ( aromDen, segDensity, ii )
else
print ( "ERROR: Aromatic density table entry for " .. aaCode .. " is nil" )
end
--
-- update table of density by aliphatic vs. non-aliphatic
--
local alipDen = tAliphatic [ Aliphatic [ aaCode ] ~= nil ]
if alipDen ~= nil then
denUpdate ( alipDen, segDensity, ii )
else
print ( "ERROR: Aliphatic density table entry for " .. aaCode .. " is nil" )
end
--
-- update table of density by hydrophobic vs. non-hydrophobic
--
local phobDen = tHydrophobic [ Hydrophobic [ aaCode ] ~= nil ]
if phobDen ~= nil then
denUpdate ( phobDen, segDensity, ii )
else
print ( "ERROR: hydrophobic density table entry for " .. aaCode .. " is nil" )
end
end
print ( "--" )
print ( "\"density by AA\"" )
print ( headStr )
tReport = tReport .. "\"density by AA\"\n" .. headStr .. "\n"
for aac, aaDen in pairs ( tAA ) do
if aaDen [ DENCOUNT ] > 0 then
aaDen [ DENMEAN ] = aaDen [ DENTOTAL ] / aaDen [ DENCOUNT ]
end
local denline =
aac
.. delim ..
AminoAcids [ aac ] [ AALONG ]
.. delim ..
aaDen [ DENCOUNT ]
.. delim ..
round ( aaDen [ DENTOTAL ] )
.. delim ..
round ( ( aaDen [ DENTOTAL ] / tSegDensity ) * 100 )
.. delim ..
round ( aaDen [ DENMEAN ] )
.. delim ..
round ( aaDen [ DENWORST ] )
.. delim ..
aaDen [ DENWORSTS ]
.. delim ..
round ( aaDen [ DENBEST ] )
.. delim ..
aaDen [ DENBESTS ]
print ( denline )
tReport = tReport .. denline .. "\n"
end
local footstr =
"totals"
.. delim ..
segCnt
.. delim ..
round ( tSegDensity )
.. delim
.. delim ..
round ( tSegDensity / segCnt )
print ( footstr )
tReport = tReport .. footstr .. "\n"
headStr =
"\"aromatic AA\""
.. delim ..
""
.. delim ..
"\"segment count\""
.. delim ..
"\"total density\""
.. delim ..
"\"% total density\""
.. delim ..
"\"mean density\""
.. delim ..
"\"worst density\""
.. delim ..
"\"worst density seg\""
.. delim ..
"\"best density\""
.. delim ..
"\"best density seg\""
.. delim
print ( "--" )
print ( "\"density by aromatic vs. non-aromatic\"" )
print ( headStr )
tReport = tReport .. "\"density by aromatic vs. non-aromatic\"\n" .. headStr .. "\n"
for aac, aaDen in pairs ( tAromatic ) do
if aaDen [ DENCOUNT ] > 0 then
aaDen [ DENMEAN ] = aaDen [ DENTOTAL ] / aaDen [ DENCOUNT ]
end
local denline =
tostring ( aac )
.. delim ..
""
.. delim ..
aaDen [ DENCOUNT ]
.. delim ..
round ( aaDen [ DENTOTAL ] )
.. delim ..
round ( ( aaDen [ DENTOTAL ] / tSegDensity ) * 100 )
.. delim ..
round ( aaDen [ DENMEAN ] )
.. delim ..
round ( aaDen [ DENWORST ] )
.. delim ..
aaDen [ DENWORSTS ]
.. delim ..
round ( aaDen [ DENBEST ] )
.. delim ..
aaDen [ DENBESTS ]
print ( denline )
tReport = tReport .. denline .. "\n"
end
headStr =
"\"aliphatic AA\""
.. delim ..
""
.. delim ..
"\"segment count\""
.. delim ..
"\"total density\""
.. delim ..
"\"% total density\""
.. delim ..
"\"mean density\""
.. delim ..
"\"worst density\""
.. delim ..
"\"worst density seg\""
.. delim ..
"\"best density\""
.. delim ..
"\"best density seg\""
.. delim
print ( "--" )
print ( "\"density by aliphatic vs. non-aliphatic\"" )
print ( headStr )
tReport = tReport .. "\"density by aliphatic vs. non-aliphatic\"\n" .. headStr .. "\n"
for aac, aaDen in pairs ( tAliphatic ) do
if aaDen [ DENCOUNT ] > 0 then
aaDen [ DENMEAN ] = aaDen [ DENTOTAL ] / aaDen [ DENCOUNT ]
end
local denline =
tostring ( aac )
.. delim ..
""
.. delim ..
aaDen [ DENCOUNT ]
.. delim ..
round ( aaDen [ DENTOTAL ] )
.. delim ..
round ( ( aaDen [ DENTOTAL ] / tSegDensity ) * 100 )
.. delim ..
round ( aaDen [ DENMEAN ] )
.. delim ..
round ( aaDen [ DENWORST ] )
.. delim ..
aaDen [ DENWORSTS ]
.. delim ..
round ( aaDen [ DENBEST ] )
.. delim ..
aaDen [ DENBESTS ]
print ( denline )
tReport = tReport .. denline .. "\n"
end
headStr =
"\"hydrophobic AA\""
.. delim ..
""
.. delim ..
"\"segment count\""
.. delim ..
"\"total density\""
.. delim ..
"\"% total density\""
.. delim ..
"\"mean density\""
.. delim ..
"\"worst density\""
.. delim ..
"\"worst density seg\""
.. delim ..
"\"best density\""
.. delim ..
"\"best density seg\""
.. delim
print ( "--" )
print ( "\"density by hydrophobic vs. non-hydrophobic\"" )
print ( headStr )
tReport = tReport .. "\"density by hydrophobic vs. non-hydrophobic\"\n" .. headStr .. "\n"
for aac, aaDen in pairs ( tHydrophobic ) do
if aaDen [ DENCOUNT ] > 0 then
aaDen [ DENMEAN ] = aaDen [ DENTOTAL ] / aaDen [ DENCOUNT ]
end
local denline =
tostring ( aac )
.. delim ..
""
.. delim ..
aaDen [ DENCOUNT ]
.. delim ..
round ( aaDen [ DENTOTAL ] )
.. delim ..
round ( ( aaDen [ DENTOTAL ] / tSegDensity ) * 100 )
.. delim ..
round ( aaDen [ DENMEAN ] )
.. delim ..
round ( aaDen [ DENWORST ] )
.. delim ..
aaDen [ DENWORSTS ]
.. delim ..
round ( aaDen [ DENBEST ] )
.. delim ..
aaDen [ DENBESTS ]
print ( denline )
tReport = tReport .. denline .. "\n"
end
print ( "--" )
print ( "\"density deviation (above/below mean density by AA)\"" )
local dendeviate = ""
for ii = 1, segCnt do
local aaCode = table [ ii ] [ 1 ]
local segDensity = subScoreCache [ "Density" ] [ ii ]
local jDenMean = tAA [ aaCode ] [ DENMEAN ]
if round ( segDensity ) == round ( jDenMean ) or tAA [ aaCode ] [ DENCOUNT ] == 1 then
dendeviate = dendeviate .. "="
elseif segDensity < jDenMean then
dendeviate = dendeviate .. "-"
else
dendeviate = dendeviate .. "+"
end
end
linotype ( dendeviate )
return tReport, dendeviate
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
for ii = 1, segCnt do
if ( protNfo.ss [ ii ] == structT ) then
if ( within_struct == false ) then
-- start of a new struct
within_struct = true
structStart = ii
structScr = 0
end
structLast = ii
if ii <= #segScoreCache then
structScr = structScr + segScoreCache [ ii ]
else
structScr = structScr + current.GetSegmentEnergyScore ( ii )
end
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 ShowDensityReport ( dReport, dendev )
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.l50 = dialog.AddLabel ( "---- density analysis ----" )
ask.dens = dialog.AddTextbox ( "density:", dReport )
ask.l70 = dialog.AddLabel ( "---- density deviation from mean AA density ----" )
ask.dev = dialog.AddTextbox ( "deviation:", dendev )
ask.OK = dialog.AddButton ( "OK", 1 )
dialog.Show ( ask )
end
function GetParms ( scrParts, ligands )
local ask = dialog.CreateDialog ( ReVersion )
local kRet = 0
repeat
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 ] )
.. " (" ..
round ( scrParts [ ii ] [ 2 ] / segCnt )
.. " / seg) ",
scrParts [ ii ] [ 3 ] )
end
ask.SECT = dialog.AddLabel ( "---- report sections ----" )
ask.kContact = dialog.AddCheckbox ( "mini contact table", kContact )
ask.kMutDet = dialog.AddCheckbox ( "mutable details", kMutDet )
if jDensity then
ask.kDensity = dialog.AddCheckbox ( "density analysis", kDensity )
end
ask.OK = dialog.AddButton ( "OK", 1 )
ask.more = dialog.AddButton ( "More", 2 )
ask.Cancel = dialog.AddButton ( "Cancel", 0 )
kRet = dialog.Show ( ask )
if kRet > 0 then
local aPart = 0
for ii = 1, #scrParts do
scrParts [ ii ] [ 3 ] = ask [ scrParts [ ii ] [ 1 ] ].value
aPart = aPart + 1
end
--
-- select all if nothing selected
--
if aPart == 0 then
for ii = 1, #scrParts do
scrParts [ ii ] [ 3 ] = true
end
end
kContact = ask.kContact.value
kMutDet = ask.kMutDet.value
if jDensity then
kDensity = ask.kDensity.value
end
if kRet == 2 then
GetMoreParms ()
end
end
until kRet < 2
if kRet == 1 then
return true, scrParts
end
return false, scrParts
end
function GetMoreParms ( )
local ask = dialog.CreateDialog ( ReVersion )
ask.DETAIL = dialog.AddLabel ( "---- additional columns ----" )
ask.kLongnm = dialog.AddCheckbox ( "long name", kLongnm )
ask.kAbbrev = dialog.AddCheckbox ( "abbreviation", kAbbrev )
ask.kHydro = dialog.AddCheckbox ( "hydropathy index", kHydro )
ask.kAtom = dialog.AddCheckbox ( "atom count", kAtom )
ask.kRotamer = dialog.AddCheckbox ( "rotamer count", kRotamer )
ask.FORMAT = dialog.AddLabel ( "---- formatting options ----" )
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.OK = dialog.AddButton ( "OK", 1 )
ask.Cancel = dialog.AddButton ( "Cancel", 0 )
local kRet = dialog.Show ( ask )
if kRet > 0 then
kLongnm = ask.kLongnm.value
kAbbrev = ask.kAbbrev.value
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
return true
end
return false
end
--
-- Ident - print identifying information at beginning and end of recipe
--
-- slugline - first line to print - normally recipe name and version
--
function Ident ( slugline )
local function round ( ii )
return ii - ii % 0.001
end
print ( slugline )
print ( "Puzzle: " .. puzzle.GetName () .. " (" .. puzzle.GetPuzzleID () .. ")" )
print ( "Track: " .. ui.GetTrackName () )
gname = user.GetGroupName ()
if gname ~= nil then
gname = " (" .. gname .. ")"
else
gname = ""
end
print ( "User: " .. user.GetPlayerName () .. gname )
local scoretype = scoreboard.GetScoreType ()
local scort = ""
if scoretype == 0 then
scort = "soloist"
elseif scoretype == 1 then
scort = "evolver"
elseif scoretype == 2 then
scort = "all hands"
elseif scoretype == 3 then
scort = "no score"
else
scort = "unknown/error"
end
print ( "Rank: " .. scoreboard.GetRank ( scoretype ) .. " (" .. scort .. ")" )
local sGroup = scoreboard.GetGroupScore ()
if sGroup ~= nil then
print ( "Group rank / score: " .. scoreboard.GetGroupRank () .. " / " .. round ( 10 * ( 800 - sGroup ) ) )
end
end
function main ()
save.Quicksave ( WAYBACK )
print ( "--" )
Ident ( ReVersion )
--
-- get protein info
--
print ( "collecting protein info, please wait" )
protNfo.setNfo ()
print ( "--" )
print ( "collecting score info, please wait" )
print ( "--" )
--
-- 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
}
]]--
--
-- FindActiveSubscores should be called first, to build subScoreCache
--
subScores, BoxScore.tSubScores, BoxScore.tSegScores = FindActiveSubscores ( true )
--
-- special check for "Density" subscore
--
for ii = 1, #subScores do
if subScores [ ii ] [ 1 ] == "Density" then
jDensity = true -- density present
kDensity = true -- select density report by default
break
end
end
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 ) )
local sRosetta = scoreboard.GetScore ()
print ( "Rosetta energy score = ".. round ( sRosetta ) )
local sRosecon = 10 * ( 800 - sRosetta )
print ( "converted Rosetta score = " .. round ( sRosecon ) )
print ( "--" )
print ( "sequence information" )
--
-- build table of non-ligand segments
--
local segTable = tablesegment ()
--
-- sequence of letters, hydrophobes, structures, locks
--
local seq, hydro, struc, types, locks, slocks, nonprot, locked, slocked = 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, nonprot, locked, slocked )
--
-- print density analysis
--
local dReport = nil
local dendev = nil
if jDensity then
dReport, dendev = DensityRat ( segTable )
end
--
-- 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 reports for copy and paste
--
ShowReport ( tReport, seq, struc )
if kDensity then
ShowDensityReport ( dReport, dendev )
end
end
--
-- exit via the cleanup function
--
cleanup ()
end
function cleanup ( errmsg )
if CLEANUPENTRY ~= nil then
return
end
CLEANUPENTRY = true
print ( "---" )
--
-- model 100 - print recipe name, puzzle, track, time, score, and gain
--
local reason
local start, stop, line, msg
if errmsg == nil then
reason = "complete"
else
--
-- model 120 - civilized error reporting,
-- thanks to Bruno K. and Jean-Bob
--
start, stop, line, msg = errmsg:find ( ":(%d+):%s()" )
if msg ~= nil then
errmsg = errmsg:sub ( msg, #errmsg )
end
if errmsg:find ( "Cancelled" ) ~= nil then
reason = "cancelled"
else
reason = "error"
end
end
Ident ( ReVersion )
if reason == "error" then
print ( "Unexpected error detected" )
print ( "Error line: " .. line )
print ( "Error: \"" .. errmsg .. "\"" )
end
save.Quickload ( WAYBACK )
end
xpcall ( main, cleanup )
--- end of recipe
