class Bio::Transmembrane::OrientedTransmembraneDomain

From Predicting transmembrane protein topology with a hidden markov model: application to complete g

Another signal shown to be associated with transmembrane helices is the abundance of positively charged residues in the part of the sequence on the cytoplasmic side of the membrane, “the positive inside rule” (von Heijne 1986) and (von Heijne 1994).

So, inside means cytosolic. So outside_in means type I transmembrane domain protein

Constants

INSIDE_OUT

The orientation can either be inside out (like a type II transmembrane domain protein)

OUTSIDE_IN

Or outside in, like a type I transmembrane domain protein)

UNKNOWN

or the whole protein is TMD, so orientation is unknown

Attributes

orientation[RW]

Public Class Methods

new(start=nil, stop=nil, orientation=nil) click to toggle source
# File lib/bio/transmembrane.rb, line 201
def initialize(start=nil, stop=nil, orientation=nil)
  @start = start.to_i unless start.nil?
  @stop = stop.to_i unless stop.nil?
  @orientation = orientation unless orientation.nil?
end