mspire-isotope 0.1.0

data/lib/mspire/isotope/nist/updater.rb

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+require 'mspire/isotope'
+
+class Mspire::Isotope::NIST::Updater
+  NIST_ISOTOPE_SITE = 'http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some'
+
+  class << self
+
+    # Creates an isotope from a nist entry.  Sets mono to false, which is not
+    # always correct (but needs to be corrected with additional info)
+    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
+
+    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
+
+    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
+
+    private
+
+    def match(string)
+      unless string.nil?
+        if string.empty?
+          nil
+        else
+          string[/= (.*)/,1]
+        end
+      end
+    end 
+  end 
+end
+
+if __FILE__ == $0
+  require 'mspire/isotope/nist'
+  Mspire::Isotope::NIST::Updater.write_nist_info(Mspire::Isotope::NIST::INFO_FILE_FULL_PATH)
+end

data/lib/mspire/isotope/version.rb

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+module Mspire
+  class Isotope
+    VERSION = "0.1.0"
+  end
+end

data/mspire-isotope.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'mspire/isotope/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "mspire-isotope"
+  spec.version       = Mspire::Isotope::VERSION
+  spec.authors       = ["John T. Prince"]
+  spec.email         = ["jtprince@gmail.com"]
+  spec.summary       = %q{mspire library holding element isotope information}
+  spec.description   = %q{mspire library holding element isotope information.  Mostly just holds constants.}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  [
+    #["nokogiri", "~> 1.6.1"],
+    #["bsearch", ">= 1.5.0"],
+  ].each do |args|
+    spec.add_dependency(*args)
+  end
+
+  [
+    ["bundler", "~> 1.6.2"],
+    ["rake"],
+    ["rspec", "~> 2.14.1"], 
+    ["rdoc", "~> 4.1.1"], 
+    ["simplecov", "~> 0.8.2"],
+  ].each do |args|
+    spec.add_development_dependency(*args)
+  end
+end

data/spec/mspire/isotope_spec.rb

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+require 'spec_helper'
+
+require 'mspire/isotope'
+
+describe Mspire::Isotope do
+
+  specify 'Mspire::Isotope[] accesses isotopes by element' do
+    carbon12 = Mspire::Isotope[:C][0]  # the lightest carbon isotope
+    carbon12.element.should == :C
+    carbon12.mass_number.should == 12
+    carbon12 = Mspire::Isotope[:C].find(&:mono)  # the most abundant (i.e., monoisotopic isotope)
+    carbon12.element.should == :C
+    carbon12.mass_number.should == 12
+    carbon12.mono.should be_true
+  end
+
+  it 'can set the element_hash to change convenience method access' do
+    Mspire::Isotope[:C][0].relative_abundance.should == 0.9891
+    Mspire::Isotope.element_hash = Mspire::Isotope::NIST::BY_ELEMENT
+    Mspire::Isotope[:C][0].relative_abundance.should == 0.9893
+  end
+
+  specify 'Mspire::Isotope::ISOTOPES has all the common isotopes and (uses Neese by default)' do
+    # frozen
+    Mspire::Isotope::ISOTOPES.size.should == 288
+    hydrogen_isotopes = Mspire::Isotope::ISOTOPES.select {|iso| iso.element == :H }
+    hydrogen_isotopes.size.should == 2
+
+    {atomic_number: 1, element: :H, mass_number: 1, atomic_mass: 1.00782503207, relative_abundance: 0.999844, average_mass: 1.00794, mono: true}.each do |k,v|
+      hydrogen_isotopes.first.send(k).should == v
+    end
+    {atomic_number: 1, element: :H, mass_number: 2, atomic_mass: 2.0141017778, relative_abundance: 0.000156, average_mass: 1.00794, mono: false}.each do |k,v|
+      hydrogen_isotopes.last.send(k).should == v
+    end
+    u = Mspire::Isotope::ISOTOPES.last
+    {atomic_number: 92, element: :U, mass_number: 238, atomic_mass: 238.0507882, relative_abundance: 0.992742, average_mass: 238.02891, mono: true}.each do |k,v|
+      u.send(k).should == v
+    end
+  end
+
+  specify 'Mspire::Isotope::BY_ELEMENT has all common isotopes by element (uses Neese by default)' do
+    [{atomic_number: 6, element: :C, mass_number: 12, atomic_mass: 12.0, relative_abundance: 0.9891, average_mass: 12.0107, mono: true}, {atomic_number: 6, element: :C, mass_number: 13, atomic_mass: 13.0033548378, relative_abundance: 0.0109, average_mass: 12.0107, mono: false}].zip(Mspire::Isotope::BY_ELEMENT[:C]) do |hash, iso|
+      hash.each do |k,v|
+        iso.send(k).should == v
+      end
+    end
+    Mspire::Isotope::BY_ELEMENT[:H].size.should == 2
+  end
+end

data/spec/spec_helper.rb

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+require 'simplecov'
+SimpleCov.start
+
+require 'rspec'
+
+TESTFILES = File.dirname(__FILE__) + '/testfiles'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.color_enabled = true
+  config.tty = true
+  config.formatter = :documentation  # :progress, :html, :textmate
+  #config.formatter = :progress # :progress, :html, :textmate
+end
+
+

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification
+name: mspire-isotope
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- John T. Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-07-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.1.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.1.1
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+description: mspire library holding element isotope information.  Mostly just holds
+  constants.
+email:
+- jtprince@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/mspire/isotope.rb
+- lib/mspire/isotope/aa.rb
+- lib/mspire/isotope/neese.rb
+- lib/mspire/isotope/nist.rb
+- lib/mspire/isotope/nist/isotope_info.yml
+- lib/mspire/isotope/nist/updater.rb
+- lib/mspire/isotope/version.rb
+- mspire-isotope.gemspec
+- spec/mspire/isotope_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: mspire library holding element isotope information
+test_files:
+- spec/mspire/isotope_spec.rb
+- spec/spec_helper.rb