rcdk 0.2.0 → 0.3.0

data/README

@@ -1,15 +1,15 @@
 =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.
+RCDK makes it possible to use the Chemistry Development Kit (CDK)
+from Ruby. CDK is a Java library for chemical informatics.
 
 ==Typical Usage
 
   require 'rubygems'
   require_gem 'rcdk'
-  require 'util'
+  require 'rcdk/util'
   
-  mol = RCDK::Util::Lang.read_smiles('c1ccccc1')
+  mol = RCDK::Util::Lang.read_smiles 'c1ccccc1'
   
   puts mol.getAtomCount # =>6
   
@@ -23,7 +23,8 @@ http://rubyforge.org/projects/rcdk
 ==Requirements
 
 RCDK was developed with Ruby 1.8.4. Earlier versions of Ruby
-may also be compatible.
+may also be compatible. Ruby Java Bridge is used to interface
+to the Java Virtual Machine.
 
 ==Installing
 
@@ -32,12 +33,20 @@ The RubyGems package can be installed using the following command
 
 gem install rcdk
 
+This command will optionally install Ruby Java Bridge, if it
+hasn't been installed yet.
+
 ==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.
+It contains bytecode from the following sources:
+
+-Chemistry Development Kit (CDK), licensed under the LGPL: http://cdk.sf.net
+
+-OPSIN, licensed under the Artistic License: http://sourceforge.net/projects/oscar3-chem/
+
+-Structure-CDK, licensed under the LGPL: http://sf.net/projects/structure
 
 ==Contact
 
-More information can be found at http://rcdk.rubyforge.org. 
+Blog: http://depth-first.com
+Email: r_apodaca at users dot sf dot net

data/Rakefile

@@ -2,7 +2,8 @@
 # RCDK - The Chemistry Development Kit for Ruby
 # =============================================
 #
-# Project Info: http://rcdk.rubyforge.org
+# Project Info: http://rubyforge.org/projects/rcdk
+# Blog: http://depth-first.com
 #
 # Copyright (C) 2006 Richard L. Apodaca
 #
@@ -26,7 +27,7 @@ require 'rake/testtask'
 require 'rake/rdoctask'
 require 'rake/gempackagetask'
 
-PKG_VERSION = "0.2.0"
+PKG_VERSION = "0.3.0"
 
 PKG_FILES = FileList[
   "Rakefile", "README",
@@ -95,7 +96,7 @@ spec = Gem::Specification.new do |s|
   s.name = 'rcdk'
   s.version = PKG_VERSION
   s.author = "Richard Apodaca"
-  s.homepage = "http://rcdk.rubyforge.org"
+  s.homepage = "http://rubyforge.org/projects/rcdk"
   s.platform = Gem::Platform::RUBY
   s.require_path = 'lib'
   s.autorequire = 'rcdk'
@@ -103,6 +104,11 @@ spec = Gem::Specification.new do |s|
   s.files = PKG_FILES
   s.summary = "A Ruby wrapper for the Chemistry Development Kit"
   s.add_dependency("rjb", ">= 1.0.0")
+  s.description = s.summary
+  s.extra_rdoc_files = ['README']
+  s.rdoc_options << '--title' << 'Ruby Chemistry Development Kit (RCDK)' <<
+                       '--main' << 'README' <<
+                       '--line-numbers'
 end
 
 Rake::GemPackageTask.new(spec) do |gem|

data/lib/rcdk.rb

@@ -2,7 +2,8 @@
 # RCDK - The Chemistry Development Kit for Ruby
 # =============================================
 #
-# Project Info: http://rcdk.rubyforge.org
+# Project Info: http://rubyforge.org/projects/rcdk
+# Blog: http://depth-first.com
 #
 # Copyright (C) 2006 Richard L. Apodaca
 #
@@ -15,18 +16,19 @@
 # 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 = '0.2.0'
+RCDK_VERSION = '0.3.0'
 CDK_VERSION = '20060714'
 STRUCTURE_CDK_VERSION = '0.1.2'
+OPSIN_VERSION = '0.1.0'
 
-Java::Classpath.add(Gem.dir + File::SEPARATOR +
-                    File.join('gems', 'rcdk-' + RCDK_VERSION, 'java', 'lib', 'cdk-' +
-CDK_VERSION + '.jar'))
-
-Java::Classpath.add(Gem.dir + File::SEPARATOR +
-                    File.join('gems', 'rcdk-' + RCDK_VERSION, 'java', 'lib', 'structure-cdk-' +
-STRUCTURE_CDK_VERSION + '.jar'))
+require 'rcdk/java'
 
+require_jar File.join(File.dirname(__FILE__), '..', 'java', 'lib', 'cdk-' + CDK_VERSION + '.jar')
+require_jar File.join(File.dirname(__FILE__), '..', 'java', 'lib', 'structure-cdk-' + STRUCTURE_CDK_VERSION + '.jar')
+require_jar File.join(File.dirname(__FILE__), '..', 'java', 'lib', 'opsin-big-' + OPSIN_VERSION + '.jar')

data/lib/rcdk/java.rb

@@ -0,0 +1,87 @@
+# =============================================
+# RCDK - The Chemistry Development Kit for Ruby
+# =============================================
+#
+# Project Info: http://rubyforge.org/projects/rcdk
+# Blog: http://depth-first.com
+#
+# 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'
+
+# Adds the fully-qualified path <tt>path_to_jarfile</tt> to the <tt>
+# CLASSPATH</tt> environment variable. Any jarfiles added after the
+# first invocation of a Java constructor will be globally ignored, i.e., <tt>
+# require</tt> all jarfiles first in your program before constructing
+# objects from them.
+def require_jar(path_to_jarfile)
+  if classpath_set?
+    ENV['CLASSPATH'] = ENV['CLASSPATH'] + File::PATH_SEPARATOR + path_to_jarfile
+  else
+    ENV['CLASSPATH'] = path_to_jarfile
+  end
+end
+
+private  
+
+# Returns false if the <tt>CLASSPATH</tt> variable is either null or
+# empty, or otherwise true.
+def classpath_set?
+  if !ENV['CLASSPATH']
+    return false
+  elsif ''.eql?(ENV['CLASSPATH'])
+    return false
+  end
+  
+  true
+end
+
+module Kernel
+
+  # Maps the packages and class name specified by <tt>qualified_class_name</tt>
+  # to a nested set of Ruby modules. The first letter of each module name is
+  # capitalized. For example, <tt>java.util.HashMap</tt> would become <tt>
+  # Java::Util::HashMap</tt>.
+  # 
+  # The first use of <tt>jrequire</tt> will render all subsequent calls
+  # to <tt>require_jar</tt> ineffective.
+  def jrequire(qualified_class_name)
+    java_class = Rjb::import(qualified_class_name)
+    package_names = qualified_class_name.to_s.split('.')
+    java_class_name = package_names.delete(package_names.last)
+    new_module = self.class
+
+    package_names.each do |package_name|
+      module_name = package_name.capitalize
+
+      if !new_module.const_defined?(module_name)
+        new_module = new_module.const_set(module_name, Module.new)
+      else
+        new_module = new_module.const_get(module_name)
+      end
+    end
+
+    return false if new_module.const_defined?(java_class_name)
+
+    new_module.const_set(java_class_name, java_class)
+
+    return true
+  end
+end

data/lib/{util.rb → rcdk/util.rb}

@@ -2,7 +2,8 @@
 # RCDK - The Chemistry Development Kit for Ruby
 # =============================================
 #
-# Project Info: http://rcdk.rubyforge.org
+# Project Info: http://rubyforge.org/projects/rcdk
+# Blog: http://depth-first.com
 #
 # Copyright (C) 2006 Richard L. Apodaca
 #
@@ -15,21 +16,27 @@
 # 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 'rcdk'
 
-StringReader = import 'java.io.StringReader'
-StringWriter = import 'java.io.StringWriter'
-
-Molecule = import 'org.openscience.cdk.Molecule'
-MDLReader = import 'org.openscience.cdk.io.MDLReader'
-MDLWriter = import 'org.openscience.cdk.io.MDLWriter'
-SmilesParser = import 'org.openscience.cdk.smiles.SmilesParser'
-SmilesGenerator = import 'org.openscience.cdk.smiles.SmilesGenerator'
-DefaultChemObjectBuilder = import 'org.openscience.cdk.DefaultChemObjectBuilder'
-StructureDiagramGenerator = import 'org.openscience.cdk.layout.StructureDiagramGenerator'
-
-ImageKit = import 'net.sf.structure.cdk.util.ImageKit'
+jrequire 'java.io.StringReader'
+jrequire 'java.io.StringWriter'
+jrequire 'org.openscience.cdk.io.MDLWriter'
+jrequire 'org.openscience.cdk.io.MDLReader'
+jrequire 'org.openscience.cdk.smiles.SmilesParser'
+jrequire 'org.openscience.cdk.smiles.SmilesGenerator'
+jrequire 'org.openscience.cdk.DefaultChemObjectBuilder'
+jrequire 'org.openscience.cdk.Molecule'
+jrequire 'org.openscience.cdk.layout.StructureDiagramGenerator'
+jrequire 'org.openscience.cdk.io.CMLReader'
+jrequire 'org.openscience.cdk.ChemFile'
+jrequire 'net.sf.structure.cdk.util.ImageKit'
+jrequire 'uk.ac.cam.ch.wwmm.opsin.NameToStructure'
 
 # The Ruby Chemistry Development Kit.
 module RCDK
@@ -37,24 +44,45 @@ module RCDK
   # Convenience methods for working with the CDK.
   module Util
     
-    # Molecular language translation. Currently molfile and SMILES
-    # are implemented.
+    # Molecular language translation. Currently molfile, SMILES,
+    # and IUPAC nomenclature (read-only) are implemented.
     class Lang
-      @@mdl_reader = MDLReader.new
-      @@mdl_writer = MDLWriter.new
-      @@smiles_parser = SmilesParser.new
-      @@smiles_generator = SmilesGenerator.new(DefaultChemObjectBuilder.getInstance)
+      include Org::Openscience::Cdk
+      include Org::Openscience::Cdk::Io
+      include Java::Io
+      include Uk::Ac::Cam::Ch::Wwmm::Opsin
+      
+      @@mdl_reader = Io::MDLReader.new
+      @@mdl_writer = Io::MDLWriter.new
+      @@smiles_parser = Smiles::SmilesParser.new
+      @@smiles_generator = Smiles::SmilesGenerator.new(DefaultChemObjectBuilder.getInstance)
+      @@cml_reader = nil
       
       # Returns a CDK <tt>Molecule</tt> given the String-based molfile
       # <tt>molfile</tt>.
       def self.read_molfile(molfile)
-        reader =
-        StringReader.new_with_sig('Ljava.lang.String;', molfile)
+        reader = StringReader.new(molfile)
         
         @@mdl_reader.setReader(reader)
         @@mdl_reader.read(Molecule.new)
       end
       
+      # Returns a CDK <tt>Molecule</tt> given the specified <tt>iupac_name</tt>.
+      def self.read_iupac(iupac_name)
+        nts = NameToStructure.getInstance
+        cml = nts.parseToCML(iupac_name)
+        
+        raise "Couldn't parse #{iupac_name}." unless cml
+        
+        string_reader = StringReader.new(cml.toXML)
+        
+        @@cml_reader = CMLReader.new unless @@cml_reader
+        @@cml_reader.setReader(string_reader)
+        
+        chem_file = @@cml_reader.read(ChemFile.new)
+        chem_file.getChemSequence(0).getChemModel(0).getSetOfMolecules.getMolecule(0)
+      end
+      
       # Returns a String-based molfile by parsing the CDK <tt>molecule</tt>.
       def self.get_molfile(molecule)
         writer = StringWriter.new
@@ -86,12 +114,13 @@ module RCDK
       def self.smiles_to_molfile(smiles)
         get_molfile(read_smiles(smiles))
       end
-      
     end
     
     # 2-D coordinate generation.
     class XY
-      @@sdg = StructureDiagramGenerator.new    
+      include Org::Openscience::Cdk     
+      
+      @@sdg = Layout::StructureDiagramGenerator.new    
       
       # Assigns 2-D coordinates to the indicated <tt>molfile</tt> string.
       def self.coordinate_molfile(molfile)
@@ -110,7 +139,8 @@ module RCDK
     
     # Raster and SVG 2-D molecular images.
     class Image
-    
+      include Net::Sf::Structure::Cdk::Util
+      
       # Writes a <tt>width</tt> by <tt>height</tt> PNG image to
       # <tt>path_to_png</tt> using <tt>molfile</tt>.
       def self.molfile_to_png(molfile, path_to_png, width, height)
@@ -155,6 +185,33 @@ module RCDK
         
         ImageKit.writeJPG(mol, width, height, path_to_jpg)
       end
+      
+      # Writes a <tt>width</tt> by <tt>height</tt> PNG image to
+      # <tt>path_to_png</tt> using <tt>iupac_name</tt>. Coordinates
+      # are automatically assigned.
+      def self.iupac_to_png(iupac_name, path_to_png, width, height)
+        mol = XY.coordinate_molecule(Lang.read_iupac(iupac_name))
+        
+        ImageKit.writePNG(mol, width, height, path_to_png)
+      end
+      
+      # Writes a <tt>width</tt> by <tt>height</tt> SVG document to
+      # <tt>path_to_svg</tt> using <tt>iupac_name</tt>. Coordinates
+      # are automatically assigned.
+      def self.iupac_to_svg(iupac_name, path_to_svg, width, height)
+        mol = XY.coordinate_molecule(Lang.read_iupac(iupac_name))
+        
+        ImageKit.writeSVG(mol, width, height, path_to_svg)
+      end
+      
+      # Writes a <tt>width</tt> by <tt>height</tt> JPG image to
+      # <tt>path_to_jpg</tt> using <tt>iupac_name</tt>. Coordinates
+      # are automatically assigned.
+      def self.iupac_to_jpg(iupac_name, path_to_jpg, width, height)
+        mol = XY.coordinate_molecule(Lang.read_iupac(iupac_name))
+        
+        ImageKit.writeJPG(mol, width, height, path_to_jpg)
+      end
     end
   end
 end

data/test/test.rb

@@ -2,7 +2,8 @@
 # RCDK - The Chemistry Development Kit for Ruby
 # =============================================
 #
-# Project Info: http://rcdk.rubyforge.org
+# Project Info: http://rubyforge.org/projects/rcdk
+# Blog: http://depth-first.com
 #
 # Copyright (C) 2006 Richard L. Apodaca
 #
@@ -15,26 +16,25 @@
 # 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'
+require 'rcdk'
+require 'rcdk/util'
 
-Java::Classpath.clear!
-Java::Classpath.add(File.join('java', 'lib', 'cdk-' + CDK_VERSION + '.jar'))
-Java::Classpath.add(File.join('java', 'lib', 'structure-cdk-' + STRUCTURE_CDK_VERSION + '.jar'))
-
-require 'util'
-
-include RCDK::Util
-
-MoleculeFactory = import 'org.openscience.cdk.templates.MoleculeFactory'
+jrequire 'org.openscience.cdk.templates.MoleculeFactory'
 
 # A very simple test suite. Woefully incomplete. Just exercises the API.
 class BasicTest < Test::Unit::TestCase
-
+  include RCDK::Util
+  include Org::Openscience::Cdk::Templates
+  
   def setup
     @benzene =
 "c1ccccc1
@@ -75,6 +75,12 @@ M  END"
     assert_equal(6, molecule.getAtomCount)
   end
   
+  def test_read_iupac
+    molecule = Lang.read_iupac('benzene')
+    
+    assert_equal(6, molecule.getAtomCount)
+  end
+  
   def test_write_smiles
     smiles = Lang.get_smiles(MoleculeFactory.makeBenzene)
     
@@ -123,7 +129,19 @@ M  END"
   end
   
   def test_smiles_to_jpg
-    Image.smiles_to_jpg('Clc1ccccc1', 'output/chlrobenzene.jpg', 200, 200)
+    Image.smiles_to_jpg('Clc1ccccc1', 'output/chlorobenzene.jpg', 200, 200)
+  end
+  
+  def test_iupac_to_png
+    Image.iupac_to_png('quinoline', 'output/quinoline.png', 200, 200)
+  end
+  
+  def test_iupac_to_svg
+    Image.iupac_to_svg('quinoline', 'output/quinoline.svg', 200, 200)
+  end
+  
+  def test_iupac_to_jpg
+    Image.iupac_to_jpg('quinoline', 'output/quinoline.jpg', 200, 200)
   end
 end
 

metadata

@@ -3,15 +3,15 @@ rubygems_version: 0.9.0
 specification_version: 1
 name: rcdk
 version: !ruby/object:Gem::Version 
-  version: 0.2.0
-date: 2006-09-24 00:00:00 -07:00
+  version: 0.3.0
+date: 2006-10-28 00:00:00 -07:00
 summary: A Ruby wrapper for the Chemistry Development Kit
 require_paths: 
 - lib
 email: 
-homepage: http://rcdk.rubyforge.org
+homepage: http://rubyforge.org/projects/rcdk
 rubyforge_project: 
-description: 
+description: A Ruby wrapper for the Chemistry Development Kit
 autorequire: rcdk
 default_executable: 
 bindir: bin
@@ -32,17 +32,22 @@ files:
 - Rakefile
 - README
 - lib/rcdk.rb
-- lib/java.rb
-- lib/util.rb
+- lib/rcdk/java.rb
+- lib/rcdk/util.rb
 - test/test.rb
 - java/lib/cdk-20060714.jar
+- java/lib/opsin-big-0.1.0.jar
 - java/lib/structure-cdk-0.1.2.jar
 test_files: []
 
-rdoc_options: []
-
-extra_rdoc_files: []
-
+rdoc_options: 
+- --title
+- Ruby Chemistry Development Kit (RCDK)
+- --main
+- README
+- --line-numbers
+extra_rdoc_files: 
+- README
 executables: []
 
 extensions: []

data/lib/java.rb

@@ -1,69 +0,0 @@
-# =============================================
-# 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