bio-chembl 0.1.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>bioruby-chembl</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+	</natures>
+</projectDescription>

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", ">= 1.0.0"
+  gem "jeweler", "~> 1.8.3"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+  gem "curb", ">= 0"
+  gem "nokogiri", "~> 1.5.5"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    curb (0.8.0)
+    git (1.2.5)
+    jeweler (1.8.3)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+      rdoc
+    json (1.7.3)
+    nokogiri (1.5.5)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
+    shoulda (3.0.1)
+      shoulda-context (~> 1.0.0)
+      shoulda-matchers (~> 1.0.0)
+    shoulda-context (1.0.0)
+    shoulda-matchers (1.0.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (>= 1.0.0)
+  curb
+  jeweler (~> 1.8.3)
+  nokogiri (~> 1.5.5)
+  rdoc (~> 3.12)
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2012 Mitsuteru Nakao
+
+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.md

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+# bio-chembl
+
+[![Build Status](https://secure.travis-ci.org/nakao/bioruby-chembl.png)](http://travis-ci.org/nakao/bioruby-chembl)
+
+[ChEMBL REST Web Service API](https://www.ebi.ac.uk/chembldb/ws) client, parser and container classes. 
+
+REST API Client
+
+```ruby
+    # Show a web service URI
+    BioChEMBL::REST::ChEMBL_URI.compound("CHEMBL1")
+
+    # GET the XML data of the ChEMBL ID CHEMBL1 
+    api = BioChEMBL::REST.new
+    api.compound("CHEMBL1")
+```
+
+Parser and container
+
+```ruby
+    cpd = BioChEMBL::Compound.find("CHEMBL1")
+    cpd.chemblId #=> "CHEMBL1"
+    cpd.slimes
+   
+    ba = cpd.bioactivities
+   
+    assay = BioChEMBL::Assay.find("CHEMBL1217643")
+    assay.bioactivities[0].target
+    assay.bioactivities[0].parent_compound
+```
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-chembl
+```
+
+## Usage
+
+```ruby
+    require 'bio-chembl'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/nakao/bio-chembl
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Todo list
+
+* BioChEMBL::Target.find_by_refesq method.
+* JSON output support (parser and address).
+* ChEMBL RDF support.
+* Local REST API server with local ChEMBL database.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-chembl](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Mitsuteru Nakao. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-chembl"
+  gem.homepage = "http://github.com/nakao/bio-chembl"
+  gem.license = "MIT"
+  gem.summary = %Q{ChEMBL REST API Client, Parser and Container}
+  gem.description = %Q{BioRuby plugin for ChEMBL REST API Client, Parser and Container classes}
+  gem.email = "mitsuteru.nakao@gmail.com"
+  gem.authors = ["Mitsuteru Nakao"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-chembl #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/bio-chembl.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{bio-chembl}
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Mitsuteru Nakao"]
+  s.date = %q{2012-07-22}
+  s.description = %q{BioRuby plugin for ChEMBL REST API Client, Parser and Container classes}
+  s.email = %q{mitsuteru.nakao@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.md"
+  ]
+  s.files = [
+    ".document",
+    ".project",
+    ".travis.yml",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.md",
+    "Rakefile",
+    "VERSION",
+    "bio-chembl.gemspec",
+    "lib/bio-chembl.rb",
+    "lib/bio-chembl/assay.rb",
+    "lib/bio-chembl/bioactivity.rb",
+    "lib/bio-chembl/chembl.rb",
+    "lib/bio-chembl/chemblid.rb",
+    "lib/bio-chembl/compound.rb",
+    "lib/bio-chembl/datamodel.rb",
+    "lib/bio-chembl/rest_api_server.rb",
+    "lib/bio-chembl/rest_client.rb",
+    "lib/bio-chembl/target.rb",
+    "test/helper.rb",
+    "test/test_bio-chembl-assay.rb",
+    "test/test_bio-chembl-assay.sh",
+    "test/test_bio-chembl-chemblid.rb",
+    "test/test_bio-chembl-chemblid.sh",
+    "test/test_bio-chembl-compound.rb",
+    "test/test_bio-chembl-compound.sh",
+    "test/test_bio-chembl-rest-client.rb",
+    "test/test_bio-chembl-rest-client.sh",
+    "test/test_bio-chembl-target.rb",
+    "test/test_bio-chembl-target.sh",
+    "test/test_bio-chembl.rb",
+    "test/test_bio-chembl.sh"
+  ]
+  s.homepage = %q{http://github.com/nakao/bio-chembl}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{ChEMBL REST API Client, Parser and Container}
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<curb>, [">= 0"])
+      s.add_development_dependency(%q<nokogiri>, ["~> 1.5.5"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, [">= 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<curb>, [">= 0"])
+      s.add_dependency(%q<nokogiri>, ["~> 1.5.5"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, [">= 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<curb>, [">= 0"])
+    s.add_dependency(%q<nokogiri>, ["~> 1.5.5"])
+  end
+end
+

data/lib/bio-chembl.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-chembl/chembl.rb'
+

data/lib/bio-chembl/assay.rb

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+require 'nokogiri'
+require 'bio-chembl/datamodel.rb'
+require 'bio-chembl/bioactivity.rb'
+
+
+module BioChEMBL
+  
+
+  
+  # ChEMBL Assay
+  #
+  # Data XML
+  # <assay>
+  #  <chemblId>CHEMBL1217643</chemblId>
+  #  <assayType>B</assayType>
+  #  <journal>Bioorg. Med. Chem. Lett.</journal>
+  #  <assayOrganism>Homo sapiens</assayOrganism>
+  #  <assayStrain>Unspecified</assayStrain>
+  #  <assayDescription>Inhibition of human hERG</assayDescription>
+  #  <numBioactivities>1</numBioactivities>
+  # </assay>
+  #
+  # 
+  class Assay
+    extend BioChEMBL::DataModel
+    
+    ATTRIBUTES = [
+      :chemblId,
+      :assayType,
+      :journal,
+      :assayOrganism,
+      :assayStrain,
+      :assayDescription,
+      :numBioactivities
+      ]
+      
+    set_attr_accessors(ATTRIBUTES)
+
+    
+    def self.parse(str)
+      case str
+      when /^</
+        format = 'xml'
+      when /^\{/
+        format = 'json'
+      else
+        raise ArgumentError, "Unexpected file format: #{str.inspect}" 
+      end
+      begin
+        eval "self.parse_#{format}(str)"
+      rescue 
+        raise NoMethodError
+      end  
+    end 
+    
+    def self.parse_xml(str)
+      xml = Nokogiri::XML(str)
+      this = new  
+      eval set_attr_values(ATTRIBUTES)
+      this
+    end 
+    
+    def self.parse_json(str)
+      raise NotImplementedError
+    end
+    
+    def self.parse_rdf(str)
+      raise NotImplementedError
+    end
+    
+    def self.find(chemblId)
+      self.parse_xml(REST.new.assays(chemblId))
+    end   
+    
+     
+    # new
+    def initialize(chemblId = nil)
+      @chemblId = chemblId
+    end 
+    
+    # Resolve the compound data by given ChEMBL ID
+    def resolve
+      resolved = self.class.find(@chemblId)
+      ATTRIBUTES.each do |attr|
+        eval "@#{attr} = resolved.#{attr}"
+      end
+    end
+    
+    # ChEMBL Bioactivity
+    def bioactivities
+      BioChEMBL::Bioactivity.parse_list_xml(REST.new.assays(@chemblId, 'bioactivities'))
+    end
+    
+  end
+
+end

data/lib/bio-chembl/bioactivity.rb

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+require 'nokogiri'
+require 'bio-chembl/datamodel.rb'
+
+
+module BioChEMBL
+
+  # BioChEMBL::Bioactivity
+  #
+  # Data XML
+  # <list>
+  #   <bioactivity>
+  #     <parent__cmpd__chemblid>CHEMBL1214402</parent__cmpd__chemblid>
+  #     <ingredient__cmpd__chemblid>CHEMBL1214402</ingredient__cmpd__chemblid>
+  #     <target__chemblid>CHEMBL240</target__chemblid>
+  #     <target__confidence>9</target__confidence>
+  #     <target__name>HERG</target__name>
+  #     <reference>Bioorg. Med. Chem. Lett., (2010) 20:15:4359</reference>
+  #     <name__in__reference>26</name__in__reference>
+  #     <organism>Homo sapiens</organism>
+  #     <bioactivity__type>IC50</bioactivity__type>
+  #     <activity__comment>Unspecified</activity__comment>
+  #     <operator>=</operator>
+  #     <units>nM</units>
+  #     <assay__chemblid>CHEMBL1217643</assay__chemblid>
+  #     <assay__type>B</assay__type>
+  #     <assay__description>Inhibition of human hERG</assay__description>
+  #     <value>5900</value>
+  #   </bioactivity>
+  # </list>
+  #
+  # Usage
+  # 
+  class Bioactivity
+    extend BioChEMBL::DataModel
+      
+    ATTRIBUTES = [
+          :parent__cmpd__chemblid,
+          :ingredient__cmpd__chemblid,
+          :target__chemblid,
+          :target__confidence,
+          :target__name,
+          :reference,
+          :name__in__reference,
+          :organism,
+          :bioactivity__type,
+          :activity__comment,
+          :operator,
+          :units,
+          :assay__chemblid,
+          :assay__type,
+          :assay__description,
+          :value
+        ]
+        
+    set_attr_accessors(ATTRIBUTES)
+      
+    def self.parse(str)
+      case str
+      when /^</
+        format = 'xml'
+      when /^\{/
+        format = 'json'
+      else
+        raise ArgumentError, "Unexpected file format: #{str.inspect}" 
+      end
+      begin
+        eval "self.parse_#{format}(str)"
+      rescue 
+        raise NoMethodError
+      end  
+    end 
+      
+    def self.parse_xml(str)
+      xml = Nokogiri::XML(str)
+      this = new
+      eval set_attr_values(ATTRIBUTES)
+      this
+    end
+      
+    # XML
+    # <list><bioactivity> ...
+    def self.parse_list_xml(str)
+      xmls = Nokogiri::XML(str)
+      xmls.xpath("/list/bioactivity").map do |cpd|
+        self.parse_xml(cpd.to_s)
+      end
+    end
+      
+    def self.parse_json(str)
+      raise NotImplementedError
+    end
+      
+    def self.parse_rdf(str)
+      raise NotImplementedError
+    end
+    
+    def parent_compound
+      require 'bio-chembl/compound.rb'
+      BioChEMBL::Compound.find(@parent__cmpd__chemblid)
+    end
+    
+    def target
+      require 'bio-chembl/target.rb'
+      BioChEMBL::Target.find(@target__chemblid)
+    end
+       
+    def assay
+      require 'bio-chembl/assay.rb'
+      BioChEMBL::Assay.find(@assay__chemblid)
+    end
+  end
+
+end