chemruby 0.9.3 → 1.1.9

data/test/{test_mol2.rb → tc_mol2.rb}

@@ -56,7 +56,7 @@ class SybylTest < Test::Unit::TestCase
   end
 
   def test_mol
-    assert_equal((0..66).to_a, @entries[0].match_by_ullmann(@entries[0]))
+    # assert_equal((0..66).to_a, @entries[0].match_by_ullmann(@entries[0]))
   end
 
 end

data/test/tc_net.rb

@@ -0,0 +1,5 @@
+
+
+class NetTest < Test::Unit::TestCase
+  fail
+end

data/test/tc_once.rb

@@ -0,0 +1,29 @@
+require 'chem'
+
+class Foo
+
+  include Once
+
+  def initialize
+    @value = 0
+  end
+
+  def get
+    @value += 1
+    @value
+  end
+
+  once :get
+
+end
+
+class OnceTest < Test::Unit::TestCase
+
+  def test_once
+    foo = Foo.new
+    assert_equal(1, foo.get)
+    assert_equal(1, foo.get)
+    assert_equal(1, foo.get)
+  end
+
+end

data/test/tc_openbabel.rb

@@ -0,0 +1,57 @@
+class OpenBabelTest < Test::Unit::TestCase
+
+  def test_chemruby_ob_conversion
+    mol = SMILES("CCC")
+    assert_raise(NoMethodError) do
+      mol.get_mol_wt # OBMol method
+    end
+    mol.use_open_babel
+    assert_in_delta(44.09562, mol.get_mol_wt, 1.0)
+  end
+
+  def test_smiles
+    mol = Chem::OpenBabel::parse_smiles("CCC")
+    assert_in_delta(44.09562, mol.get_mol_wt, 1.0)
+    assert_equal(3, mol.num_atoms)
+    assert_equal(2, mol.num_bonds)
+    mol.nodes.each do |atom|
+      assert_not_nil(atom)
+      assert_in_delta(12.0, atom.get_atomic_mass, 0.5)
+    end
+  end
+
+  # example from:
+  # http://depth-first.com/articles/2006/10/31/obruby-a-ruby-interface-to-open-babel
+  def test_smarts
+    smiles = 'CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C'
+    mol = Chem::OpenBabel::parse_smiles(smiles)
+    pat = Chem::OpenBabel::parse_smarts('C1CCCCC1')
+    assert(pat.match(mol), "must match")
+    ary = pat.get_umap_list
+    assert_equal([12, 17, 16, 15, 14, 13], ary[0])
+    assert_equal([20, 25, 24, 23, 22, 21], ary[1])
+  end
+
+  def test_load_sdf
+    sdf = Chem::OpenBabel::load_sdf($data_dir + "CID_704.sdf")
+    assert_equal(1, sdf.length)
+  end
+
+  def test_load_ob_save_ob
+    mol = Chem::OpenBabel::load_as($data_dir + "hypericin.mol", "mdl")
+    mol.ob_save_as("aa.fpt", "fpt")
+  end
+
+  def test_load_cr_save_ob
+    Chem.load($data_dir + "hypericin.mol").ob_save_as("aa.mol", "mdl")
+  end
+
+  def test_export_as
+    assert_not_nil(Chem.load($data_dir + "hypericin.mol").ob_export_as("inchi"))
+  end
+
+  def test_inchi
+    assert_not_nil(Chem.load($data_dir + "hypericin.mol").to_inchi)
+  end
+
+end

data/test/{test_prop.rb → tc_prop.rb}

@@ -16,7 +16,7 @@ class PropTest < Test::Unit::TestCase
   end
 
   def test_oxidation_number
-    mgcl2 = SMILES("ClMgCl")
+    mgcl2 = SMILES("Cl[Mg]Cl")
     mg = mgcl2.nodes.find{|n| n.element == :Mg}
     assert(2, mgcl2.oxidation_number(mg))
 

data/test/tc_pubchem.rb

@@ -0,0 +1,32 @@
+
+
+class PubChemTest < Test::Unit::TestCase
+
+  def test_pubchem_subskeys
+    mol = Chem.open_mol(File.join($data_dir, "CID_704.sdf")).to_a[0]
+    original = mol.pubchem_subskeys
+    assert_equal("11000000001111011100111000000111", ("%b" % original)[-32..-1])
+    pos = mol.pubchem_subskeys.to_bit_positions
+    assert_equal([0, 1, 2, 9, 10, 11, 14, 15, 16, 18, 19, 20, 21], pos[0..12])
+    gen_sk = mol.generate_pubchem_subskey
+
+    # Test for Section 1
+    assert_equal(("%0881b" % original)[-114..-1], ("%0881b" % gen_sk)[-114..-1])
+    # Test for Section 2
+    pos.each do |n|
+      puts Chem::PubChemSubsKey[n] if n > 115 and n < 262
+    end
+    pos2 = gen_sk.to_bit_positions
+    pos2.each do |n|
+      puts Chem::PubChemSubsKey[n] if n > 115 and n < 262
+    end
+    p mol.generate_pubchem_subskey.to_bit_positions
+    p pos
+  end
+
+  def test_path_fingerprint
+    fp = Chem.open_mol(File.join($data_dir, "hypericin.mol")).fingerprint(7, 32)
+    assert_operator(32, :<, fp)
+  end
+
+end

data/test/{test_sdf.rb → tc_sdf.rb}

@@ -1,5 +1,7 @@
 # $Id: test_sdf.rb 151 2006-02-08 08:21:08Z tanaka $
 
+require 'test/unit'
+require 'chem'
 require 'test/type_test'
 require 'chem/db/types/type_sdf'
 

data/test/{test_smiles.rb → tc_smiles.rb}

@@ -5,38 +5,10 @@ require 'test/all'
 
 require 'test/ctab_test'
 
-
-class SmilesTest < Test::Unit::TestCase
+class SmilesSampleTest < Test::Unit::TestCase
 
   include Chem::CtabTest
 
-  def test_cubane
-    Chem.parse_smiles("C12C3C4C1C5C2C3C45")
-  end
-
-  def test_atom_types
-    [
-      ["H"      , {:element => :H}],
-      ["C"      , {:element => :C,  :is_aromatic => false, :mass => 12.0107}],
-      ["c"      , {:element => :C,  :is_aromatic => true}],
-      ["se"     , {:element => :Se, :is_aromatic => true}],
-      ["[235U]" , {:element => :U,  :mass => 235.0}],
-      ["[nH]"   , {:element => :N,  :is_aromatic => true}], # Hydrogen
-      ["[OH3+]" , {:element => :O,  :hydrogen_count => 3}],
-      ["[Fe2+]" , {:element => :Fe, :charge => 2}],
-      ["[Fe++]" , {:element => :Fe, :charge => 2}],
-      ["[13CH4]", {:element => :C,  :hydrogen_count => 4, :mass => 13}],
-      ["[2H]"   , {:element => :H,  :mass => 2}],
-#      ["[C@H]"   , {:element => :H}],
-#      ["[C@@H]"   , {:element => :H}],
-    ].each do |sm, prop|
-      mol = SMILES(sm)
-      prop.each do |key, val|
-        assert_equal(val, mol.nodes[0].send(key))
-      end
-    end
-  end
-
   def setup
     @entries = []
 
@@ -52,33 +24,77 @@ class SmilesTest < Test::Unit::TestCase
       "CC(C)C(=O)O",
       "O=Cl(=O)(=O)[O-]", # Cl(=O)(=O)(=O)[O-]
       "CCCC(C(=O)O)CCC", # 4-heptanoic acid
+
       # Ring
      "C1CCCCC1", # Cyclohexane
       "C1=CCCCC1", # cyclohexene
       "c12c(cccc1)cccc2", # naphthalene
       "c1ccccc1c2ccccc2", # biphenyl 
       "C12C3C4C1C5C4C3C25", # Cubane
+
       # Isotopic specification
       "[C]", # elemental carbon
       "[12C]", # elemental carbon-12
       "[13C]", # elemental carbon-13
       "[13CH4]", # C-13 methane
+
       # Specifying double-bond configuration
       'F/C=C/F', # trans-difluoroethene
       'F\C=C\F', # trans-difluoroethene
       'F/C=C\F', # cis-difluoroethene
       'F\C=C/F', # cis-difluoroethene
+
       # Specifying tetrahedral chirality
       "N[C@@H](C)C(=O)O", # L-alanine
       "N[C@H](C)C(=O)O", # D-alanine
       "O[C@H]1CCCC[C@H]1O", # cis-resorcinol
       "C1C[C@H]2CCCC[C@H]CC1", #cis-decaline
+
       # http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=043383,niaid
       "C1=CC2=C3C(=C1)C=CC4=C3C(=CC5=C4[C@H]([C@H](C=C5)O)O)C=C2",
       "NC(Cc1c[nH]c2cc[se]c12)C(O)=O", # pointed out by Dr. ktaz
+      "S=[Co]", 
     ].each do |smiles|
       @entries.push(Chem.parse_smiles(smiles))
     end
-#        mass : NUMBER
+#       mass : NUMBER
   end
 end
+
+class SmilesTest < Test::Unit::TestCase
+
+  def test_cubane
+    Chem.parse_smiles("C12C3C4C1C5C2C3C45")
+  end
+
+  def test_atom_types
+    [
+      ["H"      , {:element => :H}],
+      ["C"      , {:element => :C,  :is_aromatic => false, :mass => 12.0107}],
+      ["c"      , {:element => :C,  :is_aromatic => true}],
+      ["[se]"     , {:element => :Se, :is_aromatic => true}],
+      ["[235U]" , {:element => :U,  :mass => 235.0}],
+      ["[nH]"   , {:element => :N,  :is_aromatic => true}], # Hydrogen
+      ["[OH3+]" , {:element => :O,  :hydrogen_count => 3}],
+      ["[Fe2+]" , {:element => :Fe, :charge => 2}],
+      ["[Fe++]" , {:element => :Fe, :charge => 2}],
+      ["[13CH4]", {:element => :C,  :hydrogen_count => 4, :mass => 13}],
+      ["[2H]"   , {:element => :H,  :mass => 2}],
+#      ["[C@H]"   , {:element => :H}],
+#      ["[C@@H]"   , {:element => :H}],
+    ].each do |sm, prop|
+      mol = SMILES(sm)
+      prop.each do |key, val|
+        assert_equal(val, mol.nodes[0].send(key))
+      end
+    end
+  end
+
+  def test_co
+    # Not cobalt
+    comp = Chem.parse_smiles("O=CO").composition
+    assert_equal(2, comp[:O])
+    assert_equal(1, comp[:C])
+  end
+
+end

data/test/tc_sssr.rb

@@ -0,0 +1 @@
+# $

data/test/tc_subcomp.rb

@@ -0,0 +1,59 @@
+# $Id: test_subcomp.rb 160 2006-02-14 06:49:37Z tanaka $
+
+require 'test/unit'
+require 'test/all'
+
+require 'chem'
+
+class SubcompTest < Test::Unit::TestCase
+
+
+  def test_bit_matrix
+    [
+      [31, 1],
+      [32, 1],
+      [33, 2],
+      [63, 2],
+      [64, 2],
+      [65, 3],
+    ].each do |bits, bytes|
+      assert_equal(bytes, Chem::BitMatrix.new(bits, bits).n_bytes)
+    end
+
+    bm = Chem::BitMatrix.new(40, 40)
+    0.upto(39) do |n|
+      bm.set(n, n)
+    end
+  end
+
+  def test_db_store
+#     db = Chem::CompoundDB.new("test")
+
+#     1.upto(10) do |n|
+#       filename = MolDir % n
+#       next if not File.exist?(filename)
+#       mol = Chem.open_mol(filename)
+#       db_id = db.store(mol)
+#       puts db_id
+#     end
+    
+#     db.close
+
+#     assert_raises(Exception) do
+#       Chem.db_search("Unexpectedly_Very_Long_File_Name_So_Please_Please_Raise_Error_Or_Program_will_Cause_Memory_Leak_It_Could_Be_Serious_Security_Problem", nil)
+#     end
+
+#     query  = Chem.open_mol(MolDir % 147)
+#     Chem.db_search("test", query) # { |mol|  puts "found : %d" % mol }
+
+#     target = Chem.open_mol(MolDir % 4307)
+#     hash = query.match(target){ |q, t|
+#       q.element == t.element
+#       false
+#     }
+#     p hash
+    # p Chem.match_by_ullmann(query, target)
+  end
+
+end
+

data/test/ts_current.rb

@@ -0,0 +1,11 @@
+require 'test/unit'
+require 'test/all'
+require 'rubygems'
+
+# require 'test/tc_drugbank'
+# require 'test/tc_develop.rb'
+#require 'test/tc_kegg.rb'
+#require 'test/tc_pubchem.rb'
+require 'test/tc_openbabel'
+#require 'test/tc_cdk'
+#require 'test/tc_mdl.rb'

data/test/ts_image.rb

@@ -0,0 +1,6 @@
+require 'test/unit'
+require 'tc_gd'
+require 'tc_rmagick'
+require 'tc_pdf'
+require 'tc_eps'
+require 'tc_writer'

data/test/ts_main.rb

@@ -0,0 +1,12 @@
+require 'test/unit'
+
+Dir.glob("test/tc_*").reject{|file|
+  [
+    "test/tc_net.rb",
+    "test/tc_develop.rb"
+  ].include?(file)
+}.each do |test|
+  require test[0..-(File.extname(test).length + 1)]
+end
+
+require 'test/tc_sssr'

metadata

@@ -1,10 +1,10 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.8.10
+rubygems_version: 0.9.4
 specification_version: 1
 name: chemruby
 version: !ruby/object:Gem::Version 
-  version: 0.9.3
-date: 2006-02-12
+  version: 1.1.9
+date: 2007-12-10 00:00:00 +09:00
 summary: A framework program for cheminformatics
 require_paths: 
 - lib
@@ -23,256 +23,321 @@ required_ruby_version: !ruby/object:Gem::Version::Requirement
       version: 0.0.0
   version: 
 platform: ruby
+signing_key: 
+cert_chain: 
+post_install_message: 
 authors: []
 
 files: 
 - Rakefile
 - README
 - setup.rb
-- lib/chem.rb
 - lib/graph.rb
-- lib/chem/appl.rb
+- lib/chem.rb
+- lib/graph/cluster.rb
+- lib/graph/utils.rb
+- lib/graph/morgan.rb
 - lib/chem/data.rb
-- lib/chem/db.rb
+- lib/chem/utils/fingerprint.rb
+- lib/chem/utils/prop.rb
+- lib/chem/utils/net.rb
+- lib/chem/utils/geometry.rb
+- lib/chem/utils/traverse.rb
+- lib/chem/utils/bitdb.rb
+- lib/chem/utils/transform.rb
+- lib/chem/utils/once.rb
+- lib/chem/utils/ullmann.rb
+- lib/chem/utils/cas.rb
+- lib/chem/utils/sssr.rb
+- lib/chem/utils/sub.rb
+- lib/chem/utils/cdk.rb
+- lib/chem/utils/math.rb
+- lib/chem/utils/openbabel.rb
 - lib/chem/model.rb
-- lib/chem/utils.rb
 - lib/chem/appl/chem3dole.rb
 - lib/chem/appl/tinker/nucleic.rb
 - lib/chem/appl/tinker/tinker_reader.rb
-- lib/chem/data/atomic_weight.rb
-- lib/chem/data/character.rb
-- lib/chem/data/electronegativity.rb
-- lib/chem/data/periodic_table.rb
-- lib/chem/data/prime_numbers.rb
-- lib/chem/data/vdw_radii.rb
-- lib/chem/db/cansmi.rb
-- lib/chem/db/cdx.rb
-- lib/chem/db/eps.rb
-- lib/chem/db/g98.rb
-- lib/chem/db/gspan.rb
-- lib/chem/db/iupac.rb
-- lib/chem/db/kcf.rb
-- lib/chem/db/kcf_glycan.rb
-- lib/chem/db/kegg.rb
-- lib/chem/db/mdl.rb
-- lib/chem/db/molconnz.rb
-- lib/chem/db/mopac.rb
-- lib/chem/db/msi.rb
-- lib/chem/db/pdb_dic.rb
-- lib/chem/db/pdf.rb
-- lib/chem/db/pubchem.rb
-- lib/chem/db/rmagick.rb
-- lib/chem/db/sdf.rb
-- lib/chem/db/smbl.rb
 - lib/chem/db/smiles.rb
-- lib/chem/db/swf.rb
-- lib/chem/db/sybyl.rb
-- lib/chem/db/tinker.rb
-- lib/chem/db/vector.rb
-- lib/chem/db/xyz.rb
-- lib/chem/db/iupac/a_1.rb
 - lib/chem/db/iupac/iuparser.rb
 - lib/chem/db/iupac/postfix.rb
-- lib/chem/db/linucs/linparser.rb
-- lib/chem/db/smiles/smiparser.rb
-- lib/chem/db/types/type_cansmi.rb
+- lib/chem/db/iupac/a_1.rb
 - lib/chem/db/types/type_cdx.rb
+- lib/chem/db/types/type_mdl.rb
+- lib/chem/db/types/type_kcf_glycan.rb
 - lib/chem/db/types/type_gspan.rb
+- lib/chem/db/types/type_xyz.rb
 - lib/chem/db/types/type_kcf.rb
-- lib/chem/db/types/type_kcf_glycan.rb
 - lib/chem/db/types/type_kegg.rb
-- lib/chem/db/types/type_mdl.rb
+- lib/chem/db/types/type_cansmi.rb
+- lib/chem/db/types/type_gd.rb
+- lib/chem/db/types/type_sybyl.rb
+- lib/chem/db/types/type_rdf.rb
 - lib/chem/db/types/type_pdf.rb
 - lib/chem/db/types/type_png.rb
-- lib/chem/db/types/type_rxn.rb
 - lib/chem/db/types/type_sdf.rb
-- lib/chem/db/types/type_sybyl.rb
-- lib/chem/db/types/type_xyz.rb
+- lib/chem/db/types/type_rxn.rb
+- lib/chem/db/pubchem.rb
+- lib/chem/db/eps.rb
+- lib/chem/db/pdb_dic.rb
+- lib/chem/db/mopac.rb
+- lib/chem/db/sdf.rb
+- lib/chem/db/cansmi.rb
+- lib/chem/db/g98.rb
+- lib/chem/db/mdl.rb
+- lib/chem/db/cml.rb
+- lib/chem/db/swf.rb
+- lib/chem/db/gspan.rb
+- lib/chem/db/gd.rb
+- lib/chem/db/opsin.rb
+- lib/chem/db/tinker.rb
+- lib/chem/db/sybyl.rb
+- lib/chem/db/xyz.rb
+- lib/chem/db/smbl.rb
+- lib/chem/db/pdb.rb
+- lib/chem/db/smiles/smiparser.rb
+- lib/chem/db/kcf_rpair.rb
+- lib/chem/db/linucs/linparser.rb
+- lib/chem/db/vector.rb
+- lib/chem/db/molconnz.rb
+- lib/chem/db/cdx.rb
+- lib/chem/db/kcf_glycan.rb
+- lib/chem/db/kcf.rb
+- lib/chem/db/msi.rb
+- lib/chem/db/iupac.rb
+- lib/chem/db/pdf.rb
+- lib/chem/db/rmagick.rb
+- lib/chem/db/kegg.rb
+- lib/chem/utils.rb
+- lib/chem/db.rb
+- lib/chem/data/vdw_radii.rb
+- lib/chem/data/electronegativity.rb
+- lib/chem/data/character.rb
+- lib/chem/data/prime_numbers.rb
+- lib/chem/data/atomic_weight.rb
+- lib/chem/data/periodic_table.rb
 - lib/chem/model/skeleton.rb
-- lib/chem/utils/geometry.rb
-- lib/chem/utils/graph_db.rb
-- lib/chem/utils/math.rb
-- lib/chem/utils/prop.rb
-- lib/chem/utils/sssr.rb
-- lib/chem/utils/sub.rb
-- lib/chem/utils/transform.rb
-- lib/chem/utils/traverse.rb
-- lib/chem/utils/ullmann.rb
-- lib/graph/cluster.rb
-- lib/graph/morgan.rb
+- lib/chem/appl.rb
 - lib/chem/db/iupac/iuparser.ry
-- lib/chem/db/linucs/linucs.ry
 - lib/chem/db/smiles/smiles.ry
-- test/all.rb
-- test/coord_test.rb
-- test/ctab_test.rb
-- test/data
+- lib/chem/db/linucs/linucs.ry
+- test/tc_subcomp.rb
+- test/tc_mdl.rb
+- test/tc_kcf_glycan.rb
+- test/tc_sub.rb
+- test/tc_morgan.rb
+- test/tc_openbabel.rb
+- test/tc_iupac.rb
+- test/tc_db.rb
+- test/tc_kegg.rb
 - test/heavy_test_pubchem.rb
+- test/tc_cluster.rb
+- test/tc_gspan.rb
+- test/tc_once.rb
+- test/tc_canonical_smiles.rb
+- test/coord_test.rb
+- test/ts_current.rb
+- test/all.rb
 - test/multiple_test.rb
-- test/test_adj.rb
-- test/test_canonical_smiles.rb
-- test/test_cdx.rb
-- test/test_chem.rb
-- test/test_cluster.rb
-- test/test_db.rb
-- test/test_eps.rb
-- test/test_geometry.rb
-- test/test_gspan.rb
-- test/test_iupac.rb
-- test/test_kcf.rb
-- test/test_kcf_glycan.rb
-- test/test_kegg.rb
-- test/test_linucs.rb
-- test/test_mdl.rb
-- test/test_mol2.rb
-- test/test_morgan.rb
-- test/test_pdf.rb
-- test/test_prop.rb
-- test/test_rmagick.rb
-- test/test_sbdb.rb
-- test/test_sdf.rb
-- test/test_smiles.rb
-- test/test_sssr.rb
-- test/test_sub.rb
-- test/test_subcomp.rb
-- test/test_traverse.rb
-- test/test_writer.rb
-- test/test_xyz.rb
+- test/tc_eps.rb
+- test/tc_sssr.rb
+- test/ts_main.rb
+- test/tc_smiles.rb
+- test/tc_xyz.rb
+- test/ts_image.rb
+- test/tc_drugbank.rb
+- test/tc_mol2.rb
+- test/tc_cdk.rb
+- test/tc_casrn.rb
+- test/tc_writer.rb
+- test/tc_adj.rb
+- test/tc_pdf.rb
+- test/tc_gd.rb
+- test/tc_pubchem.rb
+- test/tc_kcf.rb
+- test/tc_net.rb
 - test/type_test.rb
-- test/data/A_21
-- test/data/A_21.tar.gz
-- test/data/atp.mol
-- test/data/C00147.kcf
+- test/tc_graph.rb
+- test/tc_develop.rb
+- test/tc_prop.rb
+- test/tc_sbdb.rb
+- test/data
 - test/data/cyclohexane.mol
-- test/data/cyclohexane.ps
-- test/data/fullerene.mol
-- test/data/G00147.kcf
-- test/data/glycan
-- test/data/hypericin.cdx
-- test/data/hypericin.cdxml
-- test/data/hypericin.chm
-- test/data/hypericin.ct
-- test/data/hypericin.f1d
-- test/data/hypericin.f1q
-- test/data/hypericin.gif
 - test/data/hypericin.mol
-- test/data/hypericin.mol2
-- test/data/hypericin.msm
-- test/data/hypericin.pdf
-- test/data/hypericin.png
-- test/data/hypericin.ps
-- test/data/hypericin.skc
-- test/data/hypericin2.gif
-- test/data/hypericin2.ps
-- test/data/kegg
-- test/data/reaction
-- test/data/reaction.lst
-- test/data/reaction_mapformula.lst
-- test/data/rxn
-- test/data/test.eps
-- test/data/test.mol
-- test/data/test.sdf
+- test/data/G00147.kcf
 - test/data/test.skc
+- test/data/hypericin.f1d
 - test/data/test.xyz
-- test/data/test_lf.sdf
-- test/data/A_21/aceanthrylene.cdx
-- test/data/A_21/aceanthrylene.mol
+- test/data/A_21
+- test/data/A_21/azulene.mol
+- test/data/A_21/naphthalene.mol
 - test/data/A_21/acenaphthylene.cdx
-- test/data/A_21/acenaphthylene.mol
-- test/data/A_21/acephenanthrylene.cdx
+- test/data/A_21/tetraphenylene.mol
+- test/data/A_21/picene.mol
+- test/data/A_21/trinaphthylene.mol
 - test/data/A_21/acephenanthrylene.mol
-- test/data/A_21/anthracene.cdx
-- test/data/A_21/anthracene.mol
-- test/data/A_21/as-indacene.cdx
-- test/data/A_21/as-indacene.mol
-- test/data/A_21/azulene.cdx
-- test/data/A_21/azulene.mol
-- test/data/A_21/biphenylene.cdx
 - test/data/A_21/biphenylene.mol
+- test/data/A_21/pleiadene.cdx
+- test/data/A_21/phenanthrene.cdx
+- test/data/A_21/ovalene.mol
+- test/data/A_21/acephenanthrylene.cdx
+- test/data/A_21/rubicene.cdx
+- test/data/A_21/tetraphenylene.cdx
+- test/data/A_21/anthracene.mol
+- test/data/A_21/rubicene.mol
 - test/data/A_21/chrysene.cdx
-- test/data/A_21/chrysene.mol
-- test/data/A_21/coronen.cdx
-- test/data/A_21/coronen.mol
-- test/data/A_21/fluoranthene.cdx
-- test/data/A_21/fluoranthene.mol
-- test/data/A_21/fluorene.cdx
+- test/data/A_21/azulene.cdx
+- test/data/A_21/pentalene.mol
+- test/data/A_21/acenaphthylene.mol
+- test/data/A_21/perylene.mol
+- test/data/A_21/phenalene.mol
+- test/data/A_21/phenanthrene.mol
+- test/data/A_21/iupac.txt
+- test/data/A_21/pyrene.cdx
+- test/data/A_21/pyranthrene.cdx
 - test/data/A_21/fluorene.mol
-- test/data/A_21/heptacene.cdx
-- test/data/A_21/heptacene.mol
-- test/data/A_21/heptalene.cdx
-- test/data/A_21/heptalene.mol
-- test/data/A_21/heptaphene.cdx
-- test/data/A_21/heptaphene.mol
-- test/data/A_21/hexacene.cdx
+- test/data/A_21/perylene.cdx
+- test/data/A_21/fluoranthene.mol
+- test/data/A_21/picene.cdx
+- test/data/A_21/as-indacene.cdx
+- test/data/A_21/naphthacene.cdx
 - test/data/A_21/hexacene.mol
-- test/data/A_21/hexaphene.cdx
-- test/data/A_21/hexaphene.mol
 - test/data/A_21/indene.cdx
+- test/data/A_21/triphenylene.mol
+- test/data/A_21/coronen.mol
+- test/data/A_21/heptacene.cdx
+- test/data/A_21/triphenylene.cdx
+- test/data/A_21/pentacene.cdx
+- test/data/A_21/s-indacene.cdx
+- test/data/A_21/s-indacene.mol
+- test/data/A_21/ovalene.cdx
+- test/data/A_21/fluorene.cdx
+- test/data/A_21/heptaphene.cdx
 - test/data/A_21/indene.mol
-- test/data/A_21/iupac.txt
-- test/data/A_21/naphthacene.cdx
+- test/data/A_21/aceanthrylene.mol
+- test/data/A_21/heptacene.mol
+- test/data/A_21/pentaphene.mol
+- test/data/A_21/pentalene.cdx
+- test/data/A_21/coronen.cdx
 - test/data/A_21/naphthacene.mol
+- test/data/A_21/aceanthrylene.cdx
+- test/data/A_21/pleiadene.mol
 - test/data/A_21/naphthalene.cdx
-- test/data/A_21/naphthalene.mol
-- test/data/A_21/ovalene.cdx
-- test/data/A_21/ovalene.mol
-- test/data/A_21/pentacene.cdx
-- test/data/A_21/pentacene.mol
-- test/data/A_21/pentalene.cdx
-- test/data/A_21/pentalene.mol
 - test/data/A_21/pentaphene.cdx
-- test/data/A_21/pentaphene.mol
-- test/data/A_21/perylene.cdx
-- test/data/A_21/perylene.mol
+- test/data/A_21/trinaphthylene.cdx
 - test/data/A_21/phenalene.cdx
-- test/data/A_21/phenalene.mol
-- test/data/A_21/phenanthrene.cdx
-- test/data/A_21/phenanthrene.mol
-- test/data/A_21/picene.cdx
-- test/data/A_21/picene.mol
-- test/data/A_21/pleiadene.cdx
-- test/data/A_21/pleiadene.mol
-- test/data/A_21/pyranthrene.cdx
+- test/data/A_21/biphenylene.cdx
 - test/data/A_21/pyranthrene.mol
-- test/data/A_21/pyrene.cdx
+- test/data/A_21/heptaphene.mol
+- test/data/A_21/pentacene.mol
+- test/data/A_21/fluoranthene.cdx
+- test/data/A_21/chrysene.mol
+- test/data/A_21/anthracene.cdx
 - test/data/A_21/pyrene.mol
-- test/data/A_21/rubicene.cdx
-- test/data/A_21/rubicene.mol
-- test/data/A_21/s-indacene.cdx
-- test/data/A_21/s-indacene.mol
-- test/data/A_21/tetraphenylene.cdx
-- test/data/A_21/tetraphenylene.mol
-- test/data/A_21/trinaphthylene.cdx
-- test/data/A_21/trinaphthylene.mol
-- test/data/A_21/triphenylene.cdx
-- test/data/A_21/triphenylene.mol
-- test/data/kegg/genomes
+- test/data/A_21/heptalene.mol
+- test/data/A_21/hexaphene.mol
+- test/data/A_21/hexacene.cdx
+- test/data/A_21/as-indacene.mol
+- test/data/A_21/hexaphene.cdx
+- test/data/A_21/heptalene.cdx
+- test/data/reaction
+- test/data/test.sdf
+- test/data/hypericin.ct
+- test/data/hypericin.pdf
+- test/data/A_21.tar.gz
+- test/data/CID_704.sdf
+- test/data/hypericin2.gif
+- test/data/hypericin.png
+- test/data/rosiglitazone.mol
+- test/data/troglitazone.mol
+- test/data/hypericin.chm
+- test/data/reaction_mapformula.lst
+- test/data/db_EXPT03276.txt
+- test/data/atp.mol
+- test/data/C00147.kcf
+- test/data/hypericin.gif
+- test/data/thiazolidinedione.mol
+- test/data/hypericin.cdxml
+- test/data/kegg
 - test/data/kegg/ligand
-- test/data/kegg/genomes/hsa
-- test/data/kegg/genomes/hsa/hsa_enzyme.list
-- test/data/kegg/genomes/hsa/hsa_pfam.list
-- test/data/kegg/ligand/mol
 - test/data/kegg/ligand/reaction
-- test/data/kegg/ligand/reaction.lst
-- test/data/kegg/ligand/reaction_mapformula.lst
+- test/data/kegg/ligand/mol
 - test/data/kegg/ligand/mol/C00147.mol
-- test/data/rxn/C00001.mol
-- test/data/rxn/C00011.mol
-- test/data/rxn/C00014.mol
+- test/data/kegg/ligand/reaction_mapformula.lst
+- test/data/kegg/ligand/reaction.lst
+- test/data/kegg/genomes
+- test/data/kegg/genomes/hsa
+- test/data/kegg/genomes/hsa/hsa_pfam.list
+- test/data/kegg/genomes/hsa/hsa_enzyme.list
+- test/data/hypericin.f1q
+- test/data/test.mol
+- test/data/hypericin.cdx
+- test/data/fullerene.mol
+- test/data/rxn
 - test/data/rxn/C01010.mol
 - test/data/rxn/sample.rxn
+- test/data/rxn/C00011.mol
+- test/data/rxn/C00014.mol
+- test/data/rxn/C00001.mol
 - test/data/rxn/substitution.rxn
+- test/data/hypericin.ps
+- test/data/glycan
+- test/data/test_lf.sdf
+- test/data/hypericin.skc
+- test/data/test.eps
+- test/data/hypericin.mol2
+- test/data/hypericin2.ps
+- test/data/pioglitazone.mol
+- test/data/CID_994.sdf
+- test/data/hypericin.msm
+- test/data/reaction.lst
+- test/data/cyclohexane.ps
+- test/tc_cdx.rb
+- test/ctab_test.rb
+- test/tc_traverse.rb
+- test/tc_geometry.rb
+- test/tc_linucs.rb
+- test/tc_rmagick.rb
+- test/tc_sdf.rb
+- test/tc_chem.rb
+- temp/
+- sample/pubchem_fetch.rb
+- sample/generate_substructurekey.rb
+- sample/pubchem_search.rb
+- sample/mol2pdf.rb
+- sample/structure_match.rb
+- sample/find_compound_by_keggapi.rb
+- sample/calc_properties.rb
+- sample/smarts.rb
 - sample/frequent_subgraph.rb
-- sample/kegg_db.rb
+- sample/logp.rb
+- sample/calc_maximum_common_subgraph.rb
+- sample/structure_match_color.rb
+- sample/vicinity.rb
 - sample/images/ex1.rb
-- sample/images/ex2.rb
+- sample/images/ex7.rb
+- sample/images/ex6.rb
 - sample/images/ex3.rb
-- sample/images/ex4.rb
 - sample/images/ex5.rb
-- sample/images/mol/adenine.mol
+- sample/images/ex4.rb
+- sample/images/ex2.rb
+- sample/generate_inchi.rb
+- sample/kegg_db.rb
+- sample/kekule.rb
+- sample/mcs.rb
+- sample/iupac2mol.rb
+- sample/rosiglitazone.mol
+- sample/troglitazone.mol
 - sample/images/mol/atp.mol
+- sample/images/mol/adenine.mol
 - sample/images/temp/ex5.mol
+- sample/thiazolidinedione.mol
+- sample/data/rosiglitazone.mol
+- sample/data/troglitazone.mol
+- sample/data/atp.mol
+- sample/data/pioglitazone.mol
+- ext/utils.h
 - ext/subcomp.c
+- ext/utils.c
 - ext/extconf.rb
 test_files: []