class Modifications

Attributes

modifications[RW]

Public Class Methods

new(mods) click to toggle source
# File lib/ms/sim_modifications.rb, line 5
def initialize(mods)
  @modifications = mods
  @modifications = @modifications.split(/_/)
  if @modifications[0] != "false"
    get_mods
  else
    @modifications = nil
  end
  return @modifications
end

Public Instance Methods

get_mods() click to toggle source
# File lib/ms/sim_modifications.rb, line 16
def get_mods()
  mods = {}
  obo = Obo::Ontology.new(Obo::Ontology::DIR + '/mod.obo')
  @modifications.each do |mod|
    diff = nil
    residue = mod[9..mod.size-1]
    mod = (obo.id_to_element[mod[0..8]]).tagvalues
    xref = mod['xref']
    xref.each do |x|
      if x =~ /DiffFormula/
        diff = (x.split(/"/))[1]
      end
    end
    if mods[residue] == nil
      mods[residue] = [[mod['id'][0],diff]]
    else
      mds = mods[residue]
      mds<<[mod['id'][0],diff]
      mods[residue] = mds
    end
  end
  @modifications = mods
end