molecules 0.1.0 → 0.1.3

data/test/molecules/utils_test.rb

@@ -1,147 +0,0 @@
-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

@@ -1,24 +0,0 @@
-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

@@ -1,31 +0,0 @@
-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

@@ -1,3 +0,0 @@
-$:.unshift File.join(File.dirname(__FILE__), '../lib')
-
-Dir.glob("./**/*_test.rb").each {|test| require test}

data/test/tap_test_helper.rb

@@ -1,3 +0,0 @@
-require 'rubygems'
-require 'tap'
-require 'tap/test'