bio 1.3.1 → 1.4.0

data/test/unit/bio/db/kegg/test_compound.rb

@@ -0,0 +1,146 @@
+#
+# test/unit/bio/db/kegg/test_compound.rb - Unit test for Bio::KEGG::COMPOUND
+#
+# Copyright::  Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>
+# License::    The Ruby License
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/compound'
+
+module Bio
+  class TestKeggCompound < Test::Unit::TestCase
+
+    def setup
+      testdata_kegg = Pathname.new(File.join(BioRubyTestDataPath, 'KEGG')).cleanpath.to_s
+      entry = File.read(File.join(testdata_kegg, "C00025.compound"))
+      @obj = Bio::KEGG::COMPOUND.new(entry)
+    end
+
+    def test_entry_id
+      assert_equal('C00025', @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal("L-Glutamate", @obj.name)
+    end
+
+    def test_names
+      assert_equal(["L-Glutamate", "L-Glutamic acid", "L-Glutaminic acid", "Glutamate"], @obj.names)
+    end
+
+    def test_formula
+      assert_equal("C5H9NO4", @obj.formula)
+    end
+
+    def test_mass
+      assert_equal(147.0532, @obj.mass)
+    end
+
+    def test_remark
+      assert_equal("Same as: D00007", @obj.remark)
+    end
+
+    def test_reactions
+      assert_equal(["R00021", "R00093", "R00114", "R00239", "R00241", "R00243", "R00245", "R00248", "R00250", "R00251", "R00253", "R00254", "R00256", "R00257", "R00258", "R00259", "R00260", "R00261", "R00262", "R00263", "R00355", "R00372", "R00411", "R00457", "R00494", "R00525", "R00573", "R00575", "R00578", "R00609", "R00667", "R00668", "R00684", "R00694", "R00707", "R00708", "R00734", "R00768", "R00894", "R00895", "R00908", "R00942", "R00986", "R01072", "R01090", "R01155", "R01161", "R01214", "R01231", "R01339", "R01585", "R01586", "R01648", "R01654", "R01684", "R01716", "R01939", "R01956", "R02040", "R02077", "R02199", "R02237", "R02274", "R02282", "R02283", "R02285", "R02287", "R02313", "R02315", "R02433", "R02619", "R02700", "R02772", "R02773", "R02929", "R02930", "R03053", "R03120", "R03189", "R03207", "R03243", "R03248", "R03266", "R03651", "R03905", "R03916", "R03952", "R03970", "R03971", "R04028", "R04029", "R04051", "R04171", "R04173", "R04188", "R04212", "R04217", "R04234", "R04241", "R04269", "R04338", "R04438", "R04463", "R04467", "R04475", "R04529", "R04558", "R04776", "R05052", "R05085", "R05197", "R05207", "R05224", "R05225", "R05507", "R05578", "R05815", "R06423", "R06426", "R06844", "R06977", "R07275", "R07276", "R07277", "R07396", "R07414", "R07419", "R07456", "R07613", "R07643", "R07659", "R08244"], @obj.reactions)
+    end
+
+    def test_rpairs
+      assert_equal([], @obj.rpairs)
+    end
+
+    def test_pathways_as_strings
+      assert_equal(["PATH: ko00250  Alanine, aspartate and glutamate metabolism", "PATH: ko00330  Arginine and proline metabolism", "PATH: ko00340  Histidine metabolism", "PATH: ko00471  D-Glutamine and D-glutamate metabolism", "PATH: ko00480  Glutathione metabolism", "PATH: ko00650  Butanoate metabolism", "PATH: ko00660  C5-Branched dibasic acid metabolism", "PATH: ko00860  Porphyrin and chlorophyll metabolism", "PATH: ko00910  Nitrogen metabolism", "PATH: ko00970  Aminoacyl-tRNA biosynthesis", "PATH: map01060  Biosynthesis of plant secondary metabolites", "PATH: ko01064  Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid", "PATH: ko01100  Metabolic pathways", "PATH: ko02010  ABC transporters", "PATH: ko04080  Neuroactive ligand-receptor interaction", "PATH: ko04540  Gap junction", "PATH: ko04720  Long-term potentiation", "PATH: ko04730  Long-term depression", "PATH: ko04742  Taste transduction", "PATH: ko05014  Amyotrophic lateral sclerosis (ALS)", "PATH: ko05016  Huntington's disease"], @obj.pathways_as_strings)
+    end
+
+    def test_enzymes
+      assert_equal(["1.4.1.2", "1.4.1.3", "1.4.1.4", "1.4.1.13", "1.4.1.14", "1.4.3.11", "1.4.7.1", "1.5.1.9", "1.5.1.10", "1.5.1.12", "1.5.99.5", "2.1.1.21", "2.1.2.5", "2.3.1.1", "2.3.1.14", "2.3.1.35", "2.3.2.2", "2.3.2.-", "2.4.2.14", "2.4.2.-", "2.6.1.1", "2.6.1.2", "2.6.1.3", "2.6.1.4", "2.6.1.5", "2.6.1.6", "2.6.1.7", "2.6.1.8", "2.6.1.9", "2.6.1.11", "2.6.1.13", "2.6.1.16", "2.6.1.17", "2.6.1.19", "2.6.1.22", "2.6.1.23", "2.6.1.24", "2.6.1.26", "2.6.1.27", "2.6.1.29", "2.6.1.33", "2.6.1.34", "2.6.1.36", "2.6.1.38", "2.6.1.39", "2.6.1.40", "2.6.1.42", "2.6.1.48", "2.6.1.49", "2.6.1.52", "2.6.1.55", "2.6.1.57", "2.6.1.59", "2.6.1.65", "2.6.1.67", "2.6.1.68", "2.6.1.72", "2.6.1.75", "2.6.1.76", "2.6.1.79", "2.6.1.80", "2.6.1.81", "2.6.1.82", "2.6.1.83", "2.6.1.85", "2.6.1.-", "2.7.2.11", "2.7.2.13", "3.5.1.2", "3.5.1.38", "3.5.1.55", "3.5.1.65", "3.5.1.68", "3.5.1.87", "3.5.1.94", "3.5.1.96", "3.5.2.9", "3.5.3.8", "4.1.1.15", "4.1.3.27", "4.1.3.-", "5.1.1.3", "5.4.99.1", "6.1.1.17", "6.1.1.24", "6.3.1.2", "6.3.1.6", "6.3.1.11", "6.3.1.-", "6.3.2.2", "6.3.2.12", "6.3.2.17", "6.3.2.18", "6.3.4.2", "6.3.4.12", "6.3.5.1", "6.3.5.2", "6.3.5.3", "6.3.5.4", "6.3.5.5", "6.3.5.6", "6.3.5.7", "6.3.5.9", "6.3.5.10"], @obj.enzymes)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal([ "CAS: 56-86-0",
+                     "PubChem: 3327",
+                     "ChEBI: 16015",
+                     "KNApSAcK: C00001358",
+                     "PDB-CCD: GLU",
+                     "3DMET: B00007",
+                     "NIKKAJI: J9.171E" ], @obj.dblinks_as_strings)
+    end
+
+    def test_dblinks_as_hash
+      expected = {
+        "CAS"      => [ "56-86-0" ],
+        "PubChem"  => [ "3327" ],
+        "ChEBI"    => [ "16015" ],
+        "KNApSAcK" => [ "C00001358" ],
+        "PDB-CCD"  => [ "GLU" ],
+        "3DMET"    => [ "B00007" ],
+        "NIKKAJI"  => [ "J9.171E" ]
+      }
+      assert_equal(expected, @obj.dblinks_as_hash)
+      assert_equal(expected, @obj.dblinks)
+    end
+
+    def test_pathways_as_hash
+      expected = {
+        "ko00250"  => "Alanine, aspartate and glutamate metabolism",
+        "ko00330"  => "Arginine and proline metabolism",
+        "ko00340"  => "Histidine metabolism",
+        "ko00471"  => "D-Glutamine and D-glutamate metabolism",
+        "ko00480"  => "Glutathione metabolism",
+        "ko00650"  => "Butanoate metabolism",
+        "ko00660"  => "C5-Branched dibasic acid metabolism",
+        "ko00860"  => "Porphyrin and chlorophyll metabolism",
+        "ko00910"  => "Nitrogen metabolism",
+        "ko00970"  => "Aminoacyl-tRNA biosynthesis",
+        "map01060" => "Biosynthesis of plant secondary metabolites",
+        "ko01064"  =>
+        "Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid",
+        "ko01100"  => "Metabolic pathways",
+        "ko02010"  => "ABC transporters",
+        "ko04080"  => "Neuroactive ligand-receptor interaction",
+        "ko04540"  => "Gap junction",
+        "ko04720"  => "Long-term potentiation",
+        "ko04730"  => "Long-term depression",
+        "ko04742"  => "Taste transduction",
+        "ko05014"  => "Amyotrophic lateral sclerosis (ALS)",
+        "ko05016"  => "Huntington's disease"
+      }
+      assert_equal(expected, @obj.pathways_as_hash)
+      assert_equal(expected, @obj.pathways)
+    end
+
+    def test_kcf
+      assert_equal("ATOM        10
+            1   C1c C    23.8372  -17.4608
+            2   C1b C    25.0252  -16.7233
+            3   C6a C    22.6023  -16.7994
+            4   N1a N    23.8781  -18.8595
+            5   C1b C    26.2601  -17.3788
+            6   O6a O    21.4434  -17.5954
+            7   O6a O    22.6198  -15.4007
+            8   C6a C    27.4482  -16.6414
+            9   O6a O    28.6830  -17.3028
+            10  O6a O    27.4714  -15.2426
+BOND        9
+            1     1   2 1
+            2     1   3 1
+            3     1   4 1 #Down
+            4     2   5 1
+            5     3   6 1
+            6     3   7 2
+            7     5   8 1
+            8     8   9 1
+            9     8  10 2", @obj.kcf)
+    end
+
+    def test_comment
+      assert_equal('The name "glutamate" also means DL-Glutamate (see [CPD:C00302])', @obj.comment)
+    end
+  end
+end

data/test/unit/bio/db/kegg/test_drug.rb

@@ -0,0 +1,194 @@
+#
+# test/unit/bio/db/kegg/test_drug.rb - Unit test for Bio::KEGG::DRUG
+#
+# Copyright::  Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/drug.rb'
+
+module Bio
+  class TestBioKeggDRUG < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/D00063.drug')
+      @obj = Bio::KEGG::DRUG.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      expected = {
+        "ChEBI"=>["28864"],
+        "PubChem"=>["7847131"],
+        "NIKKAJI"=>["J4.533K"],
+        "PDB-CCD"=>["TOY"],
+        "DrugBank"=>["DB00684"],
+        "LigandBox"=>["D00063"],
+        "CAS"=>["32986-56-4"]
+      }
+      assert_equal(expected, @obj.dblinks_as_hash)
+      assert_equal(expected, @obj.dblinks)
+    end
+
+    def test_pathways_as_hash
+      expected = {"map07021"=>"Aminoglycosides"}
+      assert_equal(expected, @obj.pathways_as_hash)
+      assert_equal(expected, @obj.pathways)
+    end
+
+    def test_entry_id
+      assert_equal("D00063", @obj.entry_id)
+    end
+
+    def test_names
+      expected = [ "Tobramycin (JP15/USP)",
+                   "TOB", "Tobracin (TN)", "Tobrex (TN)" ]
+      assert_equal(expected, @obj.names)
+    end
+
+    def test_name
+      expected = "Tobramycin (JP15/USP)"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_formula
+      assert_equal("C18H37N5O9", @obj.formula)
+    end
+
+    def test_mass
+      assert_equal(467.2591, @obj.mass)
+    end
+
+    def test_activity
+      expected = "Antibacterial"
+      assert_equal(expected, @obj.activity)
+    end
+
+    def test_remark
+      expected = "Same as: C00397 Therapeutic category: 1317 6123 ATC code: J01GB01 S01AA12"
+      assert_equal(expected, @obj.remark)
+    end
+
+    def test_pathways_as_strings
+      expected = [ "PATH: map07021  Aminoglycosides" ]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_dblinks_as_strings
+      expected = [ "CAS: 32986-56-4",
+                   "PubChem: 7847131",
+                   "ChEBI: 28864",
+                   "DrugBank: DB00684",
+                   "PDB-CCD: TOY",
+                   "LigandBox: D00063",
+                   "NIKKAJI: J4.533K" ]
+      assert_equal(expected, @obj.dblinks_as_strings)
+    end
+
+    def test_kcf
+      expected = <<END_OF_EXPECTED_KCF
+ATOM        32
+            1   C1y C    20.6560  -20.0968
+            2   C1y C    20.6560  -21.4973
+            3   C1y C    21.8689  -22.1975
+            4   C1y C    23.0818  -21.4973
+            5   C1y C    23.0818  -20.0968
+            6   O2x O    21.8689  -19.3965
+            7   C1b C    19.4432  -19.3965
+            8   O1a O    18.2473  -20.0872
+            9   O1a O    19.4432  -22.1975
+            10  N1a N    21.8689  -23.5978
+            11  O1a O    24.3134  -22.2085
+            12  O2a O    24.3134  -19.3855
+            13  C1y C    25.4878  -18.6963
+            14  C1y C    26.7056  -19.3879
+            15  C1x C    27.9134  -18.6791
+            16  C1y C    27.9035  -17.2786
+            17  C1y C    26.6857  -16.5869
+            18  C1y C    25.4779  -17.2958
+            19  N1a N    26.7157  -20.7965
+            20  N1a N    29.0779  -16.5893
+            21  O1a O    24.2675  -16.6084
+            22  O2a O    26.6757  -15.1950
+            23  C1y C    27.8854  -14.4851
+            24  O2x O    29.0946  -15.1718
+            25  C1y C    30.3025  -14.4631
+            26  C1y C    30.2926  -13.0626
+            27  C1x C    29.0835  -12.3758
+            28  C1y C    27.8755  -13.0846
+            29  C1b C    31.5468  -15.1693
+            30  N1a N    31.5569  -16.5953
+            31  O1a O    31.5060  -12.3503
+            32  N1a N    26.6567  -12.3923
+BOND        34
+            1     1   2 1
+            2     2   3 1
+            3     3   4 1
+            4     4   5 1
+            5     5   6 1
+            6     1   6 1
+            7     1   7 1 #Up
+            8     7   8 1
+            9     2   9 1 #Down
+            10    3  10 1 #Up
+            11    4  11 1 #Down
+            12    5  12 1 #Down
+            13   13  12 1 #Down
+            14   13  14 1
+            15   14  15 1
+            16   15  16 1
+            17   16  17 1
+            18   17  18 1
+            19   13  18 1
+            20   14  19 1 #Up
+            21   16  20 1 #Up
+            22   18  21 1 #Up
+            23   17  22 1 #Down
+            24   23  22 1 #Down
+            25   23  24 1
+            26   24  25 1
+            27   25  26 1
+            28   26  27 1
+            29   27  28 1
+            30   23  28 1
+            31   25  29 1 #Up
+            32   29  30 1
+            33   26  31 1 #Down
+            34   28  32 1 #Down
+END_OF_EXPECTED_KCF
+      assert_equal(expected, @obj.kcf)
+    end
+
+    def test_comment
+      expected = "natural product"
+      assert_equal(expected, @obj.comment)
+    end
+
+    def test_products
+      expected =
+        [
+         "TOBI (Novartis Pharma) 94F9E516-6BF6-4E30-8DDE-8833C25C2560",
+         "TOBRAMYCIN (Bristol-Myers Squibb) 7305F9BB-622B-43C0-981A-56E2F226CFD7",
+         "TOBRAMYCIN (Hospira) C5A005B0-7B6F-4E30-DF92-9A20B1CA66A1",
+         "Tobramycin (Akorn-Strides) 49151A62-191A-4BA8-8B8C-BD8535F2FDB3",
+         "Tobramycin (Bausch and Lomb) A5693EC9-D2F7-4D45-90B0-A113C54840D7",
+         "Tobramycin (Falcon Pharma) 27E2C16E-19B0-4745-93EB-5CF99F94BB92",
+         "Tobramycin (Hospira) 4E115874-3637-4AED-B6AF-77D53A850208",
+         "Tobramycin (Hospira) EB02166C-18F6-4BE0-F493-AC89D65DA759",
+         "Tobramycin (X-Gen Pharma) A384641C-04E3-4AB5-B152-7408CD07B64D",
+         "Tobramycin in Sodium Chloride (Hospira) EE907146-E4A8-4578-A9B0-C8E9790E3D55",
+         "Tobrex (Alcon Lab) 4B8716C4-0FFD-49AA-9006-A3BF5B6D19A6",
+         "Tobrex (Alcon Lab) CDD423C5-A231-47D4-BF51-00B5C29E6A60"
+        ]
+      assert_equal(expected, @obj.products)
+    end
+
+  end #class TestBioKeggDRUG
+end #module Bio
+

data/test/unit/bio/db/kegg/test_enzyme.rb

@@ -0,0 +1,241 @@
+#
+# test/unit/bio/db/kegg/test_enzyme.rb - Unit test for Bio::KEGG::ENZYME
+#
+# Copyright::  Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'digest/sha1'
+require 'bio/db/kegg/enzyme'
+
+module Bio
+  class TestKeggEnzyme < Test::Unit::TestCase
+
+    def setup
+      testdata_kegg = Pathname.new(File.join(BioRubyTestDataPath,
+                                             'KEGG')).cleanpath.to_s
+      entry = File.read(File.join(testdata_kegg, "1.1.1.1.enzyme"))
+      @obj = Bio::KEGG::ENZYME.new(entry)
+    end
+
+    def test_entry
+      assert_equal("EC 1.1.1.1 Enzyme", @obj.entry)
+    end
+
+    def test_entry_id
+      assert_equal("1.1.1.1", @obj.entry_id)
+    end
+
+    def test_obsolete?
+      assert_equal(false, @obj.obsolete?)
+    end
+
+    def test_names
+      expected = [ "alcohol dehydrogenase",
+                   "aldehyde reductase",
+                   "ADH",
+                   "alcohol dehydrogenase (NAD)",
+                   "aliphatic alcohol dehydrogenase",
+                   "ethanol dehydrogenase",
+                   "NAD-dependent alcohol dehydrogenase",
+                   "NAD-specific aromatic alcohol dehydrogenase",
+                   "NADH-alcohol dehydrogenase",
+                   "NADH-aldehyde dehydrogenase",
+                   "primary alcohol dehydrogenase",
+                   "yeast alcohol dehydrogenase" ]
+      assert_equal(expected, @obj.names)
+    end
+
+    def test_name
+      assert_equal("alcohol dehydrogenase", @obj.name)
+    end
+
+    def test_classes
+      assert_equal([ "Oxidoreductases;",
+                     "Acting on the CH-OH group of donors;",
+                     "With NAD+ or NADP+ as acceptor" ], @obj.classes)
+    end
+
+    def test_sysname
+      assert_equal("alcohol:NAD+ oxidoreductase", @obj.sysname)
+    end
+
+    def test_reaction
+      expected = "an alcohol + NAD+ = an aldehyde or ketone + NADH + H+ [RN:R07326 R07327]"
+      assert_equal(expected, @obj.reaction)
+    end
+
+    def test_all_reac
+      expected = "R07326 > R00623 R00754 R02124 R04805 R04880 R05233 R05234 R06917 R06927 R08281 R08306 R08557 R08558; R07327 > R00624 R08310; (other) R07105"
+      assert_equal(expected, @obj.all_reac)
+    end
+
+    def test_iubmb_reactions
+      expected = [ "R07326 > R00623 R00754 R02124 R04805 R04880 R05233 R05234 R06917 R06927 R08281 R08306 R08557 R08558",
+                   "R07327 > R00624 R08310" ]
+      assert_equal(expected, @obj.iubmb_reactions)
+    end
+
+    def test_kegg_reactions
+      assert_equal(["R07105"], @obj.kegg_reactions)
+    end
+
+    def test_substrates
+      expected = [ "alcohol [CPD:C00069]", "NAD+ [CPD:C00003]" ]
+      assert_equal(expected, @obj.substrates)
+    end
+
+    def test_products
+      expected = [ "aldehyde [CPD:C00071]",
+                   "ketone [CPD:C01450]",
+                   "NADH [CPD:C00004]",
+                   "H+ [CPD:C00080]" ]
+      assert_equal(expected, @obj.products)
+    end
+
+    def test_inhibitors
+      assert_equal([], @obj.inhibitors)
+    end
+
+    def test_cofactors
+      assert_equal(["Zinc [CPD:C00038]"], @obj.cofactors)
+    end
+
+    def test_comment
+      expected = "A zinc protein. Acts on primary or secondary alcohols or hemi-acetals; the animal, but not the yeast, enzyme acts also on cyclic secondary alcohols."
+      assert_equal(expected, @obj.comment)
+    end
+
+    def test_pathways_as_strings
+      expected = [ "PATH: ec00010  Glycolysis / Gluconeogenesis",
+                   "PATH: ec00071  Fatty acid metabolism",
+                   "PATH: ec00260  Glycine, serine and threonine metabolism",
+                   "PATH: ec00350  Tyrosine metabolism",
+                   "PATH: ec00624  1- and 2-Methylnaphthalene degradation",
+                   "PATH: ec00641  3-Chloroacrylic acid degradation",
+                   "PATH: ec00830  Retinol metabolism",
+                   "PATH: ec00980  Metabolism of xenobiotics by cytochrome P450",
+                   "PATH: ec00982  Drug metabolism - cytochrome P450",
+                   "PATH: ec01100  Metabolic pathways" ]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_pathways_as_hash
+      expected = {
+        "ec01100" => "Metabolic pathways",
+        "ec00982" => "Drug metabolism - cytochrome P450",
+        "ec00641" => "3-Chloroacrylic acid degradation",
+        "ec00830" => "Retinol metabolism",
+        "ec00071" => "Fatty acid metabolism",
+        "ec00260" => "Glycine, serine and threonine metabolism",
+        "ec00624" => "1- and 2-Methylnaphthalene degradation",
+        "ec00350" => "Tyrosine metabolism",
+        "ec00010" => "Glycolysis / Gluconeogenesis",
+        "ec00980" => "Metabolism of xenobiotics by cytochrome P450"
+      }
+      assert_equal(expected, @obj.pathways_as_hash)
+      assert_equal(expected, @obj.pathways)
+    end
+
+    def test_orthologs_as_strings
+      expected = [ "KO: K00001  alcohol dehydrogenase",
+                   "KO: K11440  choline dehydrogenase" ]
+      assert_equal(expected, @obj.orthologs_as_strings)
+    end
+
+    def test_orthologs_as_hash
+      expected = {
+        "K11440" => "choline dehydrogenase",
+        "K00001" => "alcohol dehydrogenase"
+      }
+      assert_equal(expected, @obj.orthologs_as_hash)
+      assert_equal(expected, @obj.orthologs)
+    end
+
+    def test_genes_as_strings
+      assert_equal(759, @obj.genes_as_strings.size)
+      assert_equal("0b01addd884266d7e80fdc34f112b9a89b90cc54",
+                   Digest::SHA1.hexdigest(@obj.genes_as_strings.join("\n")))
+    end
+
+    def test_genes_as_hash
+      assert_equal(759, @obj.genes_as_hash.size)
+      assert_equal("025e77f866a7edb0eccaaabcff31df90d8e1fca1",
+                   Digest::SHA1.hexdigest(@obj.genes_as_hash.keys.sort.join(";")))
+      assert_equal(["124", "125", "126", "127", "128", "130", "131"],
+                   @obj.genes_as_hash['hsa'])
+      assert_equal(["BSU18430", "BSU26970", "BSU31050"],
+                   @obj.genes_as_hash['bsu'])
+      assert_equal(["Tpen_1006", "Tpen_1516"],
+                   @obj.genes_as_hash['tpe'])
+    end
+
+    def test_genes
+      assert_equal(759, @obj.genes.size)
+      assert_equal("025e77f866a7edb0eccaaabcff31df90d8e1fca1",
+                   Digest::SHA1.hexdigest(@obj.genes.keys.sort.join(";")))
+      assert_equal(["124", "125", "126", "127", "128", "130", "131"],
+                   @obj.genes['hsa'])
+      assert_equal(["BSU18430", "BSU26970", "BSU31050"],
+                   @obj.genes['bsu'])
+      assert_equal(["Tpen_1006", "Tpen_1516"],
+                   @obj.genes['tpe'])
+    end
+
+    def test_diseases
+      assert_equal([], @obj.diseases)
+    end
+
+    def test_motifs
+      assert_equal([], @obj.motifs)
+    end
+
+    def test_structures
+      expected = ["1A4U", "1A71", "1A72", "1ADB", "1ADC", "1ADF", "1ADG",
+                  "1AGN", "1AXE", "1AXG", "1B14", "1B15", "1B16", "1B2L",
+                  "1BTO", "1CDO", "1D1S", "1D1T", "1DEH", "1E3E", "1E3I",
+                  "1E3L", "1EE2", "1H2B", "1HDX", "1HDY", "1HDZ", "1HET",
+                  "1HEU", "1HF3", "1HLD", "1HSO", "1HSZ", "1HT0", "1HTB",
+                  "1JU9", "1JVB", "1LDE", "1LDY", "1LLU", "1M6H", "1M6W",
+                  "1MA0", "1MC5", "1MG0", "1MG5", "1MGO", "1MP0", "1N8K",
+                  "1N92", "1NTO", "1NVG", "1O2D", "1P1R", "1QLH", "1QLJ",
+                  "1QV6", "1QV7", "1R37", "1RJW", "1SBY", "1TEH", "1U3T",
+                  "1U3U", "1U3V", "1U3W", "1VJ0", "1YE3", "2EER", "2FZE",
+                  "2FZW", "2HCY", "2JHF", "2JHG", "2OHX", "2OXI", "3BTO",
+                  "3COS", "3HUD", "3I4C", "5ADH", "6ADH", "7ADH"]
+      assert_equal(expected, @obj.structures)
+    end
+
+    def test_dblinks_as_strings
+      expected = [ "ExplorEnz - The Enzyme Database: 1.1.1.1",
+                   "IUBMB Enzyme Nomenclature: 1.1.1.1",
+                   "ExPASy - ENZYME nomenclature database: 1.1.1.1",
+                   "UM-BBD (Biocatalysis/Biodegradation Database): 1.1.1.1",
+                   "BRENDA, the Enzyme Database: 1.1.1.1",
+                   "CAS: 9031-72-5" ]
+      assert_equal(expected, @obj.dblinks_as_strings)
+    end
+
+    def test_dblinks_as_hash
+      expected = {
+        "UM-BBD (Biocatalysis/Biodegradation Database)" => [ "1.1.1.1" ],
+        "ExPASy - ENZYME nomenclature database"         => [ "1.1.1.1" ],
+        "IUBMB Enzyme Nomenclature"                     => [ "1.1.1.1" ],
+        "BRENDA, the Enzyme Database"                   => [ "1.1.1.1" ],
+        "ExplorEnz - The Enzyme Database"               => [ "1.1.1.1" ],
+        "CAS"                                           => [ "9031-72-5" ]
+      }
+      assert_equal(expected, @obj.dblinks_as_hash)
+      assert_equal(expected, @obj.dblinks)
+    end
+
+  end #class TestKeggEnzyme < Test::Unit::TestCase
+end #module Bio
+