class Mspire::Ident::Pepxml::AminoacidModification
Modified aminoacid, static or variable unless otherwise stated, all attributes can be anything
Attributes
aminoacid[RW]
The amino acid (one letter code)
binary[RW]
‘Y’ if each peptide must have only modified or unmodified aminoacid, ‘N’ if a peptide may contain both modified and unmodified aminoacid
mass[RW]
Mass of modified aminoacid, Float
massdiff[RW]
Mass difference with respect to unmodified aminoacid, as a Float
peptide_terminus[RW]
whether modification can reside only at protein terminus (specified ‘n’, ‘c’, or ‘nc’)
symbol[RW]
Symbol used by search engine to designate this modification
variable[RW]
Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present
Public Class Methods
new(hash={})
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# File lib/mspire/ident/pepxml/modifications.rb, line 30 def initialize(hash={}) merge!(hash) end
Public Instance Methods
to_xml(builder=nil)
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returns the builder or an xml string if no builder supplied
# File lib/mspire/ident/pepxml/modifications.rb, line 35 def to_xml(builder=nil) xmlb = builder || Nokogiri::XML::Builder.new # note massdiff: must begin with either + (nonnegative) or - [e.g. # +1.05446 or -2.3342] consider Numeric#to_plus_minus_string in # Mspire::Ident::Pepxml attrs = [:aminoacid, :massdiff, :mass, :variable, :peptide_terminus, :symbol, :binary].map {|at| v=send(at) ; [at,v] if v }.compact hash = Hash[attrs] hash[:massdiff] = hash[:massdiff].to_plus_minus_string xmlb.aminoacid_modification(hash) builder || xmlb.doc.root.to_xml end