bio-hydropathy 0.0.1

data/.document

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

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 "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J Woodcroft
+
+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.rdoc

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+= bio-hydropathy
+
+Simple biogem to calculate amino acid hydropathy. They are calculated as proposed by
+
+    Jack Kyte, Russell F. Doolittle,
+    A simple method for displaying the hydropathic character of 
+    a protein, Journal of Molecular Biology,
+    Volume 157, Issue 1, 5 May 1982, Pages 105-132
+
+Example:
+
+    Bio::Sequence::AA.new('ACD').hydrophopathy_profile #=> [1.8, 2.5, -3.5]
+
+== Contributing to bio-bio-hydropathy
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. 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-hydropathy"
+  gem.homepage = "http://github.com/wwood/bioruby-hydropathy"
+  gem.license = "MIT"
+  gem.summary = %Q{Hydropathy scale for BioRuby}
+  gem.description = %Q{Hydropathy scale for BioRuby}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J Woodcroft"]
+  # 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
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-hydropathy #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-hydropathy.rb

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+require 'bio/sequence/aa/hydropathy'

data/lib/bio/sequence/aa/hydropathy.rb

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+require 'bio'
+
+module Bio
+  class Sequence
+    class AA
+      # Return an array of hydrophobicities, as defined by Kyte and Doolittle
+      def hydrophopathy_profile
+        profile = []
+        seq.each_char do |letter|
+          profile.push Bio::AminoAcid::Data::KYTE_DOOLITTLE_HYDROPATHY_SCALE[letter]
+        end
+        profile
+      end
+      
+      # Sum of hydropathy values for each amino acid, divided by the length of the protein
+      def grand_average_of_hydropathy
+        hydrophopathy_profile.inject{|sum,x| sum + x }.to_f/seq.length
+      end
+      alias_method :gravy, :grand_average_of_hydropathy
+    end
+  end
+  
+  
+  class AminoAcid
+    module Data
+      # Jack Kyte, Russell F. Doolittle,
+      # A simple method for displaying the hydropathic character of 
+      # a protein, Journal of Molecular Biology,
+      # Volume 157, Issue 1, 5 May 1982, Pages 105-132, ISSN 0022-2836, 10.1016/0022-2836(82)90515-0.
+      KYTE_DOOLITTLE_HYDROPATHY_SCALE = {
+        'A' => 1.8,
+        'C' => 2.5,
+        'D' => -3.5,
+        'E' => -3.5,
+        'F' => 2.8,
+        'G' => -0.4,
+        'H' => -3.2,
+        'I' => 4.5,
+        'K' => -3.9,
+        'L' => 3.8,
+        'M' => 1.9,
+        'N' => -3.5,
+        'P' => -1.6,
+        'Q' => -3.5,
+        'R' => -4.5,
+        'S' => -0.8,
+        'T' => -0.7,
+        'U' => 0.0,
+        'V' => 4.2,
+        'W' => -0.9,
+        'Y' => -1.3,
+          
+        'B' => -3.5,
+        'X' => -0.49,
+        'Z' => -3.5,
+      }
+    end
+  end
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-hydropathy'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-hydropathy.rb

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+require 'helper'
+
+class TestBioBioGravy < Test::Unit::TestCase
+  should "hydrophobicity" do
+    assert_equal [1.8, 2.5, -3.5], Bio::Sequence::AA.new('ACD').hydrophopathy_profile
+  end
+  
+  should "gravy" do 
+    assert_equal -4, (Bio::Sequence::AA.new('ACDCD').grand_average_of_hydropathy*100).to_i
+    assert_equal -4, (Bio::Sequence::AA.new('ACDCD').gravy*100).to_i
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: bio-hydropathy
+version: !ruby/object:Gem::Version 
+  hash: 29
+  prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-01-26 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id001
+  name: shoulda
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  version_requirements: *id002
+  name: bundler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 6
+        - 4
+        version: 1.6.4
+  version_requirements: *id003
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id004
+  name: rcov
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  version_requirements: *id005
+  name: bio
+  prerelease: false
+description: Hydropathy scale for BioRuby
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-hydropathy.rb
+- lib/bio/sequence/aa/hydropathy.rb
+- test/helper.rb
+- test/test_bio-hydropathy.rb
+homepage: http://github.com/wwood/bioruby-hydropathy
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: Hydropathy scale for BioRuby
+test_files: []
+