mspire 0.8.7 → 0.9.0

data/lib/mspire/mass.rb

@@ -1,49 +1,41 @@
-require 'mspire/isotope'
-require 'mspire/molecular_formula'
 
 module Mspire
   module Mass
+      end
+end
 
-    # takes a molecular formula as a string, hash or MolecularFormula object
-    # and returns the exact mass.
-    def self.formula_to_exact_mass(formula)
-      Mspire::MolecularFormula.from_any(formula).mass
-    end
+require 'mspire/molecular_formula'
+require 'mspire/mass/element'
+require 'mspire/mass/subatomic'
+require 'mspire/mass/common'
+require 'mspire/mass/aa'
 
-    MONO_STR = {
-      'h+' => 1.00727646677,
-      'e' => 0.0005486,   # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
-      'neutron' => 1.0086649156,
-    }
+module Mspire
+  module Mass
 
-    Mspire::Isotope::BY_ELEMENT.each do |el, isotopes|
-      MONO_STR[el.to_s] = isotopes.find {|iso| iso.mono }.atomic_mass
-    end
-    MONO_STR['h2o'] = %w(h h o).map {|el| MONO_STR[el] }.reduce(:+)
-    MONO_STR['oh'] = %w(o h).map {|el| MONO_STR[el] }.reduce(:+)
-    # add on deuterium
-    MONO_STR['d'] = Mspire::Isotope::BY_ELEMENT[:h].find {|iso| iso.element == :h && iso.mass_number == 2 }.atomic_mass
-
-    AVG_STR = {
-      'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)
-      'e' => 0.0005486,
-      'neutron' => 1.0086649156,
-    }
-    Mspire::Isotope::BY_ELEMENT.each do |el, isotopes|
-      AVG_STR[el.to_s] = isotopes.first.average_mass
-    end
-    AVG_STR['h2o'] = %w(h h o).map {|el| AVG_STR[el] }.reduce(:+)
-    AVG_STR['oh'] = %w(o h).map {|el| AVG_STR[el] }.reduce(:+)
+    ELECTRON = Subatomic::MONO[:e]
+    NEUTRON = Subatomic::MONO[:neutron]
+    PROTON = Subatomic::MONO[:proton]
+    H_PLUS = PROTON
+
+    class << self
+      # takes a molecular formula as a string, hash or MolecularFormula object
+      # and returns the exact mass.
+      def formula_to_exact_mass(formula)
+        Mspire::MolecularFormula.from_any(formula).mass
+      end
+      alias_method :formula, :formula_to_exact_mass
+
+      def aa_to_exact_mass(aa_seq)
+        chain_mass = aa_seq.each_char.inject(0.0) do |sum, aa_char|
+          sum + AA[aa_char]
+        end
+        chain_mass + formula_to_exact_mass('H2O')
+      end
+      alias_method :aa, :aa_to_exact_mass
 
-    # sets MONO_SYM, MONO, AVG_SYM, and AVG
-    %w(MONO AVG).each do |type|
-      const_set "#{type}_SYM", Hash[ const_get("#{type}_STR").map {|k,v| [k.to_sym, v] } ]
-      const_set type, const_get("#{type}_STR").merge( const_get("#{type}_SYM") )
     end
 
-    ELECTRON = MONO[:e]
-    NEUTRON = MONO[:neutron]
-    H_PLUS = MONO['h+']
 
   end
 end

data/lib/mspire/mass/aa.rb

@@ -1,4 +1,4 @@
-require 'mspire/mass'
+require 'mspire/mass/util'
 
 module Mspire
   module Mass
@@ -65,18 +65,22 @@ module Mspire
       }
 
       # amino_acids keys as symbols, monoisotopic masses
-      MONO_SYM = Hash[MONO_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
+      MONO_SYMBOL = Mspire::Mass::Util.symbol_keys( MONO_STRING )
 
       # amino_acids keys as symbols, average masses
-      AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
+      AVG_SYMBOL = Mspire::Mass::Util.symbol_keys( AVG_STRING )
 
-      # Monoisotopic amino acid masses keyed as symbols and also strings (all
-      # upper case).  Also includes Mspire::Mass::MONO for things like protons ('h+' and 'h2o')
-      MONO = MONO_SYM.merge(MONO_STRING).merge(Mspire::Mass::MONO)
+      # Monoisotopic amino acid masses keyed as symbols and also strings 
+      MONO = MONO_SYMBOL.merge(MONO_STRING)
 
-      # Average amino acid masses keyed as symbols and also strings (all
-      # uppder case).  Also includes Mspire::Mass::AVG for things like protons ('h+' and 'h2o')
-      AVG = AVG_SYM.merge(AVG_STRING).merge(Mspire::Mass::AVG)
+      # Average amino acid masses keyed as symbols and also strings
+      AVG = AVG_SYMBOL.merge(AVG_STRING)
+
+      class << self
+        def [](key) 
+          MONO[key]
+        end
+      end
     end
   end
 end

data/lib/mspire/mass/all.rb

@@ -0,0 +1,37 @@
+require 'mspire/mass/util'
+
+module Mspire
+  module Mass
+    # provides hashes with both Amino Acids (uppercase letters) and elements
+    # (lowercased) along with common abbreviations
+    module All
+      def self.downcase_keys(hash)
+        Hash[ hash.map {|key,val| [key.to_s.downcase, val] } ]
+      end
+
+      MONO_STRING = downcase_keys( Element::MONO_STRING )
+        .merge( downcase_keys( Common::MONO_STRING ) )
+        .merge( AA::MONO_STRING )
+        .merge( downcase_keys( Subatomic::MONO_STRING ) )
+
+      MONO_SYMBOL = Mspire::Mass::Util.symbol_keys( MONO_STRING )
+      MONO = MONO_STRING.merge( MONO_SYMBOL )
+
+      AVG_STRING = downcase_keys( Element::AVG_STRING )
+        .merge( downcase_keys( Common::AVG_STRING ) )
+        .merge( AA::AVG_STRING )
+        .merge( downcase_keys( Subatomic::MONO_STRING ) )  
+        # ^^ NOTE: we use MONO values for Subatomic since avg makes no sense
+
+      AVG_SYMBOL = Mspire::Mass::Util.symbol_keys( AVG_STRING )
+      AVG = AVG_STRING.merge( AVG_SYMBOL )
+
+      class << self
+        def [](key)
+          MONO[key]
+        end
+      end
+
+    end
+  end
+end

data/lib/mspire/mass/common.rb

@@ -0,0 +1,34 @@
+require 'mspire/mass/util'
+require 'mspire/mass/element'
+
+module Mspire
+  module Mass
+    module Common
+      mono_string = Mspire::Mass::Element::MONO_STRING
+      avg_string = Mspire::Mass::Element::AVG_STRING
+
+      MONO_STRING = {
+        'H2O' => %w(H H O).map {|el| mono_string[el] }.reduce(:+),
+        'OH' => %w(O H).map {|el| mono_string[el] }.reduce(:+),
+      }
+
+      AVG_STRING = {
+        'H2O' => %w(H H O).map {|el| avg_string[el] }.reduce(:+),
+        'OH' => %w(O H).map {|el| avg_string[el] }.reduce(:+),
+      }
+
+      MONO_SYMBOL = Mspire::Mass::Util.symbol_keys( MONO_STRING )
+      MONO = MONO_STRING.merge( MONO_SYMBOL )
+
+      AVG_SYMBOL = Mspire::Mass::Util.symbol_keys( AVG_STRING )
+      AVG = AVG_STRING.merge( AVG_SYMBOL )
+
+      class << self
+        def [](key)
+          MONO[key]
+        end
+      end
+
+    end
+  end
+end

data/lib/mspire/mass/element.rb

@@ -0,0 +1,30 @@
+require 'mspire/isotope'
+require 'mspire/mass/util'
+
+module Mspire
+  module Mass
+    module Element
+
+      AVG_STRING = {}
+      MONO_STRING = {}
+      Mspire::Isotope::BY_ELEMENT.each do |el, isotopes|
+        AVG_STRING[el.to_s] = isotopes.first.average_mass
+        MONO_STRING[el.to_s] = isotopes.find {|iso| iso.mono }.atomic_mass
+      end
+
+      MONO_STRING['D'] = Mspire::Isotope::BY_ELEMENT[:H].find {|iso| iso.element == :H && iso.mass_number == 2 }.atomic_mass
+
+      MONO_SYMBOL = Mspire::Mass::Util.symbol_keys( MONO_STRING )
+      AVG_SYMBOL = Mspire::Mass::Util.symbol_keys( AVG_STRING )
+      MONO = MONO_SYMBOL.merge(MONO_STRING)
+      AVG = AVG_SYMBOL.merge(AVG_STRING)
+
+      class << self
+        def [](key)
+          MONO[key]
+        end
+      end
+
+    end
+  end
+end

data/lib/mspire/mass/subatomic.rb

@@ -0,0 +1,27 @@
+require 'mspire/mass/util'
+require 'mspire/mass/element'
+
+module Mspire
+  module Mass
+    module Subatomic
+      MONO_STRING = {
+        'electron' => 0.0005486,   # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
+        'neutron' => 1.0086649156,
+      }
+      MONO_STRING['proton'] = Mspire::Mass::Element[:H] - MONO_STRING['electron']
+      MONO_STRING['H+'] = MONO_STRING['proton']
+      MONO_STRING['e'] = MONO_STRING['electron']
+
+      MONO_SYMBOL = Mspire::Mass::Util.symbol_keys( MONO_STRING )
+      MONO = MONO_STRING.merge( MONO_SYMBOL )
+
+      class << self
+        def [](key)
+          MONO[key]
+        end
+      end
+
+      # 'h+' => 1.00727646677,
+    end
+  end
+end

data/lib/mspire/mass/util.rb

@@ -0,0 +1,10 @@
+
+module Mspire
+  module Mass
+    module Util
+      def self.symbol_keys(hash)
+        Hash[ hash.map {|key,val| [key.to_sym, val] } ]
+      end
+    end
+  end
+end

data/lib/mspire/molecular_formula.rb

@@ -5,12 +5,12 @@ module Mspire
   class MolecularFormula < Hash
 
     class << self
-      def from_aaseq(aaseq)
+      def from_aaseq(aaseq, formula_hash=Mspire::Isotope::AA::FORMULAS)
         hash = aaseq.each_char.inject({}) do |hash,aa| 
-          hash.merge(Mspire::Isotope::AA::FORMULAS[aa]) {|h,o,n| (o ? o : 0) +n }
+          hash.merge(formula_hash[aa]) {|hash,old,new| (old ? old : 0) + new }
         end
-        hash[:h] += 2
-        hash[:o] += 1
+        hash[:H] += 2
+        hash[:O] += 1
         self.new(hash)
       end
 
@@ -19,7 +19,7 @@ module Mspire
       def from_string(mol_form_str, charge=0)
         mf = self.new({}, charge)
         mol_form_str.scan(/([A-Z][a-z]?)(\d*)/).each do |k,v| 
-          mf[k.downcase.to_sym] = (v == '' ? 1 : v.to_i)
+          mf[k.to_sym] = (v == '' ? 1 : v.to_i)
         end
         mf
       end
@@ -41,7 +41,7 @@ module Mspire
     attr_accessor :charge
 
     # Takes a hash and an optional Integer expressing the charge
-    #     {h: 22, c: 12, n: 1, o: 3, s: 2}  # case and string/sym doesn't matter
+    #     {H: 22, C: 12, N: 1, O: 3, S: 2}  # case and string/sym doesn't matter
     def initialize(hash={}, charge=0)
       @charge = charge
       self.merge!(hash)
@@ -118,13 +118,15 @@ module Mspire
     # gives the monoisotopic mass adjusted by the current charge (i.e.,
     # adds/subtracts electron masses for the charges)
     def mass(consider_electron_masses = true)
-      mss = inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::MONO[el]*cnt) }
+      mss = inject(0.0) do |sum,(el,cnt)| 
+        sum + (Mspire::Mass::Element::MONO[el]*cnt)
+      end
       mss -= (Mspire::Mass::ELECTRON * charge) if consider_electron_masses
       mss
     end
 
     def avg_mass
-      inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::AVG[el]*cnt) }
+      inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::Element::AVG[el]*cnt) }
     end
 
     # returns nil if the charge == 0

data/lib/mspire/version.rb

@@ -1,3 +1,3 @@
 module Mspire
-  VERSION = "0.8.7"
+  VERSION = "0.9.0"
 end

data/mspire.gemspec

@@ -0,0 +1,46 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'mspire/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "mspire"
+  spec.version       = Mspire::VERSION
+  spec.authors       = ["John T. Prince", "Simon Chiang"]
+  spec.email         = ["jtprince@gmail.com"]
+  spec.description   = %q{mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems}
+  spec.summary       = %q{mass spectrometry proteomics, lipidomics, and tools}
+  spec.homepage      = "http://github.com/princelab/mspire"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  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", "~> 1.5.9"],
+    ["bsearch", ">= 1.5.0"],
+    ["andand", ">= 1.3.3"],
+    ["obo", ">= 0.1.3"],
+    ["builder", "~> 3.2.0"],
+    ["bio", "~> 1.4.3"],
+    ["trollop", "~> 2.0.0"],
+  ].each do |args|
+    spec.add_dependency(*args)
+  end
+
+  [
+    ["bundler", "~> 1.3"],
+    ["rake"],
+    ["rspec", "~> 2.13.0"], 
+    ["rdoc", "~> 3.12"], 
+    ["simplecov"],
+    ["coveralls"],
+    # here because bad microsoft OS support
+    ["fftw3", "~> 0.3"],
+  ].each do |args|
+    spec.add_development_dependency(*args)
+  end
+
+end

data/spec/mspire/ident/pepxml_spec.rb

@@ -43,12 +43,12 @@ describe "creating an Mspire::Ident::Pepxml" do
               :variable => 'Y', :symbol => '*')
               # invented, for example, a protein terminating mod
             modifications << Mspire::Ident::Pepxml::TerminalModification.new( 
-              :terminus => 'c', :massdiff => 23.3333, :mass => Mspire::Mass::MONO['oh'] + 23.3333, 
+              :terminus => 'c', :massdiff => 23.3333, :mass => Mspire::Mass::Common::MONO['OH'] + 23.3333, 
               :variable => 'Y', :symbol => '[', :protein_terminus => 'c', 
               :description => 'leave protein_terminus off if not protein mod'
             )
             modifications << Mspire::Ident::Pepxml::TerminalModification.new( 
-              :terminus => 'c', :massdiff => 25.42322, :mass => Mspire::Mass::MONO['h+'] + 25.42322, 
+              :terminus => 'c', :massdiff => 25.42322, :mass => Mspire::Mass::PROTON + 25.42322, 
               :variable => 'N', :symbol => ']', :description => 'example: c term mod'
             )
             parameters.merge!( 

data/spec/mspire/isotope/aa_spec.rb

@@ -4,17 +4,17 @@ require 'mspire/isotope/aa'
 
 describe 'accessing an amino acid atom count' do
   before do
-    @alanine = {:c=>3, :h=>5, :o=>1, :n=>1, :s=>0, :p=>0, :se=>0}
+    @alanine = {:C=>3, :H=>5, :O=>1, :N=>1, :S=>0, :P=>0, :Se=>0}
   end
 
   it 'residue can be accessed with a symbol' do
     hash = Mspire::Isotope::AA::FORMULAS[:A]
-    [:c, :h, :o, :n, :s].each {|key| hash[key].should == @alanine[key] }
+    [:C, :H, :O, :N, :S].each {|key| hash[key].should == @alanine[key] }
   end
     
   it 'residue can be accessed with a string' do
     hash = Mspire::Isotope::AA::FORMULAS['A']
-    [:c, :h, :o, :n, :s].each {|key| hash[key].should == @alanine[key] }
+    [:C, :H, :O, :N, :S].each {|key| hash[key].should == @alanine[key] }
   end
 
 end

data/spec/mspire/isotope_spec.rb

@@ -6,26 +6,26 @@ describe 'Mspire::Isotope constants' do
   it 'has all the common isotopes: Mspire::Isotope::ISOTOPES' do
     # frozen
     Mspire::Isotope::ISOTOPES.size.should == 288
-    hydrogen_isotopes = Mspire::Isotope::ISOTOPES.select {|iso| iso.element == :h }
+    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: 0.999885, average_mass: 1.00794, mono: true }.each do |k,v|
+    { atomic_number: 1, element: :H, mass_number: 1, atomic_mass: 1.00782503207, relative_abundance: 0.999885, 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: 0.000115, average_mass: 1.00794, mono: false}.each do |k,v|
+    {atomic_number: 1, element: :H, mass_number: 2, atomic_mass: 2.0141017778, relative_abundance: 0.000115, 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|
+    {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
   it 'has all common isotopes by element: Mspire::Isotope::BY_ELEMENT' do
-    [{atomic_number: 6, element: :c, mass_number: 12, atomic_mass: 12.0, relative_abundance: 0.9893, average_mass: 12.0107, mono: true}, {atomic_number: 6, element: :c, mass_number: 13, atomic_mass: 13.0033548378, relative_abundance: 0.0107, average_mass: 12.0107, mono: false}].zip(Mspire::Isotope::BY_ELEMENT[:c]) do |hash, iso|
+    [{atomic_number: 6, element: :C, mass_number: 12, atomic_mass: 12.0, relative_abundance: 0.9893, average_mass: 12.0107, mono: true}, {atomic_number: 6, element: :C, mass_number: 13, atomic_mass: 13.0033548378, relative_abundance: 0.0107, 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
+    Mspire::Isotope::BY_ELEMENT[:H].size.should == 2
   end
 end

data/spec/mspire/mass/aa_spec.rb

@@ -0,0 +1,18 @@
+require 'spec_helper'
+
+require 'mspire/mass/aa'
+
+describe Mspire::Mass::AA do
+  it 'provides string and symbol access to element masses' do
+    mono = Mspire::Mass::AA::MONO
+
+    mono['C'].should == 103.0091844778
+    mono[:C].should == mono['C']
+
+    Mspire::Mass::AA[:C].should == mono[:C] # <- not a hash but a method
+
+    avg = Mspire::Mass::AA::AVG
+    avg['C'].should == 103.1429
+    avg[:C].should == avg['C']
+  end
+end