rcdk 0.1.0

data/README

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+=RCDK - The Ruby Interface for the Chemistry Development Kit (CDK)
+
+RCDK makes it possible to use the CDK library, which is written in
+Java, from Ruby.
+
+==Typical Usage
+
+  require 'rubygems'
+  require_gem 'rcdk'
+  
+  SmilesParser = import('org.openscience.cdk.smiles.SmilesParser')
+
+  parser = SmilesParser.new
+  smiles = 'c1ccccc1'
+  mol = parser.parseSmiles(smiles)
+  
+  puts mol.getAtomCount # =>6
+  
+==Downloading
+
+Both a RubyGems installation package and a full source package
+can be obtained from:
+
+http://rubyforge.org/projects/rcdk
+
+==Requirements
+
+RCDK was developed with Ruby 1.8.4. Earlier versions of Ruby
+may also be compatible.
+
+==Installing
+
+The RubyGems package can be installed using the following command
+(as root):
+
+gem install rcdk
+
+==License
+RCDK is distributed under the GNU LGPL version 2.1 (see 'LICENSE').
+It contains bytecode from the Chemistry Development Kit (CDK) distribution,
+which is itself licensed under the LGPL. The complete source code for
+the CDK can be obtained from http://sf.net/projects/cdk.
+
+==Contact
+
+More information can be found at http://rcdk.rubyforge.org. 

data/Rakefile

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+# =============================================
+# RCDK - The Chemistry Development Kit for Ruby
+# =============================================
+#
+# Project Info: http://rcdk.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.
+
+require 'rake'
+require 'rake/testtask'
+require 'rake/rdoctask'
+require 'rake/gempackagetask'
+
+PKG_VERSION = "0.1.0"
+
+PKG_FILES = FileList[
+  "Rakefile", "README",
+  "lib/**/*.rb",
+  "test/**/*",
+  "java/*.jar"
+]
+
+desc "Default task"
+task :default => [:test]
+
+desc "Clean up"
+task :clean do
+  rm_rf "dist"
+  rm_rf "doc"
+  rm_rf "pkg"
+end
+
+desc "Create the source distribution"
+task :dist do
+  rm_rf "dist"
+  
+  mkdir "dist"
+  mkdir "dist/lib"
+  mkdir "dist/java"
+  mkdir "dist/test"
+  
+  cp_r Dir.glob('*.rb'), 'dist'
+  cp_r Dir.glob('lib/*.rb'), 'dist/lib'
+  cp_r Dir.glob('java/*.jar'), 'dist/java'
+  cp_r Dir.glob('test/*.rb'), 'dist/test'
+  cp 'Rakefile', 'dist'
+  cp 'README', 'dist'
+  cp 'LICENSE', 'dist'
+end
+
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/test*.rb']
+  t.verbose = true
+end
+
+Rake::RDocTask.new do |rdoc|
+  rdoc.rdoc_dir = 'doc'
+  rdoc.title    = "Ruby CDK"
+  rdoc.rdoc_files.include('README')
+  rdoc.options << '--line-numbers'
+  rdoc.options << '--inline-source'
+  rdoc.options << '--main' << 'README'
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+spec = Gem::Specification.new do |s|
+  s.name = 'rcdk'
+  s.version = PKG_VERSION
+  s.author = "Richard Apodaca"
+  s.homepage = "http://rcdk.rubyforge.org"
+  s.platform = Gem::Platform::RUBY
+  s.require_path = 'lib'
+  s.autorequire = 'rcdk'
+  s.has_rdoc = true
+  s.files = PKG_FILES
+  s.summary = "A Ruby wrapper for the Chemistry Development Kit"
+  s.add_dependency("rjb", ">= 1.0.0")
+end
+
+Rake::GemPackageTask.new(spec) do |gem|
+  gem.need_tar = true
+  gem.need_tar_gz = true
+  gem.package_files += PKG_FILES
+end

data/lib/java.rb

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+# =============================================
+# RCDK - The Chemistry Development Kit for Ruby
+# =============================================
+#
+# Project Info: http://rcdk.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.
+
+require 'rubygems'
+require_gem 'rjb'
+require 'rjb'
+
+# Returns the Java class represented by the fully qualified name
+# <tt>klass</tt> via Ruby Java Bridge (RJB).
+def import(klass)
+  Rjb::import(klass)
+end
+
+# Configuration and use of Java classes through Ruby Java Bridge (RJB).
+module Java
+  # Configuration of classpath.
+  class Classpath
+    # Appends <tt>path</tt> to the <tt>CLASSPATH</tt> environment variable.
+    def self.add(path)
+      if set?
+        ENV['CLASSPATH'] = ENV['CLASSPATH'] + File::PATH_SEPARATOR + path
+      else
+        ENV['CLASSPATH'] = path
+      end
+    end
+    
+    # Returns false if the <tt>CLASSPATH</tt> variable is either null or
+    # empty, or otherwise true.
+    def self.set?
+      if !ENV['CLASSPATH']
+        return false
+      elsif ''.eql?(ENV['CLASSPATH'])
+        return false
+      end
+      
+      true
+    end
+    
+    # Returns the value of the <tt>CLASSPATH</tt> variable.
+    def self.get
+      ENV['CLASSPATH']
+    end
+    
+    # Sets the value of the <tt>CLASSPATH</tt> varible to <tt>nil</tt>.
+    def self.clear!
+      ENV['CLASSPATH'] = nil
+    end
+  end
+end

data/lib/rcdk.rb

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+# =============================================
+# RCDK - The Chemistry Development Kit for Ruby
+# =============================================
+#
+# Project Info: http://rcdk.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.
+
+require 'java'
+
+RCDK_VERSION = '0.1.0'
+CDK_VERSION = '20060714'
+
+Java::Classpath.add(Gem.dir + File::SEPARATOR +
+  File.join('gems', 'rcdk-' + RCDK_VERSION, 'java', 'cdk-' +
+  CDK_VERSION + '.jar'))
+
+
+

data/test/test.rb

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+# =============================================
+# RCDK - The Chemistry Development Kit for Ruby
+# =============================================
+#
+# Project Info: http://rcdk.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 'rcdk'
+require 'test/unit'
+
+Java::Classpath.add(File.join('java', 'cdk-' + '20060714' + '.jar'))
+
+SmilesParser = import('org.openscience.cdk.smiles.SmilesParser')
+
+# A very simple test suite.
+class BasicTest < Test::Unit::TestCase
+
+  # Loads the SMILES string for benzene and verifies that the resulting
+  # CDK molecule has six atoms.
+  def test_parse_smiles
+    parser = SmilesParser.new
+    smiles = 'c1ccccc1'
+    
+    mol = parser.parseSmiles(smiles)
+    
+    assert_equal(6, mol.getAtomCount)
+  end
+end
+

metadata

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+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.0
+specification_version: 1
+name: rcdk
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+date: 2006-09-13 00:00:00 -07:00
+summary: A Ruby wrapper for the Chemistry Development Kit
+require_paths: 
+- lib
+email: 
+homepage: http://rcdk.rubyforge.org
+rubyforge_project: 
+description: 
+autorequire: rcdk
+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/rcdk.rb
+- lib/java.rb
+- test/test.rb
+- java/cdk-20060714.jar
+test_files: []
+
+rdoc_options: []
+
+extra_rdoc_files: []
+
+executables: []
+
+extensions: []
+
+requirements: []
+
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rjb
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Version::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+    version: