chemruby 0.9.3

data/test/test_linucs.rb

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+#
+# test_adj.rb - Test for adjacency
+#
+#
+# $Id: test_linucs.rb 127 2006-02-03 02:47:57Z tanaka $
+#
+
+require 'test/all'
+
+require 'chem'
+require 'chem/db/linucs/linparser'
+
+class LinucsTest < Test::Unit::TestCase
+
+  def test_linucs
+    assert(true)
+#     parser = LinucsParser.new
+#     parser.parse("[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}")
+  end
+
+end

data/test/test_mdl.rb

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+# $Id: test_mdl.rb 151 2006-02-08 08:21:08Z tanaka $
+
+# Tests to ensure functionality
+
+require 'test/all'
+
+require 'test/type_test'
+require 'test/ctab_test'
+require 'test/coord_test'
+
+require 'chem'
+
+class MDLTest < Test::Unit::TestCase
+
+  include Chem::TypeTest
+  include Chem::CtabTest
+  include Chem::CoordTest
+
+  def setup
+    (@entries = []).push(Chem.open_mol($data_dir + "hypericin.mol"))
+    @parser = Chem::MDL::MdlMolecule
+    @file_type = Chem::Type::MdlMolType
+  end
+
+  def test_to_mdl
+    @entries[0].save(File.join(%w(temp save_test.mol)))
+  end
+
+  def test_bond_stereo
+    mol = Chem.open_mol($data_dir + "atp.mol")
+    types = mol.edges.inject({}){|ret, (b, a1, a2)| ret[b.stereo] ||= 0 ; ret[b.stereo] += 1 ; ret}
+    assert_equal(2, types[:down])
+    assert_equal(2, types[:up])
+    assert_equal(29, types[:not_stereo])
+  end
+
+  def test_bond_type
+    mol = Chem.open_mol($data_dir + "atp.mol")
+    types = mol.edges.inject({}){|ret, (b, a1, a2)| ret[b.bond_type] ||= 0 ; ret[b.bond_type] += 1 ; ret}
+    assert_equal(7,  types[:double])
+    assert_equal(26, types[:single])
+  end
+
+end
+

data/test/test_mol2.rb

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+# $Id: test_mdl.rb 84 2005-12-01 10:01:04Z tanaka $
+
+# Tests to ensure functionality
+
+require 'test/all'
+
+require 'test/type_test'
+require 'test/ctab_test'
+require 'test/coord_test'
+
+require 'chem'
+
+class SybylTest < Test::Unit::TestCase
+
+  include Chem::TypeTest
+  include Chem::CtabTest
+#  include Chem::CoordTest
+
+  def setup
+    (@entries = []).push(Chem.open_mol($data_dir + "hypericin.mol2"))
+    @parser = Chem::Sybyl::SybylMolecule
+    @file_type = Chem::Type::SybylType
+  end
+
+  def test_counts_line
+    mol = @entries[0]
+    assert_equal(67, mol.n_atoms)
+    assert_equal(70, mol.n_bonds)
+  end
+
+  def test_atom
+    atom = Chem::Sybyl::SybylAtom.new("     60 H60        -4.920329   -2.301872    1.618476 H         1 <1>         0.024481 ")
+    assert_equal(:H, atom.element)
+    assert_in_delta(-4.920329, atom.x, 0.0001)
+    assert_in_delta(-2.301872, atom.y, 0.0001)
+    assert_in_delta( 1.618476, atom.z, 0.0001)
+    atom2 = Chem::Sybyl::SybylAtom.new("      1 C1         -3.262565   -0.588014   -0.082185 C.3       1 <1>        -0.020001 ")
+    assert_equal(:C, atom2.element)
+  end
+
+  def test_save_sybyl_atom
+    atom = Chem::SkeletonAtom.new
+    atom.x = -3.262565
+    atom.y = -0.588014
+    atom.z = -0.082185
+
+    assert_equal("      1", atom.to_sybyl[0..7])
+#    assert_equal("", atom.to_sybyl[
+  end
+
+  def test_bond
+    bond = Chem::Sybyl::SybylBond.new("     1   10   13 1    ")
+    assert_equal(10, bond.b)
+    assert_equal(13, bond.e)
+    assert_equal( 1, bond.v)
+  end
+
+  def test_mol
+    assert_equal((0..66).to_a, @entries[0].match_by_ullmann(@entries[0]))
+  end
+
+end

data/test/test_morgan.rb

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+# $Id: test_mdl.rb 37 2005-09-23 22:58:24Z tanaka $
+
+# Tests to ensure functionality
+
+require 'test/all'
+
+require 'chem'
+
+class MorganTest < Test::Unit::TestCase
+
+  def test_morgan
+    mol = Chem.open_mol(File.join($data_dir, "hypericin.mol"))
+    ec, tec, priority = mol.morgan#_index
+    require 'set'
+    assert_equal(Set.new([82, 123, 184, 216, 164, 120, 227, 216, 164, 153,
+                   184, 123, 82, 120, 184, 216, 227, 216, 184, 123,
+                   82, 120, 164, 153, 164, 120, 82, 123, 40, 42, 51,
+                   40, 42, 42, 40, 51, 40, 42]), Set.new(ec.values))
+  end
+
+end

data/test/test_pdf.rb

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+
+require 'chem'
+
+class PDFTest < Test::Unit::TestCase
+
+  def test_pdf
+    mol = Chem.open_mol($data_dir + "hypericin.mol")
+    mol.nodes.each{|node| node.visible = true unless node.element == :C}
+    Chem.save(mol, File.join(%w(temp temp.pdf)))
+  end
+
+end

data/test/test_prop.rb

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+# $Id: test_prop.rb 73 2005-11-16 09:16:15Z tanaka $
+
+require 'test/all'
+
+require 'chem'
+
+class PropTest < Test::Unit::TestCase
+
+  def test_electro_negativity
+    assert_equal(3.16, SMILES("Cl").nodes[0].electro_negativity)
+  end
+
+  def test_natural_bond_order
+    assert_equal(4, SMILES("C").nodes[0].natural_bond_order)
+    assert_equal(3, SMILES("N").nodes[0].natural_bond_order)
+  end
+
+  def test_oxidation_number
+    mgcl2 = SMILES("ClMgCl")
+    mg = mgcl2.nodes.find{|n| n.element == :Mg}
+    assert(2, mgcl2.oxidation_number(mg))
+
+    get_en = lambda{|smiles|
+      mol = SMILES(smiles)
+      c = mol.nodes.find{|atom| atom.element == :C}
+      mol.oxidation_number(c)
+    }
+    assert_equal(-4, get_en.call("HC(H)(H)H"))
+    assert_equal(-2, get_en.call("HC(H)(H)F"))
+    assert_equal(0, get_en.call("HC(H)(F)F"))
+    assert_equal(-2, get_en.call("HC(H)(H)OH"))
+    assert_equal(0, get_en.call("HC(H)=O"))
+    assert_equal(2, get_en.call("HC(=O)OH"))
+    assert_equal(4, get_en.call("O=C=O"))
+
+    # implicit hydrogen atom
+    assert_equal(-4, get_en.call("C"))
+    assert_equal(2, get_en.call("C(=O)O"))
+    # partially implicit
+    assert_equal(0, get_en.call("C(H)(F)F"))
+    
+  end
+
+  def test_n_hydrogen
+    ch4 = SMILES("C")
+    assert_equal(4, ch4.n_hydrogen(ch4.nodes[0]))
+    hcooh = SMILES("C(=O)O")
+    c = hcooh.nodes.find{|n| n.element == :C}
+    assert_equal(1, hcooh.n_hydrogen(c))
+  end
+
+  def test_composition
+    comp = Chem.open_mol($data_dir + "rxn/C01010.mol").composition
+    assert_equal(2, comp[:C])
+    assert_equal(2, comp[:N])
+    assert_equal(3, comp[:O])
+  end
+
+  # return     1 if self.composition >  to.composition
+  # return     0 if self.composition == to.composition
+  # return    -1 if self.composition <  to.composition
+  # return false if self.composition <> to.composition
+  def test_subset_in_composition
+    comp1 = Chem.parse_smiles("CCNOC")
+    comp2 = Chem.parse_smiles("CCCCC")
+    comp3 = Chem.parse_smiles("CNOCC")
+    comp4 = Chem.parse_smiles("CNOC")
+    comp5 = Chem.parse_smiles("CCC")
+    comp6 = Chem.parse_smiles("CNNOC")
+    comp7 = Chem.parse_smiles("ClOO")
+
+    # different species
+    assert_equal(false, comp2.subset_in_composition?(comp3))
+    assert_equal(false, comp7.subset_in_composition?(comp1))
+    assert_equal(1, comp3.subset_in_composition?(comp5))
+    assert_equal(-1, comp5.subset_in_composition?(comp3))
+
+    # same species
+    assert_equal(0, comp1.subset_in_composition?(comp3))
+    assert_equal(1, comp3.subset_in_composition?(comp4))
+    assert_equal(-1, comp4.subset_in_composition?(comp3))
+    assert_equal(false, comp3.subset_in_composition?(comp6))
+
+  end
+
+end

data/test/test_rmagick.rb

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+require 'chem'
+
+class RMagickTest < Test::Unit::TestCase
+
+  def setup
+  end
+
+  def test_rmagick
+    mol = Chem.open_mol($data_dir + "hypericin.mol")
+    mol.nodes.each{|node| node.visible = true unless node.element == :C}
+    mol.save(File.join(%w(temp save_test.png)))
+
+  end
+
+end

data/test/test_sbdb.rb

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+# $Id: test_sbdb.rb 135 2006-02-06 05:48:56Z tanaka $
+
+require 'test/all'
+
+require 'chem'
+require 'chem/utils/ullmann'
+
+class SBDBTest < Test::Unit::TestCase
+
+  def test_create_db
+
+#     db = GraphDB.new("kegg")
+#     mol = Chem.parse_file($data_dir + "cyclohexane.mol")
+
+#     db.insert(mol)
+
+#     db.select(mol)
+
+#     assert(true)
+
+  end
+
+end

data/test/test_sdf.rb

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+# $Id: test_sdf.rb 151 2006-02-08 08:21:08Z tanaka $
+
+require 'test/type_test'
+require 'chem/db/types/type_sdf'
+
+require 'test/multiple_test'
+
+class SdfTest < Test::Unit::TestCase
+
+  include Chem::MultipleTest
+
+  def setup
+    @entries = Chem.open_mol($data_dir + "test.sdf")
+    @file_type = Chem::Type::SdfType
+    @mod = Chem::MDL::SdfParser
+  end
+
+  def test_autodetection
+    assert_equal(Chem::Type::SdfType, Chem::autodetect($data_dir + "test.sdf"))
+  end
+
+  def test_sdf_file
+    assert_equal(2, @entries.to_a.length)
+    @entries.each do |mol|
+      assert_not_nil(mol)
+    end
+    assert_equal(2, Chem.open_mol($data_dir + "test_lf.sdf").to_a.length)
+  end
+  
+end

data/test/test_smiles.rb

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+# $Id: test_smiles.rb 124 2006-01-16 09:15:20Z tanaka $
+require 'chem/db/smiles'
+
+require 'test/all'
+
+require 'test/ctab_test'
+
+
+class SmilesTest < 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 = []
+
+    [
+      "C", 
+     "[Au]", 
+      "[235U]",
+      "CC",
+      "CCC",
+      "C=O",
+      "C=CC=C",
+      "C#N",
+      "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
+    ].each do |smiles|
+      @entries.push(Chem.parse_smiles(smiles))
+    end
+#        mass : NUMBER
+  end
+end

data/test/test_sssr.rb

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+# $Id: test_sssr.rb 65 2005-10-25 17:17:36Z tanaka $
+
+require 'chem/utils/sssr'
+
+require 'test/all'
+require 'test/ctab_test'
+
+class SssrTest < Test::Unit::TestCase
+
+  def setup
+  end
+
+  def test_coronen
+    coronen = Chem.open_mol($data_dir + '/A_21/coronen.mol')
+    coronen.find_sssr
+  end
+
+end

data/test/test_sub.rb

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+# $Id: test_sub.rb 65 2005-10-25 17:17:36Z tanaka $
+
+require 'chem'
+
+require 'test/all'
+
+class SubTest < Test::Unit::TestCase
+
+  def setup
+    @cyclohexane = Chem.open_mol($data_dir + 'cyclohexane.mol')
+  end
+
+  def test_induced_subgraph
+    sub = @cyclohexane.induced_sub(@cyclohexane.nodes[0..2])
+    assert_equal(sub.nodes.length, 3)
+  end
+
+  def test_minus
+    sub = @cyclohexane.induced_sub(@cyclohexane.nodes[0..2])
+    sub2 = @cyclohexane - sub
+    assert_equal(sub2.nodes.length, 3)
+  end
+
+  def test_connection
+    mol = Chem.parse_smiles("CCCC.NNNNN")
+    mol2 = Chem.parse_smiles("CCCCNNNNN")
+    assert_equal(false, mol.connected?)
+    assert(mol2.connected?)
+  end
+
+  def test_divide
+    mol = Chem.parse_smiles("CC.N1NN1.OOOO")
+    ary = mol.divide
+    ary.each do |mol|
+      case mol.nodes[0].element
+      when :C
+        assert_equal(2, mol.nodes.length)
+      when :N
+        assert_equal(3, mol.nodes.length)
+      when :O
+        assert_equal(4, mol.nodes.length)
+      end
+    end
+  end
+
+end
+