class Bio::Protparam

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.

Constants

ATOM

Atomic composition of amino acids.

AVERAGE_MASS

Average isotopic masses of amino acids

DIWV

Dipeptide instability weight value for calculating instability index of proteins [10].

HALFLIFE

Estemated half-life (minutes) of N-terminal residue of a protein.

HYDROPATHY

Hydropathy values for amino acids [12].

IUPAC_CODE

IUPAC codes for amino acids.

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 N-terminal residue .

WATER_MASS

Public Class Methods

new(seq, mode=:local) click to toggle source
# 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
    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

References

↑ top