molecules 0.1.0

data/test/molecules/utils_test.rb

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+require File.join(File.dirname(__FILE__), '../molecules_test_helper.rb') 
+require 'molecules/utils'
+
+class UtilsTest < Test::Unit::TestCase
+  include Molecules::Utils
+  
+  #
+  # round test
+  #
+  
+  def test_round
+    assert_equal 0, round(0.20, 0)
+    assert_equal 0.2, round(0.20, 1)
+    assert_equal 0.2, round(0.20, 2)
+    assert_equal 0.2, round(0.20, 3)
+     
+    assert_equal 0.2, round(0.18, 1)
+    assert_equal 0.2, round(0.15, 1)
+    assert_equal 0.1, round(0.13, 1)
+    assert_equal 0.13, round(0.13, 3)
+    
+    assert_equal 10, round(13, -1)
+    assert_equal 0, round(13, -2)
+  end
+  
+  #
+  # add
+  #
+  
+  def test_add_adds_the_elements_of_b_to_a_at_corresponding_indicies
+    assert_equal [2,3,4], add([1,3,-1], [1,0,5])
+  end
+  
+  def test_add_multiplies_the_elements_of_b_by_factor
+    assert_equal [3,3,9], add([1,3,-1], [1,0,5], 2)
+    assert_equal [1,3,-1], add([1,3,-1], [1,0,5], 0)
+  end
+  
+  def test_add_removes_trailing_zeros_from_a
+    assert_equal [], add([1,1,1], [-1,-1,-1])
+  end
+  
+  def test_add_returns_a
+    a = [1,2,4]
+    assert_equal a.object_id, add(a, [1,0,4]).object_id
+  end
+  
+  def test_add_does_not_require_a_and_b_to_be_the_same_length
+    a = [1,2]
+    b = [1]
+    
+    assert_equal [2,2], add(a, b)
+    
+    a = [1,2]
+    b = [1]
+    
+    assert_equal [2,2], add(b, a)
+  end
+  
+  #
+  # multiply test
+  #
+  
+  def test_multiply_multiplies_elements_of_a_by_factor
+    assert_equal [2,4,-6], multiply([1,2,-3], 2)
+    assert_equal [-2,-4,6], multiply([1,2,-3], -2)
+  end
+  
+  def test_multiply_clears_a_for_zero_factor
+    assert_equal [], multiply([1,2,-3], 0)
+  end
+  
+  def test_mulitply_returns_a
+    a = [1,2,4]
+    assert_equal a.object_id, multiply(a, 2).object_id
+    assert_equal a.object_id, multiply(a, 0).object_id
+  end
+  
+  #
+  # count test
+  #
+  
+  def test_count_documenation
+    assert_equal [3, 2, 2] , count("abcabca", ["a", "b", "c"])
+    assert_equal [3, 4], count("abcabca", ["a", "bc"])
+  end
+  
+  #
+  # benchmark tests
+  #
+  
+  def test_round_speed
+    benchmark_test(24) do |x|
+      n = 100
+      x.report("#{n}k 1234.5678.round") do 
+        (n*10**3).times { 1234.5678.round }
+      end
+      
+      x.report("#{n}k 1234.5678 (2)") do 
+        (n*10**3).times { round(1234.5678, 2) }
+      end
+      
+      x.report("#{n}k 1234.5678 (5)") do 
+        (n*10**3).times { round(1234.5678, 5) }
+      end
+    end
+  end
+  
+  def test_add_speed
+    benchmark_test(30) do |x|
+      n = 100
+      x.report("#{n}k add([1,3,-1], [1,0,5])") do 
+        (n*10**3).times { add([1,3,-1], [1,0,5]) }
+      end
+      
+      x.report("#{n}k add([1,3,-1], [1])") do 
+        (n*10**3).times { add([1,3,-1], [1]) }
+      end
+      
+      x.report("#{n}k add([1], [1,3,-1])") do 
+        (n*10**3).times { add([1], [1,3,-1]) }
+      end
+      
+      x.report("#{n}k add([1,1,1], [-1,-1,-1])") do 
+        (n*10**3).times { add([1,1,1], [-1,-1,-1]) }
+      end
+      
+      x.report("#{n}k add([1,3,-1], [1,0,5], 2)") do 
+        (n*10**3).times { add([1,3,-1], [1,0,5], 2) }
+      end
+    end
+  end
+    
+  def test_multiply_speed
+    benchmark_test(30) do |x|
+      n = 100
+      x.report("#{n}k multiply([1,3,-1], 2)") do 
+        (n*10**3).times { multiply([1,3,-1], 2) }
+      end
+      
+      x.report("#{n}k multiply([1,3,-1], 0)") do 
+        (n*10**3).times { multiply([1,3,-1], 0) }
+      end
+    end
+  end
+  
+end

data/test/molecules_test.rb

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+require File.join(File.dirname(__FILE__), 'molecules_test_helper.rb') 
+require 'molecules'
+
+class MoleculesTest < Test::Unit::TestCase
+ 
+  include Molecules::Libraries
+  
+  def test_readme_documentation
+    r = Residue::A
+    assert_equal "Alanine", r.name
+    assert_equal "Ala", r.abbr
+    assert_equal "A", r.letter
+    assert_equal "CH(3)", r.side_chain.to_s
+    assert_in_delta 71.03711, r.mass, 0.00001
+    assert_in_delta 44.05002, r.immonium_ion_mass, 0.00001
+  
+    p = Polypeptide.new("RPPGFSPFR")
+    assert_equal "C(50)H(71)N(15)O(10)", p.to_s
+    assert_in_delta 1041.5508, p.mass , 0.0001
+  
+    caffeine = Molecules::EmpiricalFormula.parse("C8H10N4O2")
+    coffee = Molecules::EmpiricalFormula.parse("C8H10N4O2 + H2O")
+  end
+end

data/test/molecules_test_helper.rb

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+require 'rubygems'
+require 'test/unit'
+require 'benchmark'
+require 'pp'
+
+class Test::Unit::TestCase
+  include Benchmark
+
+  #
+  # mass tests
+  #
+  
+  def delta_mass
+    10**-5
+  end
+  
+  def delta_abundance
+    10**-1
+  end
+  
+  def benchmark_test(length=10, &block) 
+    if ENV["benchmark"] =~ /true/i
+      puts
+      puts method_name
+      bm(length, &block)
+    else
+      print 'b'
+    end
+  end
+  
+end

data/test/molecules_test_suite.rb

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+$:.unshift File.join(File.dirname(__FILE__), '../lib')
+
+Dir.glob("./**/*_test.rb").each {|test| require test}

data/test/tap_test_helper.rb

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+require 'rubygems'
+require 'tap'
+require 'tap/test'

metadata

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+--- !ruby/object:Gem::Specification 
+name: molecules
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Simon Chiang
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-08-11 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: constants
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.1.0
+    version: 
+description: 
+email: simon.a.chiang@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README
+- MIT-LICENSE
+files: 
+- MIT-LICENSE
+- Rakefile
+- README
+- lib/molecules.rb
+- lib/molecules/calc.rb
+- lib/molecules/empirical_formula.rb
+- lib/molecules/libraries/polypeptide.rb
+- lib/molecules/libraries/residue.rb
+- lib/molecules/utils.rb
+- tap.yml
+- test/molecules/calc_test.rb
+- test/molecules/empirical_formula_class_test.rb
+- test/molecules/empirical_formula_test.rb
+- test/molecules/libraries/polypeptide_test.rb
+- test/molecules/libraries/residue_test.rb
+- test/molecules/utils_test.rb
+- test/molecules_test.rb
+- test/molecules_test_helper.rb
+- test/molecules_test_suite.rb
+- test/tap_test_helper.rb
+has_rdoc: true
+homepage: http://bioactive.rubyforge.org/molecules/
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: bioactive
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: A library of molecules for scientific calculations in Ruby.
+test_files: 
+- test/molecules_test_suite.rb