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
- 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
# 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