Class: Bio::Protparam
 Inherits:

Object
 Object
 Bio::Protparam
 Defined in:
 lib/bio/util/protparam.rb
Overview
Description
Bio::Protparam is a class for calculating protein paramesters. This class has a similer interface to BioPerl's Bio::Tools::Protparam. However, it calculate parameters instead of throwing a query to Expasy's Protparam tool}[http://web.expasy.org/protparam/]{[1] as Bio::Tools::Protparam does.
Defined Under Namespace
Constant Summary collapse
 IUPAC_CODE =
IUPAC codes for amino acids.
{ :I => "Ile", :V => "Val", :L => "Leu", :F => "Phe", :C => "Cys", :M => "Met", :A => "Ala", :G => "Gly", :T => "Thr", :W => "Trp", :S => "Ser", :Y => "Tyr", :P => "Pro", :H => "His", :E => "Glu", :Q => "Gln", :D => "Asp", :N => "Asn", :K => "Lys", :R => "Arg", :U => "Sec", :O => "Pyl", :B => "Asx", :Z => "Glx", :X => "Xaa" }
 DIWV =
Dipeptide instability weight value for calculating instability index of proteins [10].
{ :W => { :W => 1.0, :C => 1.0, :M => 24.68, :H => 24.68, :Y => 1.0, :F => 1.0, :Q => 1.0, :N => 13.34, :I => 1.0, :R => 1.0, :D => 1.0, :P => 1.0, :T => 14.03, :K => 1.0, :E => 1.0, :V => 7.49, :S => 1.0, :G => 9.37, :A => 14.03, :L => 13.34 }, :C => { :W => 24.68, :C => 1.0, :M => 33.6, :H => 33.6, :Y => 1.0, :F => 1.0, :Q => 6.54, :N => 1.0, :I => 1.0, :R => 1.0, :D => 20.26, :P => 20.26, :T => 33.6, :K => 1.0, :E => 1.0, :V => 6.54, :S => 1.0, :G => 1.0, :A => 1.0, :L => 20.26 }, :M => { :W => 1.0, :C => 1.0, :M => 1.88, :H => 58.28, :Y => 24.68, :F => 1.0, :Q => 6.54, :N => 1.0, :I => 1.0, :R => 6.54, :D => 1.0, :P => 44.94, :T => 1.88, :K => 1.0, :E => 1.0, :V => 1.0, :S => 44.94, :G => 1.0, :A => 13.34, :L => 1.0 }, :H => { :W => 1.88, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 44.94, :F => 9.37, :Q => 1.0, :N => 24.68, :I => 44.94, :R => 1.0, :D => 1.0, :P => 1.88, :T => 6.54, :K => 24.68, :E => 1.0, :V => 1.0, :S => 1.0, :G => 9.37, :A => 1.0, :L => 1.0 }, :Y => { :W => 9.37, :C => 1.0, :M => 44.94, :H => 13.34, :Y => 13.34, :F => 1.0, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 15.91, :D => 24.68, :P => 13.34, :T => 7.49, :K => 1.0, :E => 6.54, :V => 1.0, :S => 1.0, :G => 7.49, :A => 24.68, :L => 1.0 }, :F => { :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 33.6, :F => 1.0, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 1.0, :D => 13.34, :P => 20.26, :T => 1.0, :K => 14.03, :E => 1.0, :V => 1.0, :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0 }, :Q => { :W => 1.0, :C => 6.54, :M => 1.0, :H => 1.0, :Y => 6.54, :F => 6.54, :Q => 20.26, :N => 1.0, :I => 1.0, :R => 1.0, :D => 20.26, :P => 20.26, :T => 1.0, :K => 1.0, :E => 20.26, :V => 6.54, :S => 44.94, :G => 1.0, :A => 1.0, :L => 1.0 }, :N => { :W => 9.37, :C => 1.88, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 14.03, :Q => 6.54, :N => 1.0, :I => 44.94, :R => 1.0, :D => 1.0, :P => 1.88, :T => 7.49, :K => 24.68, :E => 1.0, :V => 1.0, :S => 1.0, :G => 14.03, :A => 1.0, :L => 1.0 }, :I => { :W => 1.0, :C => 1.0, :M => 1.0, :H => 13.34, :Y => 1.0, :F => 1.0, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 1.0, :D => 1.0, :P => 1.88, :T => 1.0, :K => 7.49, :E => 44.94, :V => 7.49, :S => 1.0, :G => 1.0, :A => 1.0, :L => 20.26 }, :R => { :W => 58.28, :C => 1.0, :M => 1.0, :H => 20.26, :Y => 6.54, :F => 1.0, :Q => 20.26, :N => 13.34, :I => 1.0, :R => 58.28, :D => 1.0, :P => 20.26, :T => 1.0, :K => 1.0, :E => 1.0, :V => 1.0, :S => 44.94, :G => 7.49, :A => 1.0, :L => 1.0 }, :D => { :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 6.54, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 6.54, :D => 1.0, :P => 1.0, :T => 14.03, :K => 7.49, :E => 1.0, :V => 1.0, :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0 }, :P => { :W => 1.88, :C => 6.54, :M => 6.54, :H => 1.0, :Y => 1.0, :F => 20.26, :Q => 20.26, :N => 1.0, :I => 1.0, :R => 6.54, :D => 6.54, :P => 20.26, :T => 1.0, :K => 1.0, :E => 18.38, :V => 20.26, :S => 20.26, :G => 1.0, :A => 20.26, :L => 1.0 }, :T => { :W => 14.03, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 13.34, :Q => 6.54, :N => 14.03, :I => 1.0, :R => 1.0, :D => 1.0, :P => 1.0, :T => 1.0, :K => 1.0, :E => 20.26, :V => 1.0, :S => 1.0, :G => 7.49, :A => 1.0, :L => 1.0 }, :K => { :W => 1.0, :C => 1.0, :M => 33.6, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 24.68, :N => 1.0, :I => 7.49, :R => 33.6, :D => 1.0, :P => 6.54, :T => 1.0, :K => 1.0, :E => 1.0, :V => 7.49, :S => 1.0, :G => 7.49, :A => 1.0, :L => 7.49 }, :E => { :W => 14.03, :C => 44.94, :M => 1.0, :H => 6.54, :Y => 1.0, :F => 1.0, :Q => 20.26, :N => 1.0, :I => 20.26, :R => 1.0, :D => 20.26, :P => 20.26, :T => 1.0, :K => 1.0, :E => 33.6, :V => 1.0, :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0 }, :V => { :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 6.54, :F => 1.0, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 1.0, :D => 14.03, :P => 20.26, :T => 7.49, :K => 1.88, :E => 1.0, :V => 1.0, :S => 1.0, :G => 7.49, :A => 1.0, :L => 1.0 }, :S => { :W => 1.0, :C => 33.6, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 20.26, :N => 1.0, :I => 1.0, :R => 20.26, :D => 1.0, :P => 44.94, :T => 1.0, :K => 1.0, :E => 20.26, :V => 1.0, :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0 }, :G => { :W => 13.34, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 7.49, :F => 1.0, :Q => 1.0, :N => 7.49, :I => 7.49, :R => 1.0, :D => 1.0, :P => 1.0, :T => 7.49, :K => 7.49, :E => 6.54, :V => 1.0, :S => 1.0, :G => 13.34, :A => 7.49, :L => 1.0 }, :A => { :W => 1.0, :C => 44.94, :M => 1.0, :H => 7.49, :Y => 1.0, :F => 1.0, :Q => 1.0, :N => 1.0, :I => 1.0, :R => 1.0, :D => 7.49, :P => 20.26, :T => 1.0, :K => 1.0, :E => 1.0, :V => 1.0, :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0 }, :L => { :W => 24.68, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 33.6, :N => 1.0, :I => 1.0, :R => 20.26, :D => 1.0, :P => 20.26, :T => 1.0, :K => 7.49, :E => 1.0, :V => 1.0, :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0 } }
 HALFLIFE =
Estemated halflife (minutes) of Nterminal residue of a protein.
{ :ecoli => { :I => 600, :V => 600, :L => 2, :F => 2, :C => 600, :M => 600, :A => 600, :G => 600, :T => 600, :W => 2, :S => 600, :Y => 2, :P => 600, :H => 600, :E => 600, :Q => 600, :D => 600, :N => 600, :K => 2, :R => 2, :U => 600 }, :mammalian => { :A => 264, :R => 60, :N => 84, :D => 66, :C => 72, :Q => 48, :E => 60, :G => 30, :H => 210, :I => 1200, :L => 330, :K => 78, :M => 1800, :F => 66, :P => 1200, :S => 114, :T => 432, :W => 168, :Y => 168, :V => 6000 }, :yeast => { :A => 1200, :R => 2, :N => 3, :D => 3, :C => 1200, :Q => 10, :E => 30, :G => 1200, :H => 10, :I => 30, :L => 3, :K => 3, :M => 1200, :F => 3, :P => 1200, :S => 1200, :T => 1200, :W => 3, :Y => 10, :V => 1200 } }
 HYDROPATHY =
Hydropathy values for amino acids [12].
{ :I => 4.5 , :V => 4.2 , :L => 3.8 , :F => 2.8 , :C => 2.5 , :M => 1.9 , :A => 1.8 , :G => 0.4, :T => 0.7, :W => 0.9, :S => 0.8, :Y => 1.3, :P => 1.6, :H => 3.2, :E => 3.5, :Q => 3.5, :D => 3.5, :N => 3.5, :K => 3.9, :R => 4.5, :U => 2.5 }
 AVERAGE_MASS =
{ :I => 113.1594, :V => 99.1326, :L => 113.1594, :F => 147.1766, :C => 103.1388, :M => 131.1926, :A => 71.0788, :G => 57.0519, :T => 101.1051, :W => 186.2132, :S => 87.0782, :Y => 163.1760, :P => 97.1167, :H => 137.1411, :E => 129.1155, :Q => 128.1307, :D => 115.0886, :N => 114.1038, :K => 128.1741, :R => 156.1875, :U => 150.0388 }
 WATER_MASS =
18.01524
 ATOM =
Atomic composition of amino acids.
{ :I => {:C => 6, :H => 13, :O => 2, :N => 1, :S => 0}, # C6H13NO2 :V => {:C => 5, :H => 11, :O => 2, :N => 1, :S => 0}, # C5H11NO2 :L => {:C => 6, :H => 13, :O => 2, :N => 1, :S => 0}, # C6H13NO2 :F => {:C => 9, :H => 11, :O => 2, :N => 1, :S => 0}, # C9H11NO2 :C => {:C => 3, :H => 7 , :O => 2, :N => 1, :S => 1}, # C3H7NO2S :M => {:C => 5, :H => 11 ,:O => 2, :N => 1, :S => 1}, # C5H11NO2S :A => {:C => 3, :H => 7 , :O => 2, :N => 1, :S => 0}, # C3H7NO2 :G => {:C => 2, :H => 5 , :O => 2, :N => 1, :S => 0}, # C2H5NO2 :T => {:C => 4, :H => 9 , :O => 3, :N => 1, :S => 0}, # C4H9NO3 :W => {:C => 11,:H => 12, :O => 2, :N => 2, :S => 0}, # C11H12N2O2 :S => {:C => 3, :H => 7 , :O => 3, :N => 1, :S => 0}, # C3H7NO3 :Y => {:C => 9, :H => 11, :O => 3, :N => 1, :S => 0}, # C9H11NO3 :P => {:C => 5, :H => 9 , :O => 2, :N => 1, :S => 0}, # C5H9NO2 :H => {:C => 6, :H => 9 , :O => 2, :N => 3, :S => 0}, # C6H9N3O2 :E => {:C => 5, :H => 9 , :O => 4, :N => 1, :S => 0}, # C5H9NO4 :Q => {:C => 5, :H => 10, :O => 3, :N => 2, :S => 0}, # C5H10N2O3 :D => {:C => 4, :H => 7 , :O => 4, :N => 1, :S => 0}, # C4H7NO4 :N => {:C => 4, :H => 8 , :O => 3, :N => 2, :S => 0}, # C4H8N2O3 :K => {:C => 6, :H => 14, :O => 2, :N => 2, :S => 0}, # C6H14N2O2 :R => {:C => 6, :H => 14, :O => 2, :N => 4, :S => 0}, # C6H14N4O2 }
 PK =
pK value from Bjellqvist, et al [13]. Taking into account the decrease in pK differences between acids and bases when going from water to 8 M urea, a value of 7.5 has been assigned to the Nterminal residue .
{ :cterm => { :normal => 3.55, :D => 4.55, :E => 4.75 }, :nterm => { :A => 7.59, :M => 7.00, :S => 6.93, :P => 8.36, :T => 6.82, :V => 7.44, :E => 7.70 , :G => 7.50 }, :internal => { :D => 4.05, :E => 4.45, :H => 5.98, :C => 9.0, :Y => 10.0, :K => 10.0, :R => 12.0 } }
Instance Method Summary collapse

#initialize(seq, mode = :local) ⇒ Protparam
constructor
A new instance of Protparam.
Constructor Details
#initialize(seq, mode = :local) ⇒ Protparam
Returns a new instance of Protparam.
355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 
# File 'lib/bio/util/protparam.rb', line 355 def initialize(seq, mode=:local) if seq.kind_of?(String) && Bio::Sequence.guess(seq) == Bio::Sequence::AA @seq = Bio::Sequence::AA.new seq elsif seq.kind_of? Bio::Sequence::AA @seq = seq elsif seq.kind_of?(Bio::Sequence) && seq.guess.kind_of?(Bio::Sequence::AA) @seq = seq.guess elsif seq.kind_of?(String) && Bio::Sequence.guess(seq) == Bio::Sequence::NA raise ArgumentError, "sequence must be an AA sequence" \ "(Input sequence was guessed as a nucleotide sequence)" else raise ArgumentError, "sequence must be an AA sequence" end self.class.class_eval do include(if mode == :remote then Remote else Local end) end end 