Class: Mspire::Isotope::NIST::Updater

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/isotope/nist/updater.rb

Constant Summary collapse

NIST_ISOTOPE_SITE = 
'http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some'

Class Method Summary collapse

Class Method Details

.isotope_from_nist_line(*args) ⇒ Object

Creates an isotope from a nist entry. Sets mono to false, which is not always correct (but needs to be corrected with additional info)



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# File 'lib/mspire/isotope/nist/updater.rb', line 10

def isotope_from_nist_line(*args)
  # atomic_number and mass_number are ints
  [0,2].each {|i| args[i] = args[i].to_i }
  # element is a downcase sym
  args[1] = args[1].to_sym
  # atomic_mass, relative_abundance, and average_mass as floats
  [3, 4, 5].each {|i| args[i] = args[i][/([\w.]*)/].to_f }
  # by default call every isotope the non-monoisotopic peak
  # (will correct it as a group)
  args << false
  Mspire::Isotope.new(*args)
end

.isotopes_from_nist_site(deuterium_is_kind_of_hydrogen = true) ⇒ Object 



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# File 'lib/mspire/isotope/nist/updater.rb', line 28

def isotopes_from_nist_site(deuterium_is_kind_of_hydrogen=true)
  require 'mechanize'
  body = Mechanize.new.get(NIST_ISOTOPE_SITE).body.split("\n")
  body.delete_if {|l| l[/^(<|\/)/]}
  body.shift(22)
  isotopes = body.each_slice(8).map do |lines|
    arr = (1..4).to_a.map {|i| match lines[i] }
    rel, avg = match(lines[5]), match(lines[6])
    next if rel.nil?
    rel.size > 0 ? isotope_from_nist_line(*arr, rel, avg) : nil
  end.compact!

  # deuterium should be grouped with hydrogen, not as its own element!
  isotopes.find {|iso| iso.element == :D }.element = :H if deuterium_is_kind_of_hydrogen

  # update the mono boolean if this is the highest abundance peak
  isotopes.group_by(&:element).values.each do |set|
    set.max_by(&:relative_abundance).mono = true
  end
  isotopes
end

.write_nist_info(filename) ⇒ Object 



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# File 'lib/mspire/isotope/nist/updater.rb', line 23

def write_nist_info(filename)
  isotopes = isotopes_from_nist_site
  File.write(filename, isotopes.map {|isotope| Mspire::Isotope::MEMBERS.map {|key| isotope.send(key) }}.to_yaml)
end