Class: Bio::Transmembrane::OrientedTransmembraneDomain

Inherits:
TransmembraneDomainDefinition show all
Defined in:
lib/bio/transmembrane.rb

Overview

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

Constant Summary collapse

INSIDE_OUT =

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

'inside_out'
OUTSIDE_IN =

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

'outside_in'
UNKNOWN =

or the whole protein is TMD, so orientation is unknown

'unknown'

Instance Attribute Summary collapse

Attributes inherited from TransmembraneDomainDefinition

#start, #stop

Instance Method Summary collapse

Methods inherited from TransmembraneDomainDefinition

#<=>, #==, #intersection, #length, #overlap_length, #sequence

Constructor Details

#initialize(start = nil, stop = nil, orientation = nil) ⇒ OrientedTransmembraneDomain

Returns a new instance of OrientedTransmembraneDomain.



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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

Instance Attribute Details

#orientation ⇒ Object

Returns the value of attribute orientation.



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# File 'lib/bio/transmembrane.rb', line 199

def orientation
  @orientation
end