mspire-isotope 0.1.0

checksums.yaml

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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in mspire-isotope.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,23 @@
+Copyright (c) 2014 Brigham Young University
+author: John T. Prince
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,78 @@
+# Mspire::Isotope
+
+mspire library that can retrieve (from NIST) and yield element isotope information.  Uses Neese biological ratios by default.
+
+## Installation
+
+    gem install mspire-isotope
+
+## Usage
+
+```ruby
+require 'mspire/isotope'
+```
+
+Note: by default Neese biological isotope abundance ratios are used so H, C, N, O, S
+have slightly different ratios than straight NIST ratios.
+
+### The Isotopes hashed by element
+
+```ruby
+Mspire::Isotope::BY_ELEMENT
+carbon_isotopes = Mspire::Isotope::NIST::BY_ELEMENT[:C]
+```
+
+### An array of all isotopes
+
+```ruby
+all_isotopes = Mspire::Isotope::ISOTOPES
+```
+
+### Only the monoisotopic isotopes
+
+(the monoisotopic isotope is the one with the highest relative abundance)
+
+```ruby
+monoisotopic_isotopes = Mspire::Isotope::ISOTOPES.select(&:mono)
+```
+
+### Convenience method for access by element
+
+```ruby
+# find the lightest carbon isotope
+isotope = Mspire::Isotope[:C]
+
+# find the monoisotopic (i.e., most abundant isotope) of carbon
+isotope = Mspire::Isotope[:C].find(&:mono)
+```
+
+### Information available
+
+```ruby
+c12 = Mspire::Isotope[:C][0]
+c12.atomic_number # => 6
+c12.element # => :C,
+c12.mass_number # => 12,
+c12.atomic_mass # => 12.0,
+c12.relative_abundance # => 0.9891,
+c12.average_mass # => 12.0107,
+c12.mono # => true
+
+c13 = Mspire::Isotope[:C][1]
+...
+```
+
+### Only use NIST data
+
+```ruby
+by_element_hash = Mspire::Isotope::NIST::BY_ELEMENT
+isotope_array = Mspire::Isotope::NIST::ISOTOPES
+```
+
+What about the convenience method? You set which element_hash you are using:
+
+```ruby
+Mspire::Isotope[:C][0].relative_abundance  # => 0.9891
+Mspire::Isotope.element_hash = Mspire::Isotope::NIST::BY_ELEMENT
+Mspire::Isotope[:C][0].relative_abundance  # => 0.9893
+```

data/Rakefile

@@ -0,0 +1,24 @@
+require "bundler/gem_tasks"
+
+@module_name = Mspire::Isotope
+@gem_name = 'mspire-isotope'
+@gem_path_name = @gem_name.gsub('-','/')
+
+require "#{@gem_path_name}/version"
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = @module_name.const_get('VERSION')
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "#{@gem_name} #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/lib/mspire/isotope.rb

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+require "mspire/isotope/version"
+
+module Mspire
+  class Isotope
+    class << self
+      attr_accessor :element_hash
+      def by_element(element)
+        element_hash[element]
+      end
+      alias_method :[], :by_element
+    end
+    MEMBERS = [
+      :atomic_number, 
+      :element, 
+      :mass_number, 
+      :atomic_mass, 
+      :relative_abundance, 
+      :average_mass, 
+      :mono
+    ].each {|key| attr_accessor key }
+
+    def initialize(*args)
+      MEMBERS.zip(args) {|k,val| self.send("#{k}=", val) }
+    end
+  end
+end
+
+
+# sets Mspire::Isotope::BY_ELEMENTS and Mspire::Isotope::ISOTOPES
+require 'mspire/isotope/neese'
+module Mspire
+  class Isotope
+    BY_ELEMENT = Mspire::Isotope::Neese::BY_ELEMENT
+    ISOTOPES = Mspire::Isotope::Neese::ISOTOPES
+
+    self.element_hash = Mspire::Isotope::Neese::BY_ELEMENT
+  end
+end

data/lib/mspire/isotope/aa.rb

@@ -0,0 +1,49 @@
+require 'mspire/molecular_formula'
+
+
+module Mspire
+  class Isotope
+    module AA
+      # These represent counts for the individual residues (i.e., no extra H
+      # and OH on the ends)
+      aa_to_el_hash = {
+        'A' => { C: 3, H: 5, O: 1, N: 1, S: 0, P: 0 },
+        'C' => { C: 3, H: 5, O: 1, N: 1, S: 1, P: 0 },
+        'D' => { C: 4, H: 5, O: 3, N: 1, S: 0, P: 0 },
+        'E' => { C: 5, H: 7, O: 3, N: 1, S: 0, P: 0 },
+        'F' => { C: 9, H: 9, O: 1, N: 1, S: 0, P: 0 },
+        'G' => { C: 2, H: 3, O: 1, N: 1, S: 0, P: 0 },
+        'I' => { C: 6, H: 11, O: 1, N: 1, S: 0, P: 0 },
+        'H' => { C: 6, H: 7, O: 1, N: 3, S: 0, P: 0 },
+        'K' => { C: 6, H: 12, O: 1, N: 2, S: 0, P: 0 },
+        'L' => { C: 6, H: 11, O: 1, N: 1, S: 0, P: 0 },
+        'M' => { C: 5, H: 9, O: 1, N: 1, S: 1, P: 0 },
+        'N' => { C: 4, H: 6, O: 2, N: 2, S: 0, P: 0 },
+        'O' => { C: 12, H: 19, O: 2, N: 3, S: 0, P: 0 },
+        'P' => { C: 5, H: 7, O: 1, N: 1, S: 0, P: 0 },
+        'Q' => { C: 5, H: 8, O: 2, N: 2, S: 0, P: 0 },
+        'R' => { C: 6, H: 12, O: 1, N: 4, S: 0, P: 0 },
+        'S' => { C: 3, H: 5, O: 2, N: 1, S: 0, P: 0 },
+        'T' => { C: 4, H: 7, O: 2, N: 1, S: 0, P: 0 },
+        'U' => { C: 3, H: 5, O: 1, N: 1, S: 0, P: 0, :Se =>1 },
+        'V' => { C: 5, H: 9, O: 1, N: 1, S: 0, P: 0 },
+        'W' => { C: 11, H: 10, O: 1, N: 2, S: 0, P: 0 },
+        'Y' => { C: 9, H: 9, O: 2, N: 1, S: 0, P: 0 },
+      }
+
+      # 
+      FORMULAS_STR = Hash[ 
+        aa_to_el_hash.map {|k,v| [k, Mspire::MolecularFormula.new(v)] }
+      ]
+
+      FORMULAS_SYM = Hash[FORMULAS_STR.map {|k,v| [k.to_sym, v] }]
+
+      # string and symbol access of amino acid residues (amino acids are
+      # accessed upper case and atoms are all lower case symbols)
+      FORMULAS = FORMULAS_SYM.merge FORMULAS_STR
+      
+      # an alias for FORMULAS
+      ATOM_COUNTS = FORMULAS
+    end
+  end
+end

data/lib/mspire/isotope/neese.rb

@@ -0,0 +1,33 @@
+require 'mspire/isotope/nist'
+
+module Mspire
+  class Isotope
+    module Neese
+      RATIOS = {
+        H: [0.999844, 0.000156],
+        C: [0.9891, 0.0109],
+        N: [0.99635, 0.00365],
+        O: [0.99759, 0.00037, 0.00204],
+        S: [0.9493, 0.0076, 0.0429, 0.0002]
+      }
+
+      BY_ELEMENT = Mspire::Isotope::NIST::BY_ELEMENT.dup  # shallow copy on purpose
+
+      RATIOS.each do |el, abundances| 
+        BY_ELEMENT[el] = Mspire::Isotope::NIST::BY_ELEMENT[el].
+          zip(abundances).map do |isotope, abundance|
+          if abundance
+            new_isotope = isotope.dup
+            new_isotope.relative_abundance = abundance 
+            new_isotope
+          else
+            isotope
+          end
+        end
+      end
+
+      ISOTOPES = BY_ELEMENT.values.flatten(1).sort_by {|ist| [ist.atomic_number, ist.mass_number] }
+    end
+  end
+end
+

data/lib/mspire/isotope/nist.rb

@@ -0,0 +1,20 @@
+require 'yaml'
+require 'mspire/isotope'
+
+module Mspire::Isotope::NIST
+  INFO_FILE = 'isotope_info.yml'
+  INFO_FILE_FULL_PATH = File.expand_path(File.dirname(__FILE__) + "/nist/#{INFO_FILE}")
+
+  if File.exist?(INFO_FILE_FULL_PATH)
+
+    ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| Mspire::Isotope.new *ar }
+    BY_ELEMENT = ISOTOPES.group_by(&:element)
+
+  else
+    unless __FILE__ == $0
+      warn "no file #{INFO_FILE_FULL_PATH} to read isotope information from!"
+      warn "Note that directly running the file: lib/mspire/isotope/nist/updater.rb"
+      warn "will autogenerate this file from NIST data"
+    end
+  end
+end 

data/lib/mspire/isotope/nist/isotope_info.yml

@@ -0,0 +1,2017 @@
+---
+- - 1
+  - :H
+  - 1
+  - 1.00782503207
+  - 0.999885
+  - 1.00794
+  - true
+- - 1
+  - :H
+  - 2
+  - 2.0141017778
+  - 0.000115
+  - 1.00794
+  - false
+- - 2
+  - :He
+  - 3
+  - 3.0160293191
+  - 1.34e-06
+  - 4.002602
+  - false
+- - 2
+  - :He
+  - 4
+  - 4.00260325415
+  - 0.99999866
+  - 4.002602
+  - true
+- - 3
+  - :Li
+  - 6
+  - 6.015122795
+  - 0.0759
+  - 6.941
+  - false
+- - 3
+  - :Li
+  - 7
+  - 7.01600455
+  - 0.9241
+  - 6.941
+  - true
+- - 4
+  - :Be
+  - 9
+  - 9.0121822
+  - 1.0
+  - 9.012182
+  - true
+- - 5
+  - :B
+  - 10
+  - 10.012937
+  - 0.199
+  - 10.811
+  - false
+- - 5
+  - :B
+  - 11
+  - 11.0093054
+  - 0.801
+  - 10.811
+  - true
+- - 6
+  - :C
+  - 12
+  - 12.0
+  - 0.9893
+  - 12.0107
+  - true
+- - 6
+  - :C
+  - 13
+  - 13.0033548378
+  - 0.0107
+  - 12.0107
+  - false
+- - 7
+  - :N
+  - 14
+  - 14.0030740048
+  - 0.99636
+  - 14.0067
+  - true
+- - 7
+  - :N
+  - 15
+  - 15.0001088982
+  - 0.00364
+  - 14.0067
+  - false
+- - 8
+  - :O
+  - 16
+  - 15.99491461956
+  - 0.99757
+  - 15.9994
+  - true
+- - 8
+  - :O
+  - 17
+  - 16.9991317
+  - 0.00038
+  - 15.9994
+  - false
+- - 8
+  - :O
+  - 18
+  - 17.999161
+  - 0.00205
+  - 15.9994
+  - false
+- - 9
+  - :F
+  - 19
+  - 18.99840322
+  - 1.0
+  - 18.9984032
+  - true
+- - 10
+  - :Ne
+  - 20
+  - 19.9924401754
+  - 0.9048
+  - 20.1797
+  - true
+- - 10
+  - :Ne
+  - 21
+  - 20.99384668
+  - 0.0027
+  - 20.1797
+  - false
+- - 10
+  - :Ne
+  - 22
+  - 21.991385114
+  - 0.0925
+  - 20.1797
+  - false
+- - 11
+  - :Na
+  - 23
+  - 22.9897692809
+  - 1.0
+  - 22.98976928
+  - true
+- - 12
+  - :Mg
+  - 24
+  - 23.9850417
+  - 0.7899
+  - 24.305
+  - true
+- - 12
+  - :Mg
+  - 25
+  - 24.98583692
+  - 0.1
+  - 24.305
+  - false
+- - 12
+  - :Mg
+  - 26
+  - 25.982592929
+  - 0.1101
+  - 24.305
+  - false
+- - 13
+  - :Al
+  - 27
+  - 26.98153863
+  - 1.0
+  - 26.9815386
+  - true
+- - 14
+  - :Si
+  - 28
+  - 27.9769265325
+  - 0.92223
+  - 28.0855
+  - true
+- - 14
+  - :Si
+  - 29
+  - 28.9764947
+  - 0.04685
+  - 28.0855
+  - false
+- - 14
+  - :Si
+  - 30
+  - 29.97377017
+  - 0.03092
+  - 28.0855
+  - false
+- - 15
+  - :P
+  - 31
+  - 30.97376163
+  - 1.0
+  - 30.973762
+  - true
+- - 16
+  - :S
+  - 32
+  - 31.972071
+  - 0.9499
+  - 32.065
+  - true
+- - 16
+  - :S
+  - 33
+  - 32.97145876
+  - 0.0075
+  - 32.065
+  - false
+- - 16
+  - :S
+  - 34
+  - 33.9678669
+  - 0.0425
+  - 32.065
+  - false
+- - 16
+  - :S
+  - 36
+  - 35.96708076
+  - 0.0001
+  - 32.065
+  - false
+- - 17
+  - :Cl
+  - 35
+  - 34.96885268
+  - 0.7576
+  - 35.453
+  - true
+- - 17
+  - :Cl
+  - 37
+  - 36.96590259
+  - 0.2424
+  - 35.453
+  - false
+- - 18
+  - :Ar
+  - 36
+  - 35.967545106
+  - 0.003365
+  - 39.948
+  - false
+- - 18
+  - :Ar
+  - 38
+  - 37.9627324
+  - 0.000632
+  - 39.948
+  - false
+- - 18
+  - :Ar
+  - 40
+  - 39.9623831225
+  - 0.996003
+  - 39.948
+  - true
+- - 19
+  - :K
+  - 39
+  - 38.96370668
+  - 0.932581
+  - 39.0983
+  - true
+- - 19
+  - :K
+  - 40
+  - 39.96399848
+  - 0.000117
+  - 39.0983
+  - false
+- - 19
+  - :K
+  - 41
+  - 40.96182576
+  - 0.067302
+  - 39.0983
+  - false
+- - 20
+  - :Ca
+  - 40
+  - 39.96259098
+  - 0.96941
+  - 40.078
+  - true
+- - 20
+  - :Ca
+  - 42
+  - 41.95861801
+  - 0.00647
+  - 40.078
+  - false
+- - 20
+  - :Ca
+  - 43
+  - 42.9587666
+  - 0.00135
+  - 40.078
+  - false
+- - 20
+  - :Ca
+  - 44
+  - 43.9554818
+  - 0.02086
+  - 40.078
+  - false
+- - 20
+  - :Ca
+  - 46
+  - 45.9536926
+  - 4.0e-05
+  - 40.078
+  - false
+- - 20
+  - :Ca
+  - 48
+  - 47.952534
+  - 0.00187
+  - 40.078
+  - false
+- - 21
+  - :Sc
+  - 45
+  - 44.9559119
+  - 1.0
+  - 44.955912
+  - true
+- - 22
+  - :Ti
+  - 46
+  - 45.9526316
+  - 0.0825
+  - 47.867
+  - false
+- - 22
+  - :Ti
+  - 47
+  - 46.9517631
+  - 0.0744
+  - 47.867
+  - false
+- - 22
+  - :Ti
+  - 48
+  - 47.9479463
+  - 0.7372
+  - 47.867
+  - true
+- - 22
+  - :Ti
+  - 49
+  - 48.94787
+  - 0.0541
+  - 47.867
+  - false
+- - 22
+  - :Ti
+  - 50
+  - 49.9447912
+  - 0.0518
+  - 47.867
+  - false
+- - 23
+  - :V
+  - 50
+  - 49.9471585
+  - 0.0025
+  - 50.9415
+  - false
+- - 23
+  - :V
+  - 51
+  - 50.9439595
+  - 0.9975
+  - 50.9415
+  - true
+- - 24
+  - :Cr
+  - 50
+  - 49.9460442
+  - 0.04345
+  - 51.9961
+  - false
+- - 24
+  - :Cr
+  - 52
+  - 51.9405075
+  - 0.83789
+  - 51.9961
+  - true
+- - 24
+  - :Cr
+  - 53
+  - 52.9406494
+  - 0.09501
+  - 51.9961
+  - false
+- - 24
+  - :Cr
+  - 54
+  - 53.9388804
+  - 0.02365
+  - 51.9961
+  - false
+- - 25
+  - :Mn
+  - 55
+  - 54.9380451
+  - 1.0
+  - 54.938045
+  - true
+- - 26
+  - :Fe
+  - 54
+  - 53.9396105
+  - 0.05845
+  - 55.845
+  - false
+- - 26
+  - :Fe
+  - 56
+  - 55.9349375
+  - 0.91754
+  - 55.845
+  - true
+- - 26
+  - :Fe
+  - 57
+  - 56.935394
+  - 0.02119
+  - 55.845
+  - false
+- - 26
+  - :Fe
+  - 58
+  - 57.9332756
+  - 0.00282
+  - 55.845
+  - false
+- - 27
+  - :Co
+  - 59
+  - 58.933195
+  - 1.0
+  - 58.933195
+  - true
+- - 28
+  - :Ni
+  - 58
+  - 57.9353429
+  - 0.680769
+  - 58.6934
+  - true
+- - 28
+  - :Ni
+  - 60
+  - 59.9307864
+  - 0.262231
+  - 58.6934
+  - false
+- - 28
+  - :Ni
+  - 61
+  - 60.931056
+  - 0.011399
+  - 58.6934
+  - false
+- - 28
+  - :Ni
+  - 62
+  - 61.9283451
+  - 0.036345
+  - 58.6934
+  - false
+- - 28
+  - :Ni
+  - 64
+  - 63.927966
+  - 0.009256
+  - 58.6934
+  - false
+- - 29
+  - :Cu
+  - 63
+  - 62.9295975
+  - 0.6915
+  - 63.546
+  - true
+- - 29
+  - :Cu
+  - 65
+  - 64.9277895
+  - 0.3085
+  - 63.546
+  - false
+- - 30
+  - :Zn
+  - 64
+  - 63.9291422
+  - 0.48268
+  - 65.38
+  - true
+- - 30
+  - :Zn
+  - 66
+  - 65.9260334
+  - 0.27975
+  - 65.38
+  - false
+- - 30
+  - :Zn
+  - 67
+  - 66.9271273
+  - 0.04102
+  - 65.38
+  - false
+- - 30
+  - :Zn
+  - 68
+  - 67.9248442
+  - 0.19024
+  - 65.38
+  - false
+- - 30
+  - :Zn
+  - 70
+  - 69.9253193
+  - 0.00631
+  - 65.38
+  - false
+- - 31
+  - :Ga
+  - 69
+  - 68.9255736
+  - 0.60108
+  - 69.723
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