rcdk 0.1.0 → 0.2.0

data/README

@@ -7,12 +7,9 @@ Java, from Ruby.
 
   require 'rubygems'
   require_gem 'rcdk'
+  require 'util'
   
-  SmilesParser = import('org.openscience.cdk.smiles.SmilesParser')
-
-  parser = SmilesParser.new
-  smiles = 'c1ccccc1'
-  mol = parser.parseSmiles(smiles)
+  mol = RCDK::Util::Lang.read_smiles('c1ccccc1')
   
   puts mol.getAtomCount # =>6
   

data/Rakefile

@@ -26,23 +26,27 @@ require 'rake/testtask'
 require 'rake/rdoctask'
 require 'rake/gempackagetask'
 
-PKG_VERSION = "0.1.0"
+PKG_VERSION = "0.2.0"
 
 PKG_FILES = FileList[
   "Rakefile", "README",
   "lib/**/*.rb",
   "test/**/*",
-  "java/*.jar"
+  "java/lib/*.jar"
 ]
 
 desc "Default task"
 task :default => [:test]
 
+
+task :dist => [:rdoc]
+
 desc "Clean up"
 task :clean do
   rm_rf "dist"
   rm_rf "doc"
   rm_rf "pkg"
+  rm_rf "output"
 end
 
 desc "Create the source distribution"
@@ -50,13 +54,17 @@ task :dist do
   rm_rf "dist"
   
   mkdir "dist"
+  mkdir "dist/doc"
   mkdir "dist/lib"
   mkdir "dist/java"
+  mkdir "dist/java/lib"
+  mkdir "dist/java/src"
   mkdir "dist/test"
   
+  mv Dir.glob('doc/*'), 'dist/doc'
   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('java/lib/*.jar'), 'dist/java/lib'
   cp_r Dir.glob('test/*.rb'), 'dist/test'
   cp 'Rakefile', 'dist'
   cp 'README', 'dist'
@@ -64,6 +72,10 @@ task :dist do
 end
 
 Rake::TestTask.new do |t|
+
+  rm_rf "output"
+  mkdir "output"
+  
   t.libs << "test"
   t.test_files = FileList['test/test*.rb']
   t.verbose = true

data/lib/rcdk.rb

@@ -15,20 +15,18 @@
 # 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'
+RCDK_VERSION = '0.2.0'
 CDK_VERSION = '20060714'
+STRUCTURE_CDK_VERSION = '0.1.2'
 
 Java::Classpath.add(Gem.dir + File::SEPARATOR +
-  File.join('gems', 'rcdk-' + RCDK_VERSION, 'java', 'cdk-' +
-  CDK_VERSION + '.jar'))
-
+                    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'))
 

data/lib/util.rb

@@ -0,0 +1,160 @@
+# =============================================
+# 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.
+
+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'
+
+# The Ruby Chemistry Development Kit.
+module RCDK
+  
+  # Convenience methods for working with the CDK.
+  module Util
+    
+    # Molecular language translation. Currently molfile and SMILES
+    # are implemented.
+    class Lang
+      @@mdl_reader = MDLReader.new
+      @@mdl_writer = MDLWriter.new
+      @@smiles_parser = SmilesParser.new
+      @@smiles_generator = SmilesGenerator.new(DefaultChemObjectBuilder.getInstance)
+      
+      # 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)
+        
+        @@mdl_reader.setReader(reader)
+        @@mdl_reader.read(Molecule.new)
+      end
+      
+      # Returns a String-based molfile by parsing the CDK <tt>molecule</tt>.
+      def self.get_molfile(molecule)
+        writer = StringWriter.new
+        
+        @@mdl_writer.setWriter(writer)
+        @@mdl_writer.writeMolecule(molecule)
+        @@mdl_writer.close
+        
+        writer.toString
+      end
+      
+      # Returns a CDK <tt>Molecule</tt> by parsing <tt>smiles</tt>.
+      def self.read_smiles(smiles)
+        @@smiles_parser.parseSmiles(smiles)
+      end
+      
+      # Returns a SMILES string based on the structure of the indicated
+      # CDK <tt>molecule</tt>.
+      def self.get_smiles(molecule)
+        @@smiles_generator.createSMILES(molecule)
+      end
+      
+      # Returns a SMILES string by parsing the <tt>molfile</tt> string.
+      def self.molfile_to_smiles(molfile)
+        get_smiles(read_molfile(molfile))
+      end
+      
+      # Returns a molfiles STRING by parsing <tt>smiles</tt>.
+      def self.smiles_to_molfile(smiles)
+        get_molfile(read_smiles(smiles))
+      end
+      
+    end
+    
+    # 2-D coordinate generation.
+    class XY
+      @@sdg = StructureDiagramGenerator.new    
+      
+      # Assigns 2-D coordinates to the indicated <tt>molfile</tt> string.
+      def self.coordinate_molfile(molfile)
+        mol = coordinate_molecule(Lang.read_molfile(molfile))
+        
+        Lang.get_molfile(mol)
+      end
+      
+      # Assigns 2-D coordinates to the indicated CDK <tt>molecule</tt>.
+      def self.coordinate_molecule(molecule)
+        @@sdg.setMolecule(molecule)
+        @@sdg.generateCoordinates
+        @@sdg.getMolecule
+      end
+    end
+    
+    # Raster and SVG 2-D molecular images.
+    class Image
+    
+      # 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)
+        ImageKit.writePNG(Lang.read_molfile(molfile), 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>molfile</tt>.
+      def self.molfile_to_svg(molfile, path_to_svg, width, height)
+        ImageKit.writeSVG(Lang.read_molfile(molfile), 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>molfile</tt>.
+      def self.molfile_to_jpg(molfile, path_to_jpg, width, height)
+        ImageKit.writeJPG(Lang.read_molfile(molfile), 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>smiles</tt>. Coordinates are automatically
+      # assigned.
+      def self.smiles_to_png(smiles, path_to_png, width, height)
+        mol = XY.coordinate_molecule(Lang.read_smiles(smiles))
+        
+        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>smiles</tt>. Coordinates are automatically
+      # assigned.
+      def self.smiles_to_svg(smiles, path_to_svg, width, height)
+        mol = XY.coordinate_molecule(Lang.read_smiles(smiles))
+        
+        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>smiles</tt>. Coordinates are automatically
+      # assigned.
+      def self.smiles_to_jpg(smiles, path_to_jpg, width, height)
+        mol = XY.coordinate_molecule(Lang.read_smiles(smiles))
+        
+        ImageKit.writeJPG(mol, width, height, path_to_jpg)
+      end
+    end
+  end
+end

data/test/test.rb

@@ -15,33 +15,115 @@
 # 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'))
+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
 
-SmilesParser = import('org.openscience.cdk.smiles.SmilesParser')
+MoleculeFactory = import 'org.openscience.cdk.templates.MoleculeFactory'
 
-# A very simple test suite.
+# A very simple test suite. Woefully incomplete. Just exercises the API.
 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)
+  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    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    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"
+  end
+  
+  def test_read_molfile
+    mol = Lang.read_molfile(@benzene)
     
     assert_equal(6, mol.getAtomCount)
   end
+  
+  def test_write_molfile
+    molecule = MoleculeFactory.makeIndole
+    molfile = Lang.get_molfile(molecule)
+    
+    assert_not_equal(0, molfile.length)
+  end
+  
+  def test_read_smiles
+    molecule = Lang.read_smiles('c1ccccc1')
+    
+    assert_equal(6, molecule.getAtomCount)
+  end
+  
+  def test_write_smiles
+    smiles = Lang.get_smiles(MoleculeFactory.makeBenzene)
+    
+    assert_equal('c1ccccc1', smiles)
+  end
+  
+  def test_molfile_to_smiles
+    smiles = Lang.molfile_to_smiles(@benzene)
+    
+    assert_equal('c1ccccc1', smiles)
+  end
+  
+  def test_smiles_to_molfile
+    molfile = Lang.smiles_to_molfile('c1ccccc1')
+    
+    assert_not_equal(0, molfile.length)
+  end
+  
+  def test_coordinate_molecule
+    indole = MoleculeFactory.makeIndole
+    XY.coordinate_molecule(indole)
+  end
+  
+  def test_coordinate_molfile
+    molfile = XY.coordinate_molfile(XY.coordinate_molfile(@benzene))
+  end
+ 
+  def test_molfile_to_png
+    Image.molfile_to_png(XY.coordinate_molfile(@benzene), 'output/benzene.png', 200, 200)
+  end
+  
+  def test_molfile_to_svg
+    Image.molfile_to_svg(XY.coordinate_molfile(@benzene), 'output/benzene.svg', 200, 200)
+  end
+  
+  def test_molfile_to_jpg
+    Image.molfile_to_jpg(XY.coordinate_molfile(@benzene), 'output/benzene.jpg', 200, 200)
+  end
+  
+  def test_smiles_to_png
+    Image.smiles_to_png('Clc1ccccc1', 'output/chlorobenzene.png', 200, 200)
+  end
+  
+  def test_smiles_to_svg
+    Image.smiles_to_svg('Clc1ccccc1', 'output/chlorobenzene.svg', 200, 200)
+  end
+  
+  def test_smiles_to_jpg
+    Image.smiles_to_jpg('Clc1ccccc1', 'output/chlrobenzene.jpg', 200, 200)
+  end
 end
 

metadata

@@ -3,8 +3,8 @@ 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
+  version: 0.2.0
+date: 2006-09-24 00:00:00 -07:00
 summary: A Ruby wrapper for the Chemistry Development Kit
 require_paths: 
 - lib
@@ -33,8 +33,10 @@ files:
 - README
 - lib/rcdk.rb
 - lib/java.rb
+- lib/util.rb
 - test/test.rb
-- java/cdk-20060714.jar
+- java/lib/cdk-20060714.jar
+- java/lib/structure-cdk-0.1.2.jar
 test_files: []
 
 rdoc_options: []