mspire 0.8.7 → 0.9.0

data/spec/mspire/mass/all_spec.rb

@@ -0,0 +1,33 @@
+require 'spec_helper'
+require 'mspire/mass/all'
+
+describe Mspire::Mass::All do
+  it 'accesses elements by lower case and amino acids by upper case' do
+    {
+      'c' => 12.0,  # carbon
+      'C' => 103.00918,  # cysteine
+      'br' => 78.9183361,  # bromine
+      'd' => 2.014101779,  # deuterium
+      'D' => 115.0269430,  # aspartic acid
+      'h+' => 1.00727646677, # proton
+      'h' => 1.007825035,  # hydrogen
+      'h2o' => 18.0105647, # water
+      'oh' => 17.002739665, # oh
+      'e' => 0.0005486, # electron
+    }.each do |el, mass|
+      Mspire::Mass::All::MONO[el].should_not be_nil
+      Mspire::Mass::All::MONO[el].should == Mspire::Mass::All::MONO[el.to_sym]
+      Mspire::Mass::All::MONO[el].should be_within(0.00001).of(mass) 
+    end
+
+    { h: 1.00794, he: 4.002602, ni: 58.6934, H: 137.13928 }.each do |el, mass|
+      Mspire::Mass::All::AVG[el].should_not be_nil
+      Mspire::Mass::All::AVG[el].should == Mspire::Mass::All::AVG[el.to_sym]
+      Mspire::Mass::All::AVG[el].should be_within(0.00001).of(mass) 
+    end
+  end
+
+  it 'mono may be accessed directly' do
+    Mspire::Mass::All[:c].should == 12.0
+  end
+end

data/spec/mspire/mass/common_spec.rb

@@ -0,0 +1,17 @@
+require 'spec_helper'
+
+require 'mspire/mass/common'
+
+describe Mspire::Mass::Common do
+  it 'provides string and symbol access to common mass spec masses' do
+    mono = Mspire::Mass::Common::MONO
+
+    mono['OH'].should be_within(0.0000001).of( 17.002739651629998 )
+    mono[:OH].should == mono['OH']
+    Mspire::Mass::Common[:OH].should == mono[:OH]
+
+    avg = Mspire::Mass::Common::AVG
+    avg['OH'].should == 17.00734
+    avg[:OH].should == avg['OH']
+  end
+end

data/spec/mspire/mass/element_spec.rb

@@ -0,0 +1,17 @@
+require 'spec_helper'
+
+require 'mspire/mass/element'
+
+describe Mspire::Mass::Element do
+  it 'provides string and symbol access to element masses' do
+    mono = Mspire::Mass::Element::MONO
+
+    mono['Se'].should == 79.9165213
+    mono[:Se].should == mono['Se']
+    Mspire::Mass::Element[:Se].should == mono[:Se]
+
+    avg = Mspire::Mass::Element::AVG
+    avg['Se'].should == 78.96
+    avg[:Se].should == avg['Se']
+  end
+end

data/spec/mspire/mass/subatomic_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+require 'mspire/mass/subatomic'
+
+describe Mspire::Mass::Subatomic do
+  it 'provides string and symbol access to element masses' do
+    mono = Mspire::Mass::Subatomic::MONO
+
+    mono['neutron'].should == 1.0086649156
+    mono[:neutron].should == mono['neutron']
+    Mspire::Mass::Subatomic[:neutron].should == mono[:neutron]
+  end
+end

data/spec/mspire/mass_spec.rb

@@ -2,41 +2,12 @@ require 'spec_helper'
 
 require 'mspire/mass'
 
-describe 'Mspire::Mass' do
-  it 'can access elemental masses by string or symbol' do
-    {
-      'c' => 12.0,  # +
-      'br' => 78.9183361,  # +
-      'd' => 2.014101779,  # +
-      'f' => 18.99840322,  # +
-      'n' => 14.003074,  # +
-      'o' => 15.99491463,  # +
-      'na' => 22.9897677,  # +
-      'p' => 30.973762,  # +
-      's' => 31.9720707,  # +
-      'li' => 7.016003,  # +
-      'cl' => 34.96885272,  # +
-      'k' => 38.9637074,  # +
-      'si' => 27.9769265325, 
-      'i' => 126.904473,  # +
-      'h+' => 1.00727646677,
-      'h' => 1.007825035,  # +
-      'h2o' => 18.0105647,
-      'oh' => 17.002739665,
-      'e' => 0.0005486,
-      'se' => 79.9165196
-    }.each do |el, mass|
-      Mspire::Mass::MONO[el].should_not be_nil
-      Mspire::Mass::MONO[el].should == Mspire::Mass::MONO[el.to_sym]
-      Mspire::Mass::MONO[el].should be_within(0.00001).of(mass) 
-    end
-
-
-    { h: 1.00794, he: 4.002602, ni: 58.6934 }.each do |el, mass|
-      Mspire::Mass::AVG[el].should_not be_nil
-      Mspire::Mass::AVG[el].should == Mspire::Mass::AVG[el.to_sym]
-      Mspire::Mass::AVG[el].should be_within(0.00001).of(mass) 
-    end
+describe Mspire::Mass do
+  it 'calculates formula masses' do
+    Mspire::Mass.formula('CHCl3').should be_within(0.00001).of(117.91439)
+  end
 
+  it 'calculates peptide/protein (AA) masses' do
+    Mspire::Mass.aa('ADALL').should be_within(0.00001).of(501.27986)
   end
 end

data/spec/mspire/molecular_formula_spec.rb

@@ -8,34 +8,34 @@ describe Mspire::MolecularFormula do
   describe 'initialization' do
 
     it 'is initialized with Hash' do
-      data = {h: 22, c: 12, n: 1, o: 3, s: 2}
+      data = {H: 22, C: 12, N: 1, O: 3, S: 2}
       mf = Mspire::MolecularFormula.new(data)
-      mf.to_hash.should == {:h=>22, :c=>12, :n=>1, :o=>3, :s=>2}
+      mf.to_hash.should == {:H=>22, :C=>12, :N=>1, :O=>3, :S=>2}
       mf.to_hash.should == data
     end
 
     it 'can be initialized with charge, too' do
       mf = Mspire::MolecularFormula["H22BeC12N1O3S2Li2", 2]
-      mf.to_hash.should == {:h=>22, :be=>1, :c=>12, :n=>1, :o=>3, :s=>2, :li=>2}
+      mf.to_hash.should == {:H=>22, :Be=>1, :C=>12, :N=>1, :O=>3, :S=>2, :Li=>2}
       mf.charge.should == 2
     end
 
     it 'from_string or ::[] to make from a capitalized string formula' do
-      Mspire::MolecularFormula.from_string("H22BeC12N1O3S2Li2").to_hash.should == {:h=>22, :be=>1, :c=>12, :n=>1, :o=>3, :s=>2, :li=>2}
+      Mspire::MolecularFormula.from_string("H22BeC12N1O3S2Li2").to_hash.should == {:H=>22, :Be=>1, :C=>12, :N=>1, :O=>3, :S=>2, :Li=>2}
 
       mf = Mspire::MolecularFormula['Ni7Se3', 1]
       mf.charge.should == 1
-      mf.to_hash.should == {:ni=>7, :se=>3}
+      mf.to_hash.should == {:Ni=>7, :Se=>3}
 
       # there is no such thing as the E element, so this is going to get the
       # user in trouble.  However, this is the proper interpretation of the
       # formula.
-      Mspire::MolecularFormula['Ni7SE3'].to_hash.should == {:ni=>7, :s=>1, :e=>3}
+      Mspire::MolecularFormula['Ni7SE3'].to_hash.should == {:Ni=>7, :S=>1, :E=>3}
     end
 
     describe 'correct to_s' do
       subject {
-        Mspire::MolecularFormula.new({:c=>669, :h=>1129, :o=>185, :n=>215, :s=>4, :p=>0, :se=>0})
+        Mspire::MolecularFormula.new({:C=>669, :H=>1129, :O=>185, :N=>215, :S=>4, :P=>0, :Se=>0})
       }
       it 'to_s gives output' do
         subject.to_s.should == "C669H1129N215O185S4"
@@ -45,7 +45,7 @@ describe Mspire::MolecularFormula do
     describe 'conversion' do
 
       subject {
-        data = {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        data = {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         Mspire::MolecularFormula.new(data)
       }
 
@@ -54,13 +54,13 @@ describe Mspire::MolecularFormula do
       end
 
       it 'can be converted to a hash' do
-        subject.to_hash.should == {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        subject.to_hash.should == {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
       end
     end
 
     describe 'equality' do
       subject {
-        data = {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        data = {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         Mspire::MolecularFormula.new(data)
       }
       it 'is only equal if the charge is equal' do
@@ -73,43 +73,43 @@ describe Mspire::MolecularFormula do
 
     describe 'arithmetic' do
       subject {
-        data = {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        data = {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         Mspire::MolecularFormula.new(data, 2)
       }
       it 'can do non-destructive arithmetic' do
         orig = subject.dup
         reply = subject + MF["H2C3P2", 2]
-        reply.to_hash.should == {h: 24, c: 15, n: 1, o: 3, s: 2, be: 1, p: 2}
+        reply.to_hash.should == {H: 24, C: 15, N: 1, O: 3, S: 2, Be: 1, P: 2}
         reply.charge.should == 4
         subject.should == orig
 
         reply = subject - MF["H2C3P2", 2]
-        reply.to_hash.should == {h: 20, c: 9, n: 1, o: 3, s: 2, be: 1, p: -2}
+        reply.to_hash.should == {H: 20, C: 9, N: 1, O: 3, S: 2, Be: 1, P: -2}
         reply.charge.should == 0
         subject.should == orig
 
         by2 = subject * 2
-        by2.to_hash.should == {h: 44, c: 24, n: 2, o: 6, s: 4, be: 2}
+        by2.to_hash.should == {H: 44, C: 24, N: 2, O: 6, S: 4, Be: 2}
         by2.charge.should == 4
         subject.should == orig
 
         reply = by2 / 2
-        reply.to_hash.should == {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        reply.to_hash.should == {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         reply.charge.should == 2
         subject.should == orig
       end
 
       it 'can do destructive arithmetic' do
         orig = subject.dup
-        subject.sub!(MF["H2C3"]).to_hash.should == {h: 20, c: 9, n: 1, o: 3, s: 2, be: 1}
+        subject.sub!(MF["H2C3"]).to_hash.should == {H: 20, C: 9, N: 1, O: 3, S: 2, Be: 1}
         subject.should_not == orig
-        subject.add!(MF["H2C3"]).to_hash.should == {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        subject.add!(MF["H2C3"]).to_hash.should == {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         subject.should == orig
 
         by2 = subject.mul!(2)
         subject.should_not == orig
-        by2.to_hash.should == {h: 44, c: 24, n: 2, o: 6, s: 4, be: 2}
-        by2.div!(2).to_hash.should == {h: 22, c: 12, n: 1, o: 3, s: 2, be: 1}
+        by2.to_hash.should == {H: 44, C: 24, N: 2, O: 6, S: 4, Be: 2}
+        by2.div!(2).to_hash.should == {H: 22, C: 12, N: 1, O: 3, S: 2, Be: 1}
         by2.to_hash.should == orig
       end
 

data/spec/mspire/readme_spec.rb

@@ -83,9 +83,8 @@ describe 'performing what is on the readme' do
     aa_to_mass = Mspire::Mass::AA::MONO # a hash with residue masses
     aa_to_mass['A'] # or access by symbol - Alanine
 
-    # elements
-    Mspire::Mass::MONO[:c] # carbon
-    Mspire::Mass::MONO[:e] # electron (includes other useful symbols)
+    Mspire::Mass::Element::MONO[:C] # carbon
+    Mspire::Mass::Subatomic::MONO[:electron] # electron
   end
 
   specify 'isotopes and molecular formulas' do
@@ -95,7 +94,7 @@ describe 'performing what is on the readme' do
       isotopes = Mspire::Isotope::ISOTOPES  # 288 isotopes
       hydrogen_isotopes = isotopes.select {|iso| iso.element == :h }
 
-      c12 = Mspire::Isotope::BY_ELEMENT[:c].first
+      c12 = Mspire::Isotope::BY_ELEMENT[:C].first
       c12.atomic_number # also: mass_number atomic_mass relative_abundance average_mass
       c12.mono   # => true (this is the monoisotopic isotope)
 

data/spec/spec_helper.rb

@@ -1,6 +1,3 @@
-#$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-#$LOAD_PATH.unshift(File.dirname(__FILE__))
-
 require 'simplecov'
 SimpleCov.start
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.8.7
+  version: 0.9.0
 platform: ruby
 authors:
 - John T. Prince
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-31 00:00:00.000000000 Z
+date: 2013-08-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -272,6 +272,11 @@ files:
 - lib/mspire/mascot.rb
 - lib/mspire/mass.rb
 - lib/mspire/mass/aa.rb
+- lib/mspire/mass/all.rb
+- lib/mspire/mass/common.rb
+- lib/mspire/mass/element.rb
+- lib/mspire/mass/subatomic.rb
+- lib/mspire/mass/util.rb
 - lib/mspire/molecular_formula.rb
 - lib/mspire/mzml.rb
 - lib/mspire/mzml/activation.rb
@@ -331,6 +336,7 @@ files:
 - lib/obo/unit.rb
 - lib/openany.rb
 - lib/write_file_or_string.rb
+- mspire.gemspec
 - obo/ims.obo
 - obo/mod.obo
 - obo/ms.obo
@@ -365,6 +371,11 @@ files:
 - spec/mspire/isotope/aa_spec.rb
 - spec/mspire/isotope/distribution_spec.rb
 - spec/mspire/isotope_spec.rb
+- spec/mspire/mass/aa_spec.rb
+- spec/mspire/mass/all_spec.rb
+- spec/mspire/mass/common_spec.rb
+- spec/mspire/mass/element_spec.rb
+- spec/mspire/mass/subatomic_spec.rb
 - spec/mspire/mass_spec.rb
 - spec/mspire/molecular_formula_spec.rb
 - spec/mspire/mzml/cv_spec.rb
@@ -466,6 +477,11 @@ test_files:
 - spec/mspire/isotope/aa_spec.rb
 - spec/mspire/isotope/distribution_spec.rb
 - spec/mspire/isotope_spec.rb
+- spec/mspire/mass/aa_spec.rb
+- spec/mspire/mass/all_spec.rb
+- spec/mspire/mass/common_spec.rb
+- spec/mspire/mass/element_spec.rb
+- spec/mspire/mass/subatomic_spec.rb
 - spec/mspire/mass_spec.rb
 - spec/mspire/molecular_formula_spec.rb
 - spec/mspire/mzml/cv_spec.rb