Class: Sequest::PepXML::AAModification

Inherits:

Object

• Object
• Sequest::PepXML::AAModification

Includes:

SpecIDXML

Defined in:

lib/ms/sequest/pepxml.rb

Overview

Modified aminoacid, static or variable unless otherwise stated, all attributes can be anything

Instance Attribute Summary

• #aminoacid ⇒ Object

  The amino acid (one letter code).

• #binary ⇒ Object

  Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid.

• #mass ⇒ Object

  Mass of modified aminoacid.

• #massdiff ⇒ Object

  Must be a string!!!! Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342] consider Numeric#to_plus_minus_string at top.

• #peptide_terminus ⇒ Object

  whether modification can reside only at protein terminus (specified ‘n’, ‘c’, or ‘nc’).

• #symbol ⇒ Object

  MSial symbol used by search engine to designate this modification.

• #variable ⇒ Object

  Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present.

Instance Method Summary

• #initialize(hash = nil) ⇒ AAModification constructor

  A new instance of AAModification.

• #to_pepxml ⇒ Object

Constructor Details

#initialize(hash = nil) ⇒ AAModification

Returns a new instance of AAModification.

# File 'lib/ms/sequest/pepxml.rb', line 1136

def initialize(hash=nil)
  instance_var_set_from_hash(hash) if hash # can use unless there are weird methods
end

Instance Attribute Details

#aminoacid ⇒ Object

The amino acid (one letter code)

# File 'lib/ms/sequest/pepxml.rb', line 1116

def aminoacid
  @aminoacid
end

#binary ⇒ Object

Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid

# File 'lib/ms/sequest/pepxml.rb', line 1134

def binary
  @binary
end

#mass ⇒ Object

Mass of modified aminoacid

# File 'lib/ms/sequest/pepxml.rb', line 1123

def mass
  @mass
end

#massdiff ⇒ Object

Must be a string!!!! Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342] consider Numeric#to_plus_minus_string at top

# File 'lib/ms/sequest/pepxml.rb', line 1121

def massdiff
  @massdiff
end

#peptide_terminus ⇒ Object

whether modification can reside only at protein terminus (specified ‘n’, ‘c’, or ‘nc’)

# File 'lib/ms/sequest/pepxml.rb', line 1129

def peptide_terminus
  @peptide_terminus
end

#symbol ⇒ Object

MSial symbol used by search engine to designate this modification

# File 'lib/ms/sequest/pepxml.rb', line 1131

def symbol
  @symbol
end

#variable ⇒ Object

Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present

# File 'lib/ms/sequest/pepxml.rb', line 1126

def variable
  @variable
end

Instance Method Details

#to_pepxml ⇒ Object

# File 'lib/ms/sequest/pepxml.rb', line 1140

def to_pepxml
  # note massdiff
  short_element_xml_and_att_string("aminoacid_modification", "aminoacid=\"#{aminoacid}\" massdiff=\"#{massdiff.to_plus_minus_string}\" mass=\"#{mass}\" variable=\"#{variable}\" peptide_terminus=\"#{peptide_terminus}\" symbol=\"#{symbol}\" binary=\"#{binary}\"")
end