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)
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# 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