ms-core 0.0.12 → 0.0.13

data/Rakefile

@@ -19,6 +19,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{basic, shared functionality for mspire libraries}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince", "Simon Chiang"]
+  gem.rubyforge_project = 'mspire'
   # Dependencies in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.0.12
+0.0.13

data/lib/ms/mass/aa.rb

@@ -96,10 +96,12 @@ module Ms
       # amino_acids keys as symbols, average masses
       AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
 
-      # amino_acids keys as symbols and also strings, monoisotopic masses
-      MONO = MONO_SYM.merge(MONO_STRING)
-      # amino_acids keys as symbols and also strings, average masses
-      AVG = AVG_SYM.merge(AVG_STRING)
+      # Monoisotopic amino acid masses keyed as symbols and also strings (all
+      # upper case).  Also includes Ms::Mass::MONO for things like protons ('h+')
+      MONO = MONO_SYM.merge(MONO_STRING).merge(Ms::Mass::MONO)
+      # Average amino acid masses keyed as symbols and also strings (all
+      # uppder case).  Also includes Ms::Mass::AVG for things like protons ('h+')
+      AVG = AVG_SYM.merge(AVG_STRING).merge(Ms::Mass::AVG)
 
       ###########################################################################
       # This section is broken in 1.9 (ruby-units fault), so we generate the

data/lib/ms/mass.rb

@@ -6,18 +6,25 @@ module Ms
     PROTON = H_PLUS
 
     # lower case elements (h = Hydrogen)
-    MONO = {
+    MONO_STRING = {
       'h+' => 1.00727646677,
       'h' => 1.007825035,
       'h2o' => 18.0105647,
       'oh' => 17.002739665,
     }
+    MONO_SYM = Hash[ MONO_STRING.map {|k,v| [k.to_sym, v] } ]
+    MONO = MONO_STRING.merge(MONO_SYM)
+
     # lower case elements (h = Hydrogen)
-    AVG = {
+    AVG_STRING = {
+      'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)
       'h' => 1.00794,
       'h2o' => 18.01528, 
       'oh' => 17.00734,
     }
+    AVG_SYM = Hash[ AVG_STRING.map {|k,v| [k.to_sym, v] } ]
+    AVG = AVG_STRING.merge(AVG_SYM)
+
   end
 end
 

data/spec/ms/mass/aa_spec.rb

@@ -7,8 +7,16 @@ describe 'using a mass table' do
     Ms::Mass::AA::MONO['A'].is 71.0371137878
     Ms::Mass::AA::MONO[:A].is 71.0371137878
   end
+  it 'MONO also includes Ms::Mass::MONO' do
+    Ms::Mass::AA::MONO['oh'].is 17.002739665
+    Ms::Mass::AA::MONO[:oh].is 17.002739665
+  end
   it 'has average masses by string or symbol' do
     Ms::Mass::AA::AVG['A'].is 71.0779
     Ms::Mass::AA::AVG[:A].is 71.0779
   end
+  it 'AVG also includes Ms::Mass::AVG' do
+    Ms::Mass::AA::AVG['oh'].is 17.00734
+    Ms::Mass::AA::AVG[:oh].is 17.00734
+  end
 end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 12
-  version: 0.0.12
+  - 13
+  version: 0.0.13
 platform: ruby
 authors: 
 - John T. Prince
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-25 00:00:00 -07:00
+date: 2011-02-28 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -146,7 +146,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -3438756402400319046
+      hash: -1109965199117656197
       segments: 
       - 0
       version: "0"
@@ -160,7 +160,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: 
+rubyforge_project: mspire
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3