chemruby 0.9.3

data/test/heavy_test_pubchem.rb

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+# $Id: heavy_test_pubchem.rb 65 2005-10-25 17:17:36Z tanaka $
+
+require 'test/all'
+
+class PubChemTest < Test::Unit::TestCase
+
+  def test_fetch
+    mol = Chem.parse_smiles("CCCCC")
+    entries = mol.search_pubchem
+  end
+
+  def test_false
+    assert(true)
+  end
+
+end

data/test/multiple_test.rb

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+# $Id: multiple_test.rb 88 2005-12-27 11:52:43Z tanaka $
+
+# Parsers that parse files with multiple molecule should conform
+# MultipleTest.
+
+module Chem
+  module MultipleTest
+
+    def test_prerequisite
+      assert_not_nil(@entries)
+      assert_not_nil(@file_type)
+
+      assert_kind_of(Enumerable, @entries)
+    end
+
+    def test_respond
+      assert_respond_to(@entries, :each)
+      assert(@entries.all?{|entry| entry.respond_to?(:entry)}, "all entries responds to 'entry' method")
+    end
+
+  end
+end

data/test/test_adj.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_adj.rb 127 2006-02-03 02:47:57Z tanaka $
+#
+
+require 'test/all'
+
+require 'chem'
+
+class AdjTest < Test::Unit::TestCase
+  
+  def setup
+    @cyclohexane = Chem.open_mol($data_dir + "cyclohexane.mol")
+  end
+
+  def test_adjacent_to
+    @cyclohexane.each do |node|
+      assert_equal(@cyclohexane.adjacent_to(node).length, 2)
+    end
+  end
+
+  def test_dup
+    cyclo = @cyclohexane.deep_dup
+    cyclo.delete(cyclo.nodes[0])
+    assert_equal(5, cyclo.nodes.length)
+    assert_equal(6, @cyclohexane.nodes.length)
+  end
+
+  def est_delete#!!!BUG
+    assert_equal(6, @cyclohexane.nodes.length)
+    adj = []
+    @cyclohexane.adjacent_to(@cyclohexane.nodes[0]).each do |bond, atom|
+      adj.push(atom)
+    end
+
+    @cyclohexane.delete(@cyclohexane.nodes[0])
+
+    adj.each do |atom|
+      assert_equal(1, @cyclohexane.adjacent_to(atom).length)
+    end
+
+    @cyclohexane.nodes.each do |atom|
+      if !adj.include?(atom)
+        assert_equal(2, @cyclohexane.adjacent_to(atom).length)
+      end
+    end
+
+    assert_equal(@cyclohexane.nodes.length, 5)
+    assert_equal(@cyclohexane.edges.length, 4)
+  end
+
+end

data/test/test_canonical_smiles.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_canonical_smiles.rb 127 2006-02-03 02:47:57Z tanaka $
+#
+
+require 'test/all'
+
+class CanonicalSmilesTest < Test::Unit::TestCase
+
+#   def test_ex1
+#     mol = Chem.parse_smiles("OCC(CC)CCC(CN)CN")
+#     assert_equal("CCC(CO)CCC(CN)CN", mol.to_cansmi)
+#   end
+
+#   def test_naphthalene
+#     mol = Chem.parse_smiles("C1=CC=C2C=CC=CC2=C1")
+#     cansmi = mol.to_cansmi
+#     assert_block do
+#       "C1=CC=C2C=CC=CC2=C1" == cansmi or
+#         "C1=CC2=CC=CC=C2C=C1" == cansmi
+#     end
+#     p cansmi
+#   end
+
+#   def test_cubane
+#     mol = Chem.parse_smiles("C12C3C4C1C5C4C3C25")
+#     assert_equal("C12C3C4C1C5C2C3C45", mol.to_cansmi)
+#     p mol.to_cansmi
+#   end
+
+#   def test_melphalan
+#     mol = Chem.parse_smiles("C1=CC(=CC=C1CC(C(=O)O)N)N(CCCl)CCCl")
+#     assert_equal("C1=CC(=CC=C1CC(C(=O)O)N)N(CCCl)CCCl", mol.to_cansmi)
+#   end
+#   def test_hypericin
+#     mol = Chem.open_mol(File.join($data_dir, "hypericin.mol"))
+#     assert_equal("CC1=CC(=O)C2=C(C3=C(C=C(C4=C3C5=C6C7=C(C1=C25)C(=CC(=O)C7=C(C8=C(C=C(C4=C86)O)O)O)C)O)O)O", mol.to_cansmi)
+#   end
+
+  def test_true
+    assert(true)
+  end
+  
+end

data/test/test_cdx.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_cdx.rb 149 2006-02-08 08:02:33Z tanaka $
+#
+
+require 'test/all'
+
+require 'test/type_test'
+require 'test/ctab_test'
+require 'test/coord_test'
+
+require 'chem'
+
+class CDXTest < Test::Unit::TestCase
+
+  include Chem::TypeTest
+  include Chem::CtabTest
+  include Chem::CoordTest
+
+  def setup
+    @entries = Chem.open_mol($data_dir + "hypericin.cdx")
+    @parser = Chem::CDX
+    @file_type = Chem::Type::CdxType
+  end
+
+  def test_false
+    assert(true)
+  end
+
+end

data/test/test_chem.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_chem.rb 127 2006-02-03 02:47:57Z tanaka $
+#
+
+require 'test/all'
+
+class ChemTest < Test::Unit::TestCase
+
+  def test_auto_detection
+    Chem.open_mol($data_dir + "cyclohexane.mol")
+#    Chem.open_mol($data_dir + "cyclohexane.mol", :mol)
+    assert_raise(NotImplementedError){Chem.open_mol($data_dir + "cyclohexane.no_such_format")}
+  end
+
+end

data/test/test_cluster.rb

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+# $Id: test_mdl.rb 37 2005-09-23 22:58:24Z tanaka $
+
+# Tests to ensure functionality
+
+require 'test/all'
+
+class ClusterTest < Test::Unit::TestCase
+
+  def test_morgan
+    #    mol = Chem.open_mol(File.join($data_dir, "hypericin.mol"))
+    #mol = Chem.parse_smiles("C1CC1")
+#    require 'chem/db/smiles'
+    require 'chem/db/smiles/smiparser'
+    mol = SMILES("C1CC1")
+    assert_equal([2, 2, 2], mol.clustering_coefficient.values)
+#    ec, tec, priority = mol.morgan#_index
+  end
+
+end

data/test/test_db.rb

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+
+class DBTest < Test::Unit::TestCase
+
+  # Entry finder
+  def test_false
+#    Chem.find("")
+#    assert(false)
+  end
+
+end
+

data/test/test_eps.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_eps.rb 132 2006-02-04 19:16:50Z tanaka $
+#
+
+require 'test/unit'
+
+require 'test/all'
+
+require 'chem'
+
+class EpsTest < Test::Unit::TestCase
+
+  def setup
+    @mol = Chem.open_mol($data_dir + 'test.mol')
+  end
+
+  def test_eps
+#    assert_nothing_raised(Chem.save(mols, File.join(%w(temp temp.eps))))
+  end
+
+end

data/test/test_geometry.rb

@@ -0,0 +1,11 @@
+
+
+
+class MDLTest < Test::Unit::TestCase
+
+  def test_false
+    mol = SMILES("CCC")
+    mol.assign_2d_geometry
+  end
+
+end

data/test/test_gspan.rb

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+
+require 'test/all'
+
+require 'test/type_test'
+require 'test/ctab_test'
+require 'test/coord_test'
+
+require 'chem'
+
+class GSpanTest < Test::Unit::TestCase
+
+  include Chem::CtabTest
+
+  def setup
+    (@entries = []).push(Chem::GSpan.parse("(6) 0 (0f6) 0 (1f6) 0 (2f6) 0 (3f6) 0 (4f8) 0 (1f6)"))
+    @entries.push Chem::GSpan.parse("(6) 0 (0f6) 0 (1f6) 0 (2f6) 0 (3f6) 0 (4f6) 0 (b0) 0 (5f6) 0 (6f8) 0 (4f6)")
+    @parser = Chem::GSpan
+  end
+
+  def test_gspan
+    mols = []
+    mols.push(Chem.open_mol($data_dir + "hypericin.mol"))
+    mols.push(Chem.open_mol($data_dir + "cyclohexane.mol"))
+    Chem.save(mols, File.join(%w(temp temp.fp)))
+  end
+
+
+end

data/test/test_iupac.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_iupac.rb 127 2006-02-03 02:47:57Z tanaka $
+#
+
+require 'chem/db/iupac'
+
+require 'test/all'
+require 'test/ctab_test'
+
+class IupacTest < Test::Unit::TestCase
+
+  def setup
+    @parser = IupacParser.new
+  end
+
+  def test_a_1
+    ["3-Methylpentane",
+     "2,3,5-Trimethylhexane",
+     "Isopropyl",
+     "7-(1,2-Dimethylpentyl)-5-ethyltridecane",
+     "7,7-Bis(2,4-dimethylhexyl)-3-ethyl-5,9,11-trimethyltridecane",
+    ]
+    ["hexane",
+     "hexylhexane", # Invalid IUPAC name
+     "1,2-dihexylhexane", # Invalid IUPAC name
+     "5-Methyl-6-propylnonane",
+#     "6-(1-methylbutyl)-8-(2-methylbutyl)tridecane",
+    ].each do |name|
+      @parser.parse(name)
+    end
+    assert(true)
+  end
+end

data/test/test_kcf.rb

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+
+
+require 'test/all'
+
+require 'test/type_test'
+require 'test/ctab_test'
+require 'test/coord_test'
+
+require 'chem'
+
+class KCFTest < Test::Unit::TestCase
+
+  include Chem::TypeTest
+  include Chem::CtabTest
+  include Chem::CoordTest
+
+  def setup
+    (@entries = []).push(Chem.open_mol($data_dir + "C00147.kcf"))
+    require 'chem/db/kcf'
+    @parser = Chem::KEGG::KCF
+    @file_type = Chem::Type::KCFType
+  end
+
+end

data/test/test_kcf_glycan.rb

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+require 'test/all'
+
+class KCFGlycanTest < Test::Unit::TestCase
+
+  def test_true
+    Chem.open_mol($data_dir + "G00147.kcf")
+#    assert(false)
+  end
+
+end

data/test/test_kegg.rb

@@ -0,0 +1,118 @@
+#
+# test_kegg.rb - Test for KEGG
+#
+#
+# $Id: test_kegg.rb 151 2006-02-08 08:21:08Z tanaka $
+#
+
+require 'test/all'
+require 'test/multiple_test'
+require 'test/type_test'
+
+require 'chem/db/kegg'
+
+class KeggOpenTest < Test::Unit::TestCase
+
+  def test_open
+    # environment dependent test!
+    #dir = "/home/tanaka/share/data/kegg"
+    kegg = Chem.open_kegg(File.join($data_dir, "kegg"))
+
+    compound = kegg["C00147"]
+    assert(10, compound.nodes.length)
+    assert(11, compound.edges.length)
+
+    reaction = kegg["R00001"]
+    assert_not_nil(reaction)
+    assert_equal([[["C00147", 1]], [["C00009", 1]]], reaction.map_formula)
+
+    m_formula = reaction.map_formula
+    compound = kegg[m_formula[0][0][0]]
+    assert_not_nil(compound)
+    assert_equal(10, compound.nodes.length)
+
+  end
+
+end
+
+
+__END__
+#obsolete
+Chem::Kegg.kegg_compound_folder = $data_dir
+
+class KeggReactionTest < Test::Unit::TestCase
+
+  include Chem::MultipleTest
+  include Chem::TypeTest
+
+  def setup
+    @entries   = Chem.parse_file(File.join($data_dir, "kegg", "ligand", "reaction"))
+    @parser    = Chem::Kegg::KeggReactionParser
+    @file_type = Chem::KeggReactionType
+  end
+
+  def test_entry
+    @entries.each do |entry|
+      assert_respond_to(entry, :entry)
+    end
+  end
+
+end
+
+class KeggReactionLstTest < Test::Unit::TestCase
+
+  include Chem::MultipleTest
+  include Chem::TypeTest
+
+  def setup
+    @entries   = Chem.open_mol(File.join($data_dir, "kegg", "ligand", "reaction.lst"))
+    @parser    = Chem::Kegg::KeggReactionLstParser
+    @file_type = Chem::KeggReactionLstType
+  end
+
+  def test_entry
+    @entries.each do |rxn|
+      assert_equal("2 C00890", rxn.compounds[0][0][0])
+    end
+  end
+
+end
+
+class KeggReactionMapTest < Test::Unit::TestCase
+  include Chem::MultipleTest
+  include Chem::TypeTest
+
+  def setup
+    @entries = Chem.open_mol(File.join($data_dir, "kegg", "ligand", "reaction_mapformula.lst"))
+    @parser = Chem::Kegg::KeggReactionMapParser
+    @file_type = Chem::KeggReactionMapType
+  end
+
+end
+
+class KeggGlycanTest < Test::Unit::TestCase
+
+  include Chem::MultipleTest
+  include Chem::TypeTest
+
+  def setup
+    @entries = Chem.open_mol(File.join($data_dir, "glycan"))
+    @parser = Chem::Kegg::KeggGlycanParser
+    @file_type = Chem::KeggGlycanType
+  end
+
+end
+
+class KeggPfamTest < Test::Unit::TestCase
+
+  def test_false
+    kegg = Chem.open_kegg(File.join($data_dir, "kegg"))
+    cadherin = kegg["pf:Cadherin"]
+    assert_not_nil(cadherin)
+    gene = cadherin["hsa"]
+    human = kegg["hsa"]
+    assert_not_nil(gene)
+  end
+
+end
+