RubyGems - chemruby - Versions diffs - 0.9.3 → 1.1.9 - Mend

chemruby 0.9.3 → 1.1.9

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (127) hide show

data/README +2 -2
data/Rakefile +67 -63
data/ext/extconf.rb +2 -0
data/ext/subcomp.c +461 -320
data/ext/utils.c +56 -0
data/ext/utils.h +13 -0
data/lib/chem.rb +34 -8
data/lib/chem/db.rb +8 -0
data/lib/chem/db/cansmi.rb +1 -1
data/lib/chem/db/cdx.rb +1 -1
data/lib/chem/db/cml.rb +52 -0
data/lib/chem/db/gd.rb +64 -0
data/lib/chem/db/gspan.rb +2 -2
data/lib/chem/db/kcf_rpair.rb +34 -0
data/lib/chem/db/kegg.rb +35 -1
data/lib/chem/db/mdl.rb +75 -34
data/lib/chem/db/opsin.rb +24 -0
data/lib/chem/db/pdb.rb +105 -0
data/lib/chem/db/pdf.rb +2 -0
data/lib/chem/db/pubchem.rb +1071 -88
data/lib/chem/db/rmagick.rb +5 -3
data/lib/chem/db/sdf.rb +28 -2
data/lib/chem/db/smiles/smiles.ry +27 -25
data/lib/chem/db/smiles/smiparser.rb +29 -27
data/lib/chem/db/types/type_gd.rb +35 -0
data/lib/chem/db/types/type_gspan.rb +2 -2
data/lib/chem/db/types/type_kcf.rb +19 -0
data/lib/chem/db/types/type_kegg.rb +2 -0
data/lib/chem/db/types/type_mdl.rb +1 -1
data/lib/chem/db/types/type_png.rb +5 -1
data/lib/chem/db/types/type_rdf.rb +22 -0
data/lib/chem/db/types/type_xyz.rb +1 -1
data/lib/chem/db/vector.rb +19 -3
data/lib/chem/model.rb +5 -2
data/lib/chem/utils.rb +17 -1
data/lib/chem/utils/bitdb.rb +49 -0
data/lib/chem/utils/cas.rb +28 -0
data/lib/chem/utils/cdk.rb +403 -0
data/lib/chem/utils/fingerprint.rb +98 -0
data/lib/chem/utils/geometry.rb +8 -0
data/lib/chem/utils/net.rb +303 -0
data/lib/chem/utils/once.rb +28 -0
data/lib/chem/utils/openbabel.rb +204 -0
data/lib/chem/utils/sssr.rb +33 -25
data/lib/chem/utils/sub.rb +6 -0
data/lib/chem/utils/transform.rb +9 -8
data/lib/chem/utils/ullmann.rb +138 -95
data/lib/graph.rb +5 -6
data/lib/graph/utils.rb +8 -0
data/sample/calc_maximum_common_subgraph.rb +27 -0
data/sample/calc_properties.rb +9 -0
data/sample/data/atp.mol +69 -0
data/sample/data/pioglitazone.mol +58 -0
data/sample/data/rosiglitazone.mol +55 -0
data/sample/data/troglitazone.mol +70 -0
data/sample/find_compound_by_keggapi.rb +19 -0
data/sample/generate_inchi.rb +7 -0
data/sample/generate_substructurekey.rb +11 -0
data/sample/images/ex6.rb +17 -0
data/sample/images/ex7.rb +18 -0
data/sample/iupac2mol.rb +8 -0
data/sample/kekule.rb +13 -0
data/sample/logp.rb +4 -0
data/sample/mcs.rb +13 -0
data/sample/mol2pdf.rb +8 -0
data/sample/pubchem_fetch.rb +8 -0
data/sample/pubchem_search.rb +12 -0
data/sample/rosiglitazone.mol +57 -0
data/sample/smarts.rb +10 -0
data/sample/structure_match.rb +8 -0
data/sample/structure_match_color.rb +22 -0
data/sample/thiazolidinedione.mol +19 -0
data/sample/troglitazone.mol +232 -0
data/sample/vicinity.rb +8 -0
data/test/data/CID_704.sdf +236 -0
data/test/data/CID_994.sdf +146 -0
data/test/data/db_EXPT03276.txt +321 -0
data/test/data/pioglitazone.mol +58 -0
data/test/data/rosiglitazone.mol +55 -0
data/test/data/thiazolidinedione.mol +19 -0
data/test/data/troglitazone.mol +70 -0
data/test/{test_adj.rb → tc_adj.rb} +0 -0
data/test/{test_canonical_smiles.rb → tc_canonical_smiles.rb} +0 -0
data/test/tc_casrn.rb +17 -0
data/test/tc_cdk.rb +89 -0
data/test/{test_cdx.rb → tc_cdx.rb} +0 -0
data/test/{test_chem.rb → tc_chem.rb} +0 -0
data/test/{test_cluster.rb → tc_cluster.rb} +0 -0
data/test/{test_db.rb → tc_db.rb} +0 -0
data/test/tc_develop.rb +38 -0
data/test/tc_drugbank.rb +13 -0
data/test/{test_eps.rb → tc_eps.rb} +0 -0
data/test/tc_gd.rb +8 -0
data/test/{test_geometry.rb → tc_geometry.rb} +0 -0
data/test/tc_graph.rb +15 -0
data/test/{test_gspan.rb → tc_gspan.rb} +0 -0
data/test/{test_iupac.rb → tc_iupac.rb} +0 -0
data/test/{test_kcf.rb → tc_kcf.rb} +0 -0
data/test/{test_kcf_glycan.rb → tc_kcf_glycan.rb} +0 -0
data/test/{test_kegg.rb → tc_kegg.rb} +13 -0
data/test/{test_linucs.rb → tc_linucs.rb} +0 -0
data/test/{test_mdl.rb → tc_mdl.rb} +20 -0
data/test/{test_mol2.rb → tc_mol2.rb} +1 -1
data/test/{test_morgan.rb → tc_morgan.rb} +0 -0
data/test/tc_net.rb +5 -0
data/test/tc_once.rb +29 -0
data/test/tc_openbabel.rb +57 -0
data/test/{test_pdf.rb → tc_pdf.rb} +0 -0
data/test/{test_prop.rb → tc_prop.rb} +1 -1
data/test/tc_pubchem.rb +32 -0
data/test/{test_rmagick.rb → tc_rmagick.rb} +0 -0
data/test/{test_sbdb.rb → tc_sbdb.rb} +0 -0
data/test/{test_sdf.rb → tc_sdf.rb} +2 -0
data/test/{test_smiles.rb → tc_smiles.rb} +46 -30
data/test/tc_sssr.rb +1 -0
data/test/{test_sub.rb → tc_sub.rb} +0 -0
data/test/tc_subcomp.rb +59 -0
data/test/{test_traverse.rb → tc_traverse.rb} +0 -0
data/test/{test_writer.rb → tc_writer.rb} +0 -0
data/test/{test_xyz.rb → tc_xyz.rb} +0 -0
data/test/ts_current.rb +11 -0
data/test/ts_image.rb +6 -0
data/test/ts_main.rb +12 -0
metadata +259 -194
data/lib/chem/utils/graph_db.rb +0 -146
data/test/test_sssr.rb +0 -18
data/test/test_subcomp.rb +0 -37

data/test/data/pioglitazone.mol ADDED

@@ -0,0 +1,58 @@
+pioglitazone.mol
+  ChemDraw06080600242D
+ 26 27  0  0  0  0  0  0  0  0999 V2000
+   -4.2782    0.4874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.2782   -0.3376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.5637   -0.7501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8493   -0.3376    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8493    0.4874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.0086   -0.3376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7231   -0.7501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4376   -0.3376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.7231    0.8999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.9927   -0.7501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.9927   -1.5751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1520   -0.7501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8665   -0.3376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6202   -0.6731    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    4.1722   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7597    0.6544    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    2.9527    0.4829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9927   -0.1463    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3396    1.0350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    3.8977    1.5751    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
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+  4  5  1  0
+  5  6  2  0
+  6  1  1  0
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+ 13 14  1  0
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+ 19 20  1  0
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+ 21 22  1  0
+ 22 23  1  0
+ 23 19  1  0
+ 21 24  2  0
+ 23 25  2  0
+M  END

data/test/data/rosiglitazone.mol ADDED

@@ -0,0 +1,55 @@
+Rosiglitazone.mol
+  ChemDraw06090600212D
+ 24 26  0  0  0  0  0  0  0  0999 V2000
+    3.0227    0.7707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.8477    0.7707    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    4.1026    1.5553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.4352    2.0402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    2.7677    1.5553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5378    0.1032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7128    0.1032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3003    0.8177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.4753    0.8177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0628    0.1032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.4753   -0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3003   -0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7622    0.1032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1747   -0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.9997   -0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -3.6497   -0.6113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4747   -0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.8872   -1.3257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4747   -2.0402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.6497   -2.0402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  1  1  0
+  1  6  1  0
+  6  7  1  0
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+ 15 16  1  0
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+ 17 20  2  0
+ 20 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  2  0
+ 24 17  1  0
+M  END

data/test/data/thiazolidinedione.mol ADDED

@@ -0,0 +1,19 @@
+thiazolidinedione.mol
+  ChemDraw06080600152D
+  7  7  0  0  0  0  0  0  0  0999 V2000
+   -0.6898   -0.3011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1352   -0.3011    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3901    0.4836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2773    0.9685    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9448    0.4836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1747    0.7385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1747   -0.9685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  1  1  0
+  3  6  2  0
+  1  7  2  0
+M  END

data/test/data/troglitazone.mol ADDED

@@ -0,0 +1,70 @@
+troglitazone.mol
+  ChemDraw06080600252D
+ 31 34  0  0  0  0  0  0  0  0999 V2000
+   -4.2071    0.3052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.2071   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4927   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7782   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7782    0.3052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4927    0.7177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.0637   -0.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3492   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -3.4927   -1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  2  0
+  3  4  1  0
+  4  5  2  0
+  5  6  1  0
+  6  1  2  0
+  4  7  1  0
+  7  8  1  0
+  8  9  1  0
+  9 10  1  0
+ 10  5  1  0
+  8 11  1  0
+  8 12  1  0
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+ 20 21  1  0
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+ 24 25  1  0
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+ 25 26  2  0
+ 23 27  2  0
+  6 28  1  0
+  2 29  1  0
+  1 30  1  0
+  3 31  1  0
+M  END

data/test/{test_adj.rb → tc_adj.rb} RENAMED

File without changes

data/test/{test_canonical_smiles.rb → tc_canonical_smiles.rb} RENAMED

File without changes

data/test/tc_casrn.rb ADDED

@@ -0,0 +1,17 @@
+require 'test/unit'
+class CASRNTest < Test::Unit::TestCase
+  def test_validity
+    [
+      ["aaa", false],
+      ["107-07-3", true],
+      ["107-07-4", false],
+      ["aa-07-3", false],
+    ].each do |casrn, test|
+      assert_equal(casrn.is_valid_casrn?, test)
+    end
+  end
+end

data/test/tc_cdk.rb ADDED

@@ -0,0 +1,89 @@
+class CDKTest < Test::Unit::TestCase
+  def test_load_cdk_save_ob
+    mol  = Chem::CDK::parse_smiles("C1CCC=N1")
+    mol2 = mol.cdk_generate_2D
+    mol2.use_open_babel
+    mol2.ob_save_as("temp/cdk2ob.mol", "mdl")
+  end
+  def t#est_random_generator
+    mol1 = Chem::CDK::parse_smiles("C1CCC=N1").cdk_generate_2D_mol
+    mol1.cdk_save_as("temp/original.png")
+    mol2 = mol1.cdk_generate_randomly.cdk_generate
+    mol2.cdk_save_as("temp/random.png")
+  end
+  def test_load_mdl
+    mol = Chem::CDK::parse_mdl(File.open($data_dir + "troglitazone.mol").read)
+#    mol.cdk_save_as("temp/troglitazone.png")
+  end
+  def test_load_cr_save_structure
+    troglitazone = Chem.load($data_dir + "troglitazone.mol")
+    mol = troglitazone.cdk_generate_2D
+#    mol.cdk_save_as("temp/troglitazone.png")
+  end
+  def test_common_subgraphs
+    troglitazone = Chem.load($data_dir + "troglitazone.mol")
+    pioglitazone = Chem.load($data_dir + "pioglitazone.mol")
+    troglitazone.cdk_mcs(pioglitazone).each_with_index do |mcs, i|
+      hash = mcs.match(troglitazone)[0]
+      hash.each do |from, to|
+        to.visible   = true
+        to.color   = [1, 0, 0]
+      end
+      troglitazone.save("temp/#{i}.pdf")
+      troglitazone.nodes.each{|atom| atom.color = [0, 0, 0]}
+      # RuntimeError: Fail: unknown method name `setMolecule'
+#      mol = mcs.cdk_generate_2D # ??
+#      mcs.cdk_save_as("temp/mcs-#{i}.png")
+#      mcs.save("temp.pdf")
+    end
+  end
+  def test_wiener
+  end
+  def get_sample
+    Chem.load($data_dir + "troglitazone.mol")
+  end
+  def test_CPSA
+    t = get_sample
+    t.cdk_CPSA.all?{|n| assert(n.kind_of?(Numeric))}
+  end
+  def test_RotatableBondsCount
+    t = get_sample
+    p t.cdk_RotatableBondsCount
+  end
+  def test_load
+#    Chem::CDK::load($data_dir + "troglitgazone")
+  end
+  def test_find_all_rings
+    t = get_sample
+#    p t.cdk_find_all_rings
+  end
+  def test_sssr
+    t = get_sample
+    require 'pp'
+    t.cdk_sssr.each do |ring|
+      p ring.length
+    end
+  end
+  def test_all_rings
+    t = get_sample
+    require 'pp'
+    t.cdk_find_all_rings.each do |ring|
+      p ring.length
+    end
+  end
+end

data/test/{test_cdx.rb → tc_cdx.rb} RENAMED

File without changes

data/test/{test_chem.rb → tc_chem.rb} RENAMED

File without changes

data/test/{test_cluster.rb → tc_cluster.rb} RENAMED

File without changes

data/test/{test_db.rb → tc_db.rb} RENAMED

File without changes

data/test/tc_develop.rb ADDED

@@ -0,0 +1,38 @@
+MolDir = "/home/tanaka/data/kegg/ligand/mol/C%05d.mol"
+class DevelopmentTest < Test::Unit::TestCase
+  def test_net
+    # p Chem.search("pparg", :db => :pubmed)
+    # search adenine
+    res = Chem.search("CCC", :db => :pubchem)
+#    res = Chem.search("C1=NC2=C(N1)C(=NC=N2)N", :db => :pubchem)
+    sleep 3
+    res.fetch_all
+    #res.retrieve
+  end
+end
+__END__
+class PendingTest < Test::Unit::TestCase
+  def test_raise
+    BitDatabase.new("temp/test.fng", 80) do |db|
+      assert_raise(Exception){ db.push([81]) }
+      db.push([24, 30, 32, 55])
+    end
+  end
+  def test_fingerprint
+    BitDatabase.open("temp/test2.fng", 80) do |db|
+      db.push([24, 30, 31, 32, 55])
+      assert(true)
+    end
+    BitDatabase.search("temp/test2.fng", [24, 30, 55])
+  end
+end

data/test/tc_drugbank.rb ADDED

@@ -0,0 +1,13 @@
+# tentatively stopped
+# class DrugBankTest < Test::Unit::TestCase
+#   def test_load
+#     entry = Chem::DrugBankEntry.load($data_dir + "db_EXPT03276.txt")
+#     assert_equal(6, entry.creation_date.month)
+#     assert_nil(entry.update_date)
+#     assert_equal("EXPT03276", entry.accession_no)
+#     assert_equal(403.477, entry.molecular_weight)
+#     assert_nil(entry.melting_point)
+#   end
+# end

data/test/{test_eps.rb → tc_eps.rb} RENAMED

File without changes

data/test/tc_gd.rb ADDED

@@ -0,0 +1,8 @@
+require 'chem'
+class GDTest < Test::Unit::TestCase
+  def test_gd
+    mol = Chem.open_mol($data_dir + "cyclohexane.mol")
+  end
+end

data/test/{test_geometry.rb → tc_geometry.rb} RENAMED

File without changes

data/test/tc_graph.rb ADDED

@@ -0,0 +1,15 @@
+class DummyGraph
+  include Graph
+end
+class GraphTest < Test::Unit::TestCase
+  def test_to_mdl
+    graph = DummyGraph.new
+    graph.nodes = [1, 2, 3]
+    graph.edges = [[0, 1, 2], [1, 2, 3]]
+    assert_equal([1, 3], graph.terminal_nodes)
+  end
+end

data/test/{test_gspan.rb → tc_gspan.rb} RENAMED

File without changes

data/test/{test_iupac.rb → tc_iupac.rb} RENAMED

File without changes

data/test/{test_kcf.rb → tc_kcf.rb} RENAMED

File without changes

data/test/{test_kcf_glycan.rb → tc_kcf_glycan.rb} RENAMED

File without changes

data/test/{test_kegg.rb → tc_kegg.rb} RENAMED

@@ -13,6 +13,19 @@ require 'chem/db/kegg'
 class KeggOpenTest < Test::Unit::TestCase
+  def test_coc
+    Chem::KEGG["C00147"]
+    assert_instance_of(Chem::KEGG::EC, Chem::KEGG["EC1.2.3.4"], "EC1.2.3.4")
+    assert_instance_of(Chem::KEGG::EC, Chem::KEGG["EC1.2.3.*"], "EC1.2.3.*")
+    assert_instance_of(Chem::KEGG::EC, Chem::KEGG["EC10.20.30.*"], "EC10.20.30.*")
+    assert_raises(Chem::KEGGException){
+      Chem::KEGG["Unknown"]
+    }
+    assert_raises(Chem::KEGGException){
+      Chem::KEGG["EC1"]
+    }
+  end
   def test_open
     # environment dependent test!
     #dir = "/home/tanaka/share/data/kegg"

data/test/{test_linucs.rb → tc_linucs.rb} RENAMED

File without changes

data/test/{test_mdl.rb → tc_mdl.rb} RENAMED

@@ -41,5 +41,25 @@ class MDLTest < Test::Unit::TestCase
     assert_equal(26, types[:single])
   end
+  def test_mdl_header
+    #  -ISIS-  02070623502D
+    mol = Chem.open_mol($data_dir + "atp.mol")
+    assert_equal("-ISIS-  ", mol.program_name)
+    assert_equal(DateTime.new(2006, 2, 7, 23, 50), mol.date_time)
+    assert_equal("2D", mol.dimensional_codes)
+  end
+  def test_save_mdl
+    mol = Chem.open_mol($data_dir + "atp.mol")
+    mol.save(File.join("temp", "save_test.mol"))
+    now = DateTime.now
+    mol = Chem.open_mol(File.join(%w(temp save_test.mol)))
+    assert_equal(now.year,  mol.date_time.year)
+    assert_equal(now.mday,  mol.date_time.mday)
+    assert_equal(now.month, mol.date_time.month)
+    assert_equal(now.hour,  mol.date_time.hour)
+    assert_equal(now.min,   mol.date_time.min)
+  end
 end