chemruby 0.9.3

data/test/test_subcomp.rb

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+# $Id: test_subcomp.rb 101 2006-01-06 22:26:49Z tanaka $
+
+require 'test/unit'
+require 'test/all'
+
+require 'chem'
+
+class SubcompTest < Test::Unit::TestCase
+
+  def setup
+    @mol = Chem.open_mol($data_dir + 'hypericin.mol')
+  end
+
+#   def test_mol
+#     mol = Chem.open_mol($data_dir + 'hypericin.mol')
+#     #assert_equal(mol.nodes.length, mol.match_by_ullmann(mol).length)
+#   end
+
+#   def test_match_by_atom
+#     mol2 = Chem.parse_smiles("CCCBrCC")
+#     mol = Chem.parse_smiles("CCBr")
+#     assert_equal(mol.nodes.length, mol.match_by_ullmann(mol2).length);
+#   end
+
+  def test_search
+    @mol.match_by_ullmann(@mol)
+  end
+
+#   def test_exhaustive
+#     cyclopropane = SMILES("C1CCC1")
+#     match = cyclopropane.match_by_ullmann(cyclopropane)
+#     assert_equal([0, 1, 2, 3], match)
+#     match = cyclopropane.match_exhaustively(cyclopropane)
+#   end
+
+end
+

data/test/test_traverse.rb

@@ -0,0 +1,29 @@
+# $Id: test_traverse.rb 65 2005-10-25 17:17:36Z tanaka $
+
+require 'test/all'
+
+class TraverseTest < Test::Unit::TestCase
+
+  def setup
+    @cyclohexane = Chem.open_mol($data_dir + 'cyclohexane.mol')
+  end
+
+  def test_bfs
+    i = 0
+    @cyclohexane.bfs do |from, to|
+      i += 1
+      # Block should return true if you want to continue traversing this branch!
+      true
+    end
+    assert_equal(i, 6)
+  end
+
+  def test_dfs
+    i = 0
+    @cyclohexane.dfs do |from, to, bond|
+      i += 1
+    end
+    assert_equal(i, 6)
+  end
+
+end

data/test/test_writer.rb

@@ -0,0 +1,13 @@
+# $Id: test_writer.rb 65 2005-10-25 17:17:36Z tanaka $
+
+require 'test/all'
+
+class WriterTest < Test::Unit::TestCase
+
+  def test_undefined_writer
+    assert(true)
+#     mol = Chem.parse_smiles("CCCC")
+#     assert_raise(mol.to_hoge)
+  end
+
+end

data/test/test_xyz.rb

@@ -0,0 +1,15 @@
+# $Id: test_xyz.rb 156 2006-02-09 02:00:47Z tanaka $
+
+require 'test/all'
+require 'test/type_test'
+
+class XyzTest < Test::Unit::TestCase
+  include Chem::TypeTest
+
+  def setup
+    (@entries = []).push Chem.open_mol($data_dir + "test.xyz")
+    @parser = Chem::XYZ::XyzMolecule
+    @file_type = Chem::Type::XyzType
+  end
+
+end

data/test/type_test.rb

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+# $Id: type_test.rb 61 2005-10-12 09:17:39Z tanaka $
+
+module Chem
+  # A test module for testing ``autodetect'' mechanism
+  # Modules that test autodetection must conform this test.
+
+  module TypeTest
+
+    def test_db_mod
+      assert(@file_type.respond_to?(:parse),
+             "Type modules must respond to parse(file) method")
+      assert(@file_type.respond_to?(:detect_file),
+             "Type modules must respond to detect_file method")
+      assert(@file_type.respond_to?(:detect_type),
+             "Type modules must respond to detect_type method")
+    end
+
+    def test_autodetect
+      @entries.each do |entry|
+#        assert_instance_of(@parser, entry)
+      end
+    end
+
+  end
+end

metadata

@@ -0,0 +1,290 @@
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.8.10
+specification_version: 1
+name: chemruby
+version: !ruby/object:Gem::Version 
+  version: 0.9.3
+date: 2006-02-12
+summary: A framework program for cheminformatics
+require_paths: 
+- lib
+email: 
+homepage: 
+rubyforge_project: 
+description: 
+autorequire: chem
+default_executable: 
+bindir: bin
+has_rdoc: false
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      version: 0.0.0
+  version: 
+platform: ruby
+authors: []
+
+files: 
+- Rakefile
+- README
+- setup.rb
+- lib/chem.rb
+- lib/graph.rb
+- lib/chem/appl.rb
+- lib/chem/data.rb
+- lib/chem/db.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/types/type_cdx.rb
+- lib/chem/db/types/type_gspan.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_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/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/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
+- test/heavy_test_pubchem.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/type_test.rb
+- test/data/A_21
+- test/data/A_21.tar.gz
+- test/data/atp.mol
+- test/data/C00147.kcf
+- 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/test.skc
+- 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/acenaphthylene.cdx
+- test/data/A_21/acenaphthylene.mol
+- test/data/A_21/acephenanthrylene.cdx
+- 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/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/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/hexacene.mol
+- test/data/A_21/hexaphene.cdx
+- test/data/A_21/hexaphene.mol
+- test/data/A_21/indene.cdx
+- test/data/A_21/indene.mol
+- test/data/A_21/iupac.txt
+- test/data/A_21/naphthacene.cdx
+- test/data/A_21/naphthacene.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/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/pyranthrene.mol
+- test/data/A_21/pyrene.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/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/C00147.mol
+- test/data/rxn/C00001.mol
+- test/data/rxn/C00011.mol
+- test/data/rxn/C00014.mol
+- test/data/rxn/C01010.mol
+- test/data/rxn/sample.rxn
+- test/data/rxn/substitution.rxn
+- sample/frequent_subgraph.rb
+- sample/kegg_db.rb
+- sample/images/ex1.rb
+- sample/images/ex2.rb
+- sample/images/ex3.rb
+- sample/images/ex4.rb
+- sample/images/ex5.rb
+- sample/images/mol/adenine.mol
+- sample/images/mol/atp.mol
+- sample/images/temp/ex5.mol
+- ext/subcomp.c
+- ext/extconf.rb
+test_files: []
+
+rdoc_options: []
+
+extra_rdoc_files: []
+
+executables: []
+
+extensions: 
+- ext/extconf.rb
+requirements: []
+
+dependencies: []
+