rbtk 0.1.0-jruby

data/LICENSE

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+The MIT License
+
+Copyright (c) 2007 Richard L. Apodaca
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+ 

data/README

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+= Rubidium: Cheminformatics for Ruby
+
+{Project Home Page}[http://rbtk.rubyforge.org]
+
+{RubyForge Project}[http://rubyforge.org/projects/rbtk]
+
+== DESCRIPTION
+
+Rubidium is a full-featured cheminformatics scripting environment for Ruby. It provides a clean, well-documented interface to the best open source cheminformatics software.
+
+== Dependencies
+
+* {JRuby 1.0.0}[http://jruby.codehaus.org]
+
+== Download
+
+Rubidium can be {downloaded from RubyForge}[http://rubyforge.org/frs/?group_id=4671]
+
+== Installation
+
+<tt>$ jruby -S gem install rbtk</tt>
+
+== Examples
+
+===Convert Benzene SMILES into InChI
+  require 'rubidium/lang'
+
+  c = Rubidium::Converter.new
+
+  c.set_formats 'smi', 'inchi'
+  c.convert 'c1ccccc1' => "InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H"
+
+===Create a CDK molecule from a SMILES string and count its atoms.
+
+  require 'cdk/lang'
+
+  r = CDK::SmilesReader.new
+  mol = r.read 'c1ccccc1'
+
+  mol.atom_count # => 6
+
+== Authors
+
+Copyright (C) 2007 {Richard L. Apodaca}[http://depth-first.com]
+
+== Acknowledgments
+
+This library combines capabilities from a variety of open source projects:
+
+- {Chemistry Development Kit}[http://cdk.sf.net], distributed under the {GNU Lesser GPL}[http://www.opensource.org/licenses/lgpl-license.php]
+
+Many thanks to those contributing to these projects.
+
+Rubidium was made possible with the support of {Metamolecular, LLC}[http://metamolecular.com].
+
+== License
+
+This library is distributed under the MIT License.  Please see the LICENSE[link://files/LICENSE.html] file for more details.
+
+

data/Rakefile

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+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+
+require 'rake'
+require 'rake/testtask'
+require 'rake/rdoctask'
+require 'rake/gempackagetask'
+
+PKG_VERSION = "0.1.0"
+
+desc "Default task"
+task :default => [:test]
+
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/*_test.rb']
+  t.verbose = true
+end
+
+rd = Rake::RDocTask.new do |rdoc|
+      rdoc.rdoc_dir = 'doc'
+      rdoc.title    = "Rubidium: Cheminformatics for Ruby"
+      rdoc.rdoc_files.include('README', 'LICENSE')
+      rdoc.options << '--line-numbers'
+      rdoc.options << '--inline-source'
+      rdoc.options << '--main' << 'README'
+      rdoc.rdoc_files.include('lib/**/*.rb')
+    end
+
+PKG_FILES = FileList[
+  "Rakefile", "README", "LICENSE",
+  "lib/**/*.rb",
+  "test/**/*",
+  "ext/lib/*.jar"
+]
+
+spec = Gem::Specification.new do |s|
+  s.name = 'rbtk'
+  s.version = PKG_VERSION
+  s.author = "Richard L. Apodaca"
+  s.homepage = "http://rubyforge.org/projects/rbtk"
+  s.platform = 'jruby'
+  s.require_path = 'lib'
+  s.autorequire = 'rubidium'
+  s.has_rdoc = true
+  s.files = PKG_FILES
+  s.summary = "The Ruby Cheminformatics Toolkit"
+  s.description = s.summary
+  s.extra_rdoc_files = rd.rdoc_files.reject { |fn| fn =~ /\.rb$/ }.to_a
+  s.rdoc_options = rd.options
+end
+
+Rake::GemPackageTask.new(spec) do |gem|
+  gem.need_tar_gz = true
+  gem.package_files += PKG_FILES
+end

data/lib/cdk.rb

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+=begin
+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+=end
+
+$:.unshift File.join(File.dirname(__FILE__), "..")
+
+require 'java'
+require 'ext/lib/cdk-1.0.1.jar'
+
+# Selected functionality from the Chemistry Development
+# Kit. Convenience layer for commonly-used CDK tasks.
+module CDK
+
+end

data/lib/cdk/lang.rb

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+=begin
+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+=end
+
+$:.unshift File.join(File.dirname(__FILE__), "..")
+
+require 'cdk'
+
+module CDK
+
+  # String-based molfile reader.
+  class MolfileReader
+    import 'java.io.StringReader'
+    import 'org.openscience.cdk.io.MDLReader'
+    import 'org.openscience.cdk.Molecule'
+
+    def initialize
+      @reader = MDLReader.new
+    end
+
+    # Returns the molecule encoded by the given molfile.
+    #
+    # call-seq:
+    #   MolfileReader.read(molfile) => org.openscience.cdk.Molecule
+    #
+    def read molfile
+      @reader.set_reader StringReader.new(molfile)
+      @reader.read Molecule.new
+    end
+  end
+
+  # String-based InChI reader.
+  class InChIReader
+    import 'org.openscience.cdk.inchi.InChIGeneratorFactory'
+    import 'org.openscience.cdk.Molecule'
+
+    def initialize
+      @factory = InChIGeneratorFactory.new
+    end
+
+    # Returns the molecule encoded by the given InChI
+    # string.
+    #
+    # call-seq:
+    #  InChIReader.read(inchi) => org.openscience.cdk.Molecule
+    #
+    def read inchi
+      Molecule.new @factory.getInChIToStructure(inchi).atom_container
+    end
+  end
+
+  # String-based SMILES reader.
+  class SmilesReader
+    import 'org.openscience.cdk.smiles.SmilesParser'
+
+    def initialize
+      @reader = SmilesParser.new
+    end
+
+    # Returns the molecule encoded by the given SMILES
+    # string.
+    #
+    # call-seq:
+    #  InChIReader.read(inchi) => org.openscience.cdk.Molecule
+    #
+    def read smiles
+      @reader.parse_smiles smiles
+    end
+  end
+
+  # String-based molfile writer.
+  class MolfileWriter
+    import 'java.io.StringWriter'
+    import 'org.openscience.cdk.io.MDLWriter'
+
+    def initialize
+      @writer = MDLWriter.new
+    end
+
+    # Returns the molfile representation of the given molecule.
+    #
+    # call-seq:
+    #  MolfileWriter.write(mol) => string
+    #
+    def write mol
+      string_writer = StringWriter.new
+
+      @writer.set_writer string_writer
+      @writer.write_molecule mol
+      @writer.close
+
+      string_writer.to_string
+    end
+  end
+
+  # String-based InChI writer.
+  class InChIWriter
+    import 'org.openscience.cdk.inchi.InChIGeneratorFactory'
+    import 'org.openscience.cdk.tools.HydrogenAdder'
+
+    def initialize
+      @factory = InChIGeneratorFactory.new
+      @hydrogen_adder = HydrogenAdder.new
+    end
+
+    # Returns the InChI representation of the given molecule.
+    #
+    # call-seq:
+    #  InChIWriter.write(mol) => string
+    #
+    def write mol
+      @hydrogen_adder.add_implicit_hydrogens_to_satisfy_valency mol
+      @factory.getInChIGenerator(mol).inchi
+    end
+  end
+
+  # String-based SMILES writer.
+  class SmilesWriter
+    import 'java.io.StringWriter'
+    import 'org.openscience.cdk.io.SMILESWriter'
+
+    def initialize
+      @writer = SMILESWriter.new
+    end
+
+    # Returns the SMILES representation of the given molecule.
+    #
+    #
+    # call-seq:
+    #  SmilesWriter.write(mol) => string
+    #
+    def write mol
+      string_writer = StringWriter.new
+
+      @writer.set_writer string_writer
+      @writer.write mol
+      @writer.close
+
+      string_writer.to_string.strip
+    end
+  end
+end

data/lib/rubidium.rb

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+=begin
+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+=end
+
+# TODO: This file will ultimately be used to determine
+# whether JRuby or MRI is being used. If MRI, then the
+# file 'rubidium/java' will be included, giving the same
+# interface to Java classes and methods as JRuby.
+
+# Main module for Rubidium.
+module Rubidium
+
+end

data/lib/rubidium/lang.rb

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+=begin
+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+=end
+
+$:.unshift File.join(File.dirname(__FILE__), "..")
+
+module Rubidium
+  require 'cdk/lang'
+
+  # A general-purpose molecular language converter.
+  #
+  # Usage:
+  # 
+  #  require 'rubidium/lang'
+  #
+  #  c = Rubidium::Converter.new # Defaults to toolkit = 'CDK'
+  #
+  #  c.set_formats 'smi', 'inchi'
+  #  c.convert 'c1ccccc1' # => "InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H"
+  #  c.molecule # returns the molecule representing benzene
+  #
+  class Converter
+    attr_accessor :molecule
+    attr_reader :in_format
+    attr_reader :out_format
+    attr_reader :toolkit
+
+    # Constructs a CDK converter by default.
+    def initialize(toolkit = 'CDK')
+      @toolkit = toolkit
+      @readers = create_readers
+      @writers = create_writers
+    end
+
+    # Sets the input and output formats for this Converter.
+    # CDK converters recognize the input formats: 'mol'
+    # (MDL V2000 molfile); 'inchi', and 'smi' (SMILES).
+    # Recognized output formats are: 'mol', 'inchi', and
+    # 'smi'.
+    def set_formats in_format, out_format
+      set_in_format in_format
+      set_out_format out_format
+
+      true
+    end
+
+    # Converts given input based on the formats
+    # defined in #set_formats.
+    #
+    # call-seq:
+    #  convert(input) => string
+    #
+    def convert input
+      read input
+      write
+    end
+
+    # Sets the input format to one of the formats
+    # defined in #set_formats.
+    def set_in_format format
+      raise "No input format matching #{format}" unless @readers[format]
+
+      @in_format = format
+    end
+
+    # Sets the output format to one of the formats
+    # defined in #set_formats.
+    def set_out_format format
+      raise "No output format matching #{format}" unless @writers[format]
+
+      @out_format = format
+    end
+
+    # Reads the molecule encoded by +input+ in the format
+    # defined by #in_format.
+    #
+    # call-seq:
+    #  input(input) => boolean
+    #
+    def read input
+      raise "No input format" unless @in_format
+
+      @molecule = @readers[@in_format].read input
+
+      @molecule != nil
+    end
+
+    # Writes the molecule encoded by the previous call to
+    # #read in the format defined by #out_format.
+    #
+    # call-seq:
+    #  write => string
+    #
+    def write
+      raise "No output format" unless @out_format
+
+      @writers[@out_format].write @molecule
+    end
+
+    private
+
+    def create_readers
+      {'mol'   => CDK::MolfileReader.new,
+       'inchi' => CDK::InChIReader.new,
+       'smi'   => CDK::SmilesReader.new}
+    end
+
+    def create_writers
+      {'mol'   => CDK::MolfileWriter.new,
+       'inchi' => CDK::InChIWriter.new,
+       'smi'   => CDK::SmilesWriter.new}
+    end
+  end
+end 

data/test/converter_test.rb

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+# ==================================
+# Rubidium: Cheminformatics for Ruby
+# ==================================
+#
+# Copyright (C) 2007 Richard L. Apodaca
+#
+# http://rbtk.rubyforge.org
+#
+# This library is open source software distributed under
+# the terms of the MIT License. See the LICENSE file for
+# details.
+
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require 'test/unit'
+require 'rubidium/lang'
+
+class TestConverter < Test::Unit::TestCase
+  def test_create_conversion
+    c = Rubidium::Converter.new
+
+    assert_not_nil c
+  end
+
+  def test_set_valid_in_format
+    c = Rubidium::Converter.new
+
+    assert_nothing_raised{c.set_in_format 'smi'}
+    assert_equal 'smi', c.in_format
+  end
+
+  def test_set_invalid_in_format
+    c = Rubidium::Converter.new
+
+    assert_raise(RuntimeError){c.set_in_format 'nonsense'}
+  end
+
+  def test_read_valid_input
+    c = Rubidium::Converter.new
+
+    c.set_in_format 'smi'
+
+    assert_nothing_raised{c.read 'c1ccccc1'}
+
+    assert_not_nil c.molecule
+    assert_equal 6, c.molecule.atom_count
+  end
+
+  def test_read_invalid_input
+    c = Rubidium::Converter.new
+
+    c.set_in_format 'smi'
+
+    assert_raise(NativeException){c.read 'nonsense'}
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.3
+specification_version: 1
+name: rbtk
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+date: 2007-11-06 00:00:00 -08:00
+summary: The Ruby Cheminformatics Toolkit
+require_paths: 
+- lib
+email: 
+homepage: http://rubyforge.org/projects/rbtk
+rubyforge_project: 
+description: The Ruby Cheminformatics Toolkit
+autorequire: rubidium
+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: jruby
+signing_key: 
+cert_chain: 
+post_install_message: 
+authors: 
+- Richard L. Apodaca
+files: 
+- Rakefile
+- README
+- LICENSE
+- lib/rubidium/lang.rb
+- lib/cdk/lang.rb
+- lib/rubidium.rb
+- lib/cdk.rb
+- test/converter_test.rb
+- ext/lib/cdk-1.0.1.jar
+test_files: []
+
+rdoc_options: 
+- --line-numbers
+- --inline-source
+- --main
+- README
+extra_rdoc_files: 
+- README
+- LICENSE
+executables: []
+
+extensions: []
+
+requirements: []
+
+dependencies: []
+