rino 0.1.0

data/test/test.rb

@@ -0,0 +1,386 @@
+# =================================
+# Rino - The InChI Toolkit for Ruby
+# =================================
+#
+# Project Info:  http://rino.rubyforge.org
+#
+# Copyright (C) 2006 Richard L. Apodaca
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License version 2.1 as published by the Free Software
+# Foundation.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free
+# Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor
+# Boston, MA 02111-1301, USA.
+
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require 'rino'
+require 'test/unit'
+
+class TestBenzene < Test::Unit::TestCase
+
+  def setup
+    @benzene =
+"c1ccccc1
+JME 2004.10 Thu Jun 01 18:20:16 EDT 2006
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+    0.0000    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2124    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2124    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  1  3  1  0  0  0  0
+  2  4  1  0  0  0  0
+  3  5  2  0  0  0  0
+  4  6  2  0  0  0  0
+  5  6  1  0  0  0  0
+M  END"
+
+  @ferrocene =
+"
+  ACD/Labs0709041143  
+
+ 22 40  0  0  0  0  0  0  0  0 22 V2000
+    8.4529  -17.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5359  -11.9699    0.0000 Fe  0  2  0  0  0  0  0  0  0  0  0  0
+    7.8254  -15.2493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.4796  -17.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.2545  -15.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5392  -13.9965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.3819   -8.5463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.7543   -6.5318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.5739   -6.5392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9574   -8.5592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.6776   -9.7992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.6151  -17.0901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.6981  -11.7960    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
+   15.9876  -15.0756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   18.6419  -17.0822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.4168  -15.0627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.7014  -13.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.5441   -8.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   18.9165   -6.3580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.7361   -6.3655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.1196   -8.3855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.8398   -9.6254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  2  0  0  0  0
+  1  4  1  0  0  0  0
+  2  7  1  0  0  0  0
+  2  8  1  0  0  0  0
+  2  9  1  0  0  0  0
+  2 10  1  0  0  0  0
+  2 11  1  0  0  0  0
+  2  4  1  0  0  0  0
+  2  5  1  0  0  0  0
+  2  6  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  6  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  7 11  2  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  2  0  0  0  0
+ 10 11  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 12 14  1  0  0  0  0
+ 12 15  1  0  0  0  0
+ 13 18  1  0  0  0  0
+ 13 19  1  0  0  0  0
+ 13 20  1  0  0  0  0
+ 13 21  1  0  0  0  0
+ 13 22  1  0  0  0  0
+ 13 15  1  0  0  0  0
+ 13 16  1  0  0  0  0
+ 13 17  1  0  0  0  0
+ 13 14  1  0  0  0  0
+ 14 17  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 16 17  1  0  0  0  0
+ 18 22  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 19 20  1  0  0  0  0
+ 20 21  1  0  0  0  0
+ 21 22  1  0  0  0  0
+A    1
+CH
+M  CHG  1   2   2
+A    3
+CH
+A    4
+CH-
+A    5
+CH
+A    6
+CH
+A    7
+CH
+A    8
+CH-
+A    9
+CH
+A   10
+CH
+A   11
+CH
+M  END
+"
+
+@c60 =
+"BUCKMINSTERFULLERENE
+  USERSTR 07209813162D 1   1.0         0.0    115862
+
+ 60 90  0  0  0  0  0  0  0  0999 V2000
+    7.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -3.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   10.0000   27.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   14.0000    8.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -6.0000   27.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -10.0000    8.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    2.0000   32.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -17.0000   30.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    2.0000   44.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   22.0000   30.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -17.0000   42.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -25.0000   22.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -8.0000   49.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -28.0000   46.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -10.0000   61.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   13.0000   49.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   22.0000   42.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   14.0000   61.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   32.0000   47.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   29.0000   22.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   25.0000   11.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   40.0000   24.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   34.0000    3.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    8.0000   -3.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -3.0000   -3.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   14.0000  -13.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -9.0000  -13.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -21.0000   11.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -29.0000    3.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -36.0000   24.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   48.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   45.0000    5.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   61.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   56.0000   -2.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    8.0000  -23.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -3.0000  -23.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   13.0000  -35.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   -7.0000  -35.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -41.0000    5.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -44.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -51.0000   -2.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -57.0000   16.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -31.0000   57.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -21.0000   65.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -42.0000   65.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -24.0000   77.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   25.0000   65.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   34.0000   58.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   27.0000   77.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   44.0000   65.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -38.0000   77.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -48.0000   90.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   40.0000   77.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   50.0000   90.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   65.0000    5.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+   80.0000    1.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    3.0000  -42.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+    3.0000  -60.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -61.0000    5.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  -79.0000    0.0000    0.0000 C   0  0  0     0  0  0  0  0  0
+  1  2  2  0   0  0  0
+  1  3  1  0   0  0  0
+  1  4  1  0   0  0  0
+  2  5  1  0   0  0  0
+  2  6  1  0   0  0  0
+  3 10  2  0   0  0  0
+  3  7  1  0   0  0  0
+  4 24  2  0   0  0  0
+  4 21  1  0   0  0  0
+  5  7  2  0   0  0  0
+  5  8  1  0   0  0  0
+  6 28  1  0   0  0  0
+  6 25  2  0   0  0  0
+  7  9  1  0   0  0  0
+  8 11  2  0   0  0  0
+  8 12  1  0   0  0  0
+  9 16  2  0   0  0  0
+  9 13  1  0   0  0  0
+ 10 20  1  0   0  0  0
+ 10 17  1  0   0  0  0
+ 11 13  1  0   0  0  0
+ 11 14  1  0   0  0  0
+ 12 30  2  0   0  0  0
+ 12 28  1  0   0  0  0
+ 13 15  2  0   0  0  0
+ 14 43  2  0   0  0  0
+ 14 30  1  0   0  0  0
+ 15 44  1  0   0  0  0
+ 15 18  1  0   0  0  0
+ 16 17  1  0   0  0  0
+ 16 18  1  0   0  0  0
+ 17 19  2  0   0  0  0
+ 18 47  2  0   0  0  0
+ 19 22  1  0   0  0  0
+ 19 48  1  0   0  0  0
+ 20 21  1  0   0  0  0
+ 20 22  2  0   0  0  0
+ 21 23  2  0   0  0  0
+ 22 31  1  0   0  0  0
+ 23 32  1  0   0  0  0
+ 23 26  1  0   0  0  0
+ 24 25  1  0   0  0  0
+ 24 26  1  0   0  0  0
+ 25 27  1  0   0  0  0
+ 26 35  2  0   0  0  0
+ 27 36  2  0   0  0  0
+ 27 29  1  0   0  0  0
+ 28 29  2  0   0  0  0
+ 29 39  1  0   0  0  0
+ 30 40  1  0   0  0  0
+ 31 32  2  0   0  0  0
+ 31 33  1  0   0  0  0
+ 32 34  1  0   0  0  0
+ 33 55  2  0   0  0  0
+ 33 50  1  0   0  0  0
+ 34 55  1  0   0  0  0
+ 34 37  2  0   0  0  0
+ 35 36  1  0   0  0  0
+ 35 37  1  0   0  0  0
+ 36 38  1  0   0  0  0
+ 37 57  1  0   0  0  0
+ 38 57  2  0   0  0  0
+ 38 41  1  0   0  0  0
+ 39 40  2  0   0  0  0
+ 39 41  1  0   0  0  0
+ 40 42  1  0   0  0  0
+ 41 59  2  0   0  0  0
+ 42 45  2  0   0  0  0
+ 42 59  1  0   0  0  0
+ 43 44  1  0   0  0  0
+ 43 45  1  0   0  0  0
+ 44 46  2  0   0  0  0
+ 45 51  1  0   0  0  0
+ 46 51  1  0   0  0  0
+ 46 49  1  0   0  0  0
+ 47 48  1  0   0  0  0
+ 47 49  1  0   0  0  0
+ 48 50  2  0   0  0  0
+ 49 53  2  0   0  0  0
+ 50 53  1  0   0  0  0
+ 51 52  2  0   0  0  0
+ 52 54  1  0   0  0  0
+ 52 60  1  0   0  0  0
+ 53 54  1  0   0  0  0
+ 54 56  2  0   0  0  0
+ 55 56  1  0   0  0  0
+ 56 58  1  0   0  0  0
+ 57 58  1  0   0  0  0
+ 58 60  2  0   0  0  0
+ 59 60  1  0   0  0  0
+M  END
+"
+
+@s_phenylethanol =
+"C[C@H](O)c1ccccc1
+JME 2004.10 Sun Jun 04 14:52:53 EDT 2006
+
+  9  9  0  0  0  0  0  0  0  0999 V2000
+    4.8497    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    4.2000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2124    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2124    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  9  1  0  0  0  0
+  9  2  1  1  0  0  0
+  3  4  2  0  0  0  0
+  3  5  1  0  0  0  0
+  4  6  1  0  0  0  0
+  5  7  2  0  0  0  0
+  6  8  2  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+M  END
+"
+  @reader = Rino::MolfileReader.new
+  end
+
+  def test_benzene_inchi
+    inchi = @reader.read(@benzene)
+
+    assert_equal("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H", inchi)
+  end
+
+  def test_s_phenylethanol_inchi
+    inchi = @reader.read(@s_phenylethanol)
+
+    assert_equal("InChI=1/C8H10O/c1-7(9)8-5-3-2-4-6-8/h2-7,9H,1H3/t7-/m0/s1", inchi)
+  end
+
+  def test_ferrocene_inchi
+    inchi = @reader.read(@ferrocene)
+
+    assert_equal("InChI=1/2C5H5.2C5.2Fe/c4*1-2-4-5-3-1;;/h2*1-5H;;;;/q;;2*-1;;+2", inchi)
+  end
+
+  def test_c60_inchi
+    inchi = @reader.read(@c60)
+
+    assert_equal("InChI=1/C60/c1-2-5-6-3(1)8-12-10-4(1)9-11-7(2)17-21-13(5)23-24-14(6)22-18(8)28-20(12)30-26-16(10)15(9)25-29-19(11)27(17)37-41-31(21)33(23)43-44-34(24)32(22)42-38(28)48-40(30)46-36(26)35(25)45-39(29)47(37)55-49(41)51(43)57-52(44)50(42)56(48)59-54(46)53(45)58(55)60(57)59", inchi)
+  end
+  
+  def test_bad_molfile
+    fail = true
+    
+    begin
+      inchi = @reader.read("Bad molfile")
+    rescue
+     fail = false
+    end
+    
+    if fail
+      flunk
+    end
+  end
+
+  def test_benzene_compress
+    @reader.options.clear
+
+    inchi = @reader.read(@benzene)
+    assert_equal("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H", inchi)
+
+    @reader.options << "-Compress"
+
+    inchi = @reader.read(@benzene)
+
+    assert_equal("InChI=1/C6H6/cAE1ABFD/hAF1", inchi)
+
+    @reader.options.clear
+
+    inchi = @reader.read(@benzene)
+    assert_equal("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H", inchi)
+  end
+end
+
+
+

metadata

@@ -0,0 +1,130 @@
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.0
+specification_version: 1
+name: rino
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+date: 2006-08-16 00:00:00 -07:00
+summary: A Ruby wrapper for the C InChI toolkit
+require_paths: 
+- lib
+email: 
+homepage: http://rino.rubyforge.org
+rubyforge_project: 
+description: 
+autorequire: rino
+default_executable: 
+bindir: bin
+has_rdoc: true
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      version: 0.0.0
+  version: 
+platform: ruby
+signing_key: 
+cert_chain: 
+post_install_message: 
+authors: 
+- Richard Apodaca
+files: 
+- Rakefile
+- README
+- lib/rino.rb
+- lib/clean_tempfile.rb
+- test/test.rb
+- ext/src/aux2atom.h
+- ext/src/comdef.h
+- ext/src/e_0dstereo.h
+- ext/src/e_comdef.h
+- ext/src/e_ctl_data.h
+- ext/src/e_ichicomp.h
+- ext/src/e_ichierr.h
+- ext/src/e_ichi_io.h
+- ext/src/e_ichi_parms.h
+- ext/src/e_ichisize.h
+- ext/src/e_inchi_atom.h
+- ext/src/e_inpdef.h
+- ext/src/e_mode.h
+- ext/src/e_readmol.h
+- ext/src/e_readstru.h
+- ext/src/e_util.h
+- ext/src/extr_ct.h
+- ext/src/ichi_bns.h
+- ext/src/ichicano.h
+- ext/src/ichicant.h
+- ext/src/ichicomn.h
+- ext/src/ichicomp.h
+- ext/src/ichidrp.h
+- ext/src/ichierr.h
+- ext/src/ichi.h
+- ext/src/ichimain.h
+- ext/src/ichimake.h
+- ext/src/ichinorm.h
+- ext/src/ichiparm.h
+- ext/src/ichiring.h
+- ext/src/ichisize.h
+- ext/src/ichister.h
+- ext/src/ichitaut.h
+- ext/src/ichitime.h
+- ext/src/inchi_api.h
+- ext/src/inchi_dll.h
+- ext/src/inchi_dll_main.h
+- ext/src/inpdef.h
+- ext/src/lreadmol.h
+- ext/src/mode.h
+- ext/src/strutil.h
+- ext/src/util.h
+- ext/src/e_0dstereo.c
+- ext/src/e_ichi_io.c
+- ext/src/e_ichimain.c
+- ext/src/e_ichi_parms.c
+- ext/src/e_inchi_atom.c
+- ext/src/e_mol2atom.c
+- ext/src/e_readinch.c
+- ext/src/e_readmol.c
+- ext/src/e_readstru.c
+- ext/src/e_util.c
+- ext/src/ichi_bns.c
+- ext/src/ichican2.c
+- ext/src/ichicano.c
+- ext/src/ichicans.c
+- ext/src/ichiisot.c
+- ext/src/ichilnct.c
+- ext/src/ichimak2.c
+- ext/src/ichimake.c
+- ext/src/ichimap1.c
+- ext/src/ichimap2.c
+- ext/src/ichimap4.c
+- ext/src/ichinorm.c
+- ext/src/ichiparm.c
+- ext/src/ichiprt1.c
+- ext/src/ichiprt2.c
+- ext/src/ichiprt3.c
+- ext/src/ichiqueu.c
+- ext/src/ichiring.c
+- ext/src/ichisort.c
+- ext/src/ichister.c
+- ext/src/ichitaut.c
+- ext/src/inchi_dll.c
+- ext/src/inchi_dll_main.c
+- ext/src/ruby_inchi_main.c
+- ext/src/runichi.c
+- ext/src/strutil.c
+- ext/src/util.c
+- ext/ruby_inchi_main.so
+test_files: []
+
+rdoc_options: []
+
+extra_rdoc_files: []
+
+executables: []
+
+extensions: 
+- ext/extconf.rb
+requirements: []
+
+dependencies: []
+