bio-protparam 0.1.0

data/.document

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

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"
+
+gem "bio", ">= 1.4.2"
+
+group :development, :test do
+  gem "minitest", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.4"
+end

data/LICENSE.txt

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+Copyright (c) 2012 hryk <hiroyuki@1vq9.com>
+
+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-protparam
+
+[![Build Status](https://secure.travis-ci.org/hryk/bioruby-protparam.png)](http://travis-ci.org/hryk/bioruby-protparam)
+
+`bio-protparam` adds Bio::Protparam class. Bio::Protparam has same interface and
+function as Bio::Tools::Protparam class of BioPerl, except that it calculate
+parameters instead of throwing query to Expasy protparam tool.
+
+**Note: this software is under active development!**
+
+## Installation
+
+```sh
+    gem install bio-protparam
+```
+
+## Usage
+
+```ruby
+    require 'bio-protparam'
+    
+    protparam = Bio::Protparam.new("MYNNYNLCHIRTINWEEIITGPSAMYSYVY...")
+    # Return Mw
+    protparam.molecular_weight
+    # Return pI
+    protparam.theorettical_pI
+
+```
+
+The API doc is on [rdoc.info](http://rdoc.info/github/hryk/bioruby-protparam/). For
+more code examples see the test files in the source tree.
+
+## 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-protparam](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 hryk. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-protparam
+
+{<img
+src="https://secure.travis-ci.org/hryk/bioruby-protparam.png"
+/>}[http://travis-ci.org/#!/hryk/bioruby-protparam]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-protparam
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-protparam'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/hryk/bioruby-protparam
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== 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 http://biogems.info/index.html#bio-protparam
+
+== Copyright
+
+Copyright (c) 2012 hryk. 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.name = "bio-protparam"
+  gem.homepage = "http://github.com/hryk/bioruby-protparam"
+  gem.license = "MIT"
+  gem.summary = %Q{A Protparam compatible utility for BioRuby.}
+  gem.description = %Q{Bio::Protparam has same interface and function as Bio::Tools::Protparam class of BioPerl, except that it calculate parameters instead of throwing query to Expasy protparam tool.}
+  gem.email = "hiroyuki@1vq9.com"
+  gem.authors = ["hryk"]
+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-protparam #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/bio-protparam.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/util/protparam'
+

data/lib/bio/util/protparam.rb

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+# encoding: utf-8
+#
+#
+# = bio/appl/protparam.rb - A Class to Calculate Protein Parameters.
+#
+# Copyright:: Copyright (C) 2012
+#             Hiroyuki Nakamura <hiroyuki@1vq9.com>
+# License::   The Ruby License
+#
+require 'rational'
+
+module Bio
+  ##
+  # == Description
+  #
+  # Bio::Protparam is a class for calculating protein paramesters. This class
+  # has a similer interface to BioPerl's Bio::Tools::Protparam. However, it
+  # calculate parameters instead of throwing a query to Expasy's {Protparam
+  # tool}[http://web.expasy.org/protparam/]{[1]}[rdoc-label:1] as Bio::Tools::Protparam does.
+  #
+  class Protparam
+
+    # {IUPAC codes}[http://www.bioinformatics.org/sms2/iupac.html] for amino acids.
+    IUPAC_CODE = {
+      :I => "Ile",
+      :V => "Val",
+      :L => "Leu",
+      :F => "Phe",
+      :C => "Cys",
+      :M => "Met",
+      :A => "Ala",
+      :G => "Gly",
+      :T => "Thr",
+      :W => "Trp",
+      :S => "Ser",
+      :Y => "Tyr",
+      :P => "Pro",
+      :H => "His",
+      :E => "Glu",
+      :Q => "Gln",
+      :D => "Asp",
+      :N => "Asn",
+      :K => "Lys",
+      :R => "Arg",
+      :U => "Sec",
+      :O => "Pyl",
+      :B => "Asx",
+      :Z => "Glx",
+      :X => "Xaa"
+    }
+
+    # Dipeptide instability weight value for calculating instability index of proteins {[10]}[rdoc-label:10].
+    DIWV = {
+      :W => {
+        :W => 1.0,   :C => 1.0,   :M => 24.68, :H => 24.68, :Y => 1.0, :F => 1.0,    :Q => 1.0,
+        :N => 13.34, :I => 1.0,   :R => 1.0,   :D => 1.0,   :P => 1.0, :T => -14.03, :K => 1.0,
+        :E => 1.0,   :V => -7.49, :S => 1.0,   :G => -9.37, :A => -14.03, :L => 13.34
+      },
+      :C => {
+        :W => 24.68, :C => 1.0, :M => 33.6, :H => 33.6, :Y => 1.0, :F => 1.0, :Q => -6.54, :N => 1.0,
+        :I => 1.0, :R => 1.0, :D => 20.26, :P => 20.26, :T => 33.6, :K => 1.0, :E => 1.0, :V => -6.54,
+        :S => 1.0, :G => 1.0, :A => 1.0, :L => 20.26
+      },
+      :M => {
+        :W => 1.0, :C => 1.0, :M => -1.88, :H => 58.28, :Y => 24.68, :F => 1.0, :Q => -6.54,
+        :N => 1.0, :I => 1.0, :R => -6.54, :D => 1.0, :P => 44.94, :T => -1.88, :K => 1.0, :E => 1.0,
+        :V => 1.0, :S => 44.94, :G => 1.0, :A => 13.34, :L => 1.0
+      },
+      :H => {
+        :W => -1.88, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 44.94, :F => -9.37, :Q => 1.0,
+        :N => 24.68, :I => 44.94, :R => 1.0, :D => 1.0, :P => -1.88, :T => -6.54, :K => 24.68,
+        :E => 1.0, :V => 1.0, :S => 1.0, :G => -9.37, :A => 1.0, :L => 1.0
+      },
+      :Y => {
+        :W => -9.37, :C => 1.0, :M => 44.94, :H => 13.34, :Y => 13.34, :F => 1.0, :Q => 1.0,
+        :N => 1.0, :I => 1.0, :R => -15.91, :D => 24.68, :P => 13.34, :T => -7.49, :K => 1.0,
+        :E => -6.54, :V => 1.0, :S => 1.0, :G => -7.49, :A => 24.68, :L => 1.0
+      },
+      :F => {
+        :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 33.6, :F => 1.0, :Q => 1.0, :N => 1.0,
+        :I => 1.0, :R => 1.0, :D => 13.34, :P => 20.26, :T => 1.0, :K => -14.03, :E => 1.0,
+        :V => 1.0, :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :Q => {
+        :W => 1.0, :C => -6.54, :M => 1.0, :H => 1.0, :Y => -6.54, :F => -6.54, :Q => 20.26,
+        :N => 1.0, :I => 1.0, :R => 1.0, :D => 20.26, :P => 20.26, :T => 1.0, :K => 1.0, :E => 20.26,
+        :V => -6.54, :S => 44.94, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :N => {
+        :W => -9.37, :C => -1.88, :M => 1.0, :H => 1.0,    :Y => 1.0,   :F => -14.03, :Q => -6.54,
+        :N => 1.0,   :I => 44.94, :R => 1.0, :D => 1.0,    :P => -1.88, :T => -7.49,  :K => 24.68,
+        :E => 1.0,   :V => 1.0,   :S => 1.0, :G => -14.03, :A => 1.0,   :L => 1.0
+      },
+      :I => {
+        :W => 1.0,   :C => 1.0, :M => 1.0, :H => 13.34, :Y => 1.0, :F => 1.0,   :Q => 1.0, :N => 1.0,
+        :I => 1.0,   :R => 1.0, :D => 1.0, :P => -1.88, :T => 1.0, :K => -7.49, :E => 44.94,
+        :V => -7.49, :S => 1.0, :G => 1.0, :A => 1.0,   :L => 20.26
+      },
+      :R => {
+        :W => 58.28, :C => 1.0, :M => 1.0, :H => 20.26, :Y => -6.54, :F => 1.0, :Q => 20.26,
+        :N => 13.34, :I => 1.0, :R => 58.28, :D => 1.0, :P => 20.26, :T => 1.0, :K => 1.0, :E => 1.0,
+        :V => 1.0, :S => 44.94, :G => -7.49, :A => 1.0, :L => 1.0
+      },
+      :D => {
+        :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => -6.54, :Q => 1.0, :N => 1.0,
+        :I => 1.0, :R => -6.54, :D => 1.0, :P => 1.0, :T => -14.03, :K => -7.49, :E => 1.0,
+        :V => 1.0, :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :P => {
+        :W => -1.88, :C => -6.54, :M => -6.54, :H => 1.0, :Y => 1.0, :F => 20.26, :Q => 20.26,
+        :N => 1.0, :I => 1.0, :R => -6.54, :D => -6.54, :P => 20.26, :T => 1.0, :K => 1.0, :E => 18.38,
+        :V => 20.26, :S => 20.26, :G => 1.0, :A => 20.26, :L => 1.0
+      },
+      :T => {
+        :W => -14.03, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 13.34, :Q => -6.54,
+        :N => -14.03, :I => 1.0, :R => 1.0, :D => 1.0, :P => 1.0, :T => 1.0, :K => 1.0, :E => 20.26,
+        :V => 1.0, :S => 1.0, :G => -7.49, :A => 1.0, :L => 1.0
+      },
+      :K => {
+        :W => 1.0, :C => 1.0, :M => 33.6, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 24.68, :N => 1.0,
+        :I => -7.49, :R => 33.6, :D => 1.0, :P => -6.54, :T => 1.0, :K => 1.0, :E => 1.0, :V => -7.49,
+        :S => 1.0, :G => -7.49, :A => 1.0, :L => -7.49
+      },
+      :E => {
+        :W => -14.03, :C => 44.94, :M => 1.0, :H => -6.54, :Y => 1.0, :F => 1.0, :Q => 20.26,
+        :N => 1.0, :I => 20.26, :R => 1.0, :D => 20.26, :P => 20.26, :T => 1.0, :K => 1.0, :E => 33.6,
+        :V => 1.0, :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :V => {
+        :W => 1.0, :C => 1.0, :M => 1.0, :H => 1.0, :Y => -6.54, :F => 1.0, :Q => 1.0, :N => 1.0,
+        :I => 1.0, :R => 1.0, :D => -14.03, :P => 20.26, :T => -7.49, :K => -1.88, :E => 1.0,
+        :V => 1.0, :S => 1.0, :G => -7.49, :A => 1.0, :L => 1.0
+      },
+      :S => {
+        :W => 1.0, :C => 33.6, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 20.26, :N => 1.0,
+        :I => 1.0, :R => 20.26, :D => 1.0, :P => 44.94, :T => 1.0, :K => 1.0, :E => 20.26, :V => 1.0,
+        :S => 20.26, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :G => {
+        :W => 13.34, :C => 1.0, :M => 1.0, :H => 1.0, :Y => -7.49, :F => 1.0, :Q => 1.0, :N => -7.49,
+        :I => -7.49, :R => 1.0, :D => 1.0, :P => 1.0, :T => -7.49, :K => -7.49, :E => -6.54,
+        :V => 1.0, :S => 1.0, :G => 13.34, :A => -7.49, :L => 1.0
+      },
+      :A => {
+        :W => 1.0, :C => 44.94, :M => 1.0, :H => -7.49, :Y => 1.0, :F => 1.0, :Q => 1.0, :N => 1.0,
+        :I => 1.0, :R => 1.0, :D => -7.49, :P => 20.26, :T => 1.0, :K => 1.0, :E => 1.0, :V => 1.0,
+        :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0
+      },
+      :L => {
+        :W => 24.68, :C => 1.0, :M => 1.0, :H => 1.0, :Y => 1.0, :F => 1.0, :Q => 33.6, :N => 1.0,
+        :I => 1.0, :R => 20.26, :D => 1.0, :P => 20.26, :T => 1.0, :K => -7.49, :E => 1.0, :V => 1.0,
+        :S => 1.0, :G => 1.0, :A => 1.0, :L => 1.0
+      }
+    }
+
+    # Estemated half-life of N-terminal residue of a protein.
+    HALFLIFE = {
+      :ecoli => {
+        :I => 600,
+        :V => 600,
+        :L => 2,
+        :F => 2,
+        :C => 600,
+        :M => 600,
+        :A => 600,
+        :G => 600,
+        :T => 600,
+        :W => 2,
+        :S => 600,
+        :Y => 2,
+        :P => 600,
+        :H => 600,
+        :E => 600,
+        :Q => 600,
+        :D => 600,
+        :N => 600,
+        :K => 2,
+        :R => 2,
+        :U => 600
+      },
+      :mammalian => {
+        :A => 264,
+        :R => 60,
+        :N => 84,
+        :D => 66,
+        :C => 72,
+        :Q => 48,
+        :E => 60,
+        :G => 30,
+        :H => 210,
+        :I => 1200,
+        :L => 330,
+        :K => 78,
+        :M => 1800,
+        :F => 66,
+        :P => 1200,
+        :S => 114,
+        :T => 432,
+        :W => 168,
+        :Y => 168,
+        :V => 6000
+      },
+      :yeast => {
+        :A => 1200,
+        :R => 2,
+        :N => 3,
+        :D => 3,
+        :C => 1200,
+        :Q => 10,
+        :E => 30,
+        :G => 1200,
+        :H => 10,
+        :I => 30,
+        :L => 3,
+        :K => 3,
+        :M => 1200,
+        :F => 3,
+        :P => 1200,
+        :S => 1200,
+        :T => 1200,
+        :W => 3,
+        :Y => 10,
+        :V => 1200
+      }
+    }
+
+    ##  TOP-IDP
+    ##
+    ##  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2676888/
+    ##
+    # TOP_IDP = {
+    #   :I => -0.486,
+    #   :V => -0.121,
+    #   :L => -0.326,
+    #   :F => -0.697,
+    #   :C => 0.02,
+    #   :M => -0.397,
+    #   :A => 0.06,
+    #   :G => 0.166,
+    #   :T => 0.059,
+    #   :W => -0.884,
+    #   :S => 0.341,
+    #   :Y => -0.510,
+    #   :P => 0.987,
+    #   :H => 0.303,
+    #   :E => 0.736,
+    #   :Q => 0.318,
+    #   :D => 0.192,
+    #   :N => 0.007,
+    #   :K => 0.586,
+    #   :R => 0.180,
+    #   :U => 0.02
+    # }
+
+    # Hydropathy values for amino acids {[12]}[rdoc-label:12].
+    HYDROPATHY = {
+      :I => 4.5 ,
+      :V => 4.2 ,
+      :L => 3.8 ,
+      :F => 2.8 ,
+      :C => 2.5 ,
+      :M => 1.9 ,
+      :A => 1.8 ,
+      :G => -0.4,
+      :T => -0.7,
+      :W => -0.9,
+      :S => -0.8,
+      :Y => -1.3,
+      :P => -1.6,
+      :H => -3.2,
+      :E => -3.5,
+      :Q => -3.5,
+      :D => -3.5,
+      :N => -3.5,
+      :K => -3.9,
+      :R => -4.5,
+      :U => 2.5
+    }
+
+    # {Average isotopic masses of amino acids}[http://web.expasy.org/findmod/findmod_masses.html#AA]
+    AVERAGE_MASS = {
+      :I => 113.1594,
+      :V => 99.1326,
+      :L => 113.1594,
+      :F => 147.1766,
+      :C => 103.1388,
+      :M => 131.1926,
+      :A => 71.0788,
+      :G => 57.0519,
+      :T => 101.1051,
+      :W => 186.2132,
+      :S => 87.0782,
+      :Y => 163.1760,
+      :P => 97.1167,
+      :H => 137.1411,
+      :E => 129.1155,
+      :Q => 128.1307,
+      :D => 115.0886,
+      :N => 114.1038,
+      :K => 128.1741,
+      :R => 156.1875,
+      :U => 150.0388
+    }
+    WATER_MASS = 18.01524
+
+    # Atomic composition of amino acids.
+    ATOM = {
+      :I => {:C => 6, :H => 13, :O => 2, :N => 1, :S => 0}, # C6H13NO2
+      :V => {:C => 5, :H => 11, :O => 2, :N => 1, :S => 0}, # C5H11NO2
+      :L => {:C => 6, :H => 13, :O => 2, :N => 1, :S => 0}, # C6H13NO2
+      :F => {:C => 9, :H => 11, :O => 2, :N => 1, :S => 0}, # C9H11NO2
+      :C => {:C => 3, :H => 7 , :O => 2, :N => 1, :S => 1}, # C3H7NO2S
+      :M => {:C => 5, :H => 11 ,:O => 2, :N => 1, :S => 1}, # C5H11NO2S
+      :A => {:C => 3, :H => 7 , :O => 2, :N => 1, :S => 0}, # C3H7NO2
+      :G => {:C => 2, :H => 5 , :O => 2, :N => 1, :S => 0}, # C2H5NO2
+      :T => {:C => 4, :H => 9 , :O => 3, :N => 1, :S => 0}, # C4H9NO3
+      :W => {:C => 11,:H => 12, :O => 2, :N => 2, :S => 0}, # C11H12N2O2
+      :S => {:C => 3, :H => 7 , :O => 3, :N => 1, :S => 0}, # C3H7NO3
+      :Y => {:C => 9, :H => 11, :O => 3, :N => 1, :S => 0}, # C9H11NO3
+      :P => {:C => 5, :H => 9 , :O => 2, :N => 1, :S => 0}, # C5H9NO2
+      :H => {:C => 6, :H => 9 , :O => 2, :N => 3, :S => 0}, # C6H9N3O2
+      :E => {:C => 5, :H => 9 , :O => 4, :N => 1, :S => 0}, # C5H9NO4
+      :Q => {:C => 5, :H => 10, :O => 3, :N => 2, :S => 0}, # C5H10N2O3
+      :D => {:C => 4, :H => 7 , :O => 4, :N => 1, :S => 0}, # C4H7NO4
+      :N => {:C => 4, :H => 8 , :O => 3, :N => 2, :S => 0}, # C4H8N2O3
+      :K => {:C => 6, :H => 14, :O => 2, :N => 2, :S => 0}, # C6H14N2O2
+      :R => {:C => 6, :H => 14, :O => 2, :N => 4, :S => 0}, # C6H14N4O2
+    }
+
+    ##
+    #
+    # pK value from Bjellqvist, et al {[13]}[rdoc-label:13].
+    # Taking into account the decrease in pK differences
+    # between acids and bases when going from water
+    # to 8 M urea, a value of 7.5 has been assigned to the
+    # N-terminal residue .
+    #
+    PK = {
+      :cterm => {
+        :normal => 3.55, :D => 4.55, :E => 4.75
+      },
+      :nterm => {
+        :A => 7.59, :M => 7.00, :S => 6.93,  :P => 8.36,
+        :T => 6.82, :V => 7.44, :E => 7.70 , :G => 7.50
+      },
+      :internal => {
+        :D => 4.05, :E => 4.45, :H => 5.98, :C => 9.0,
+        :Y => 10.0, :K => 10.0, :R => 12.0
+      }
+    }
+
+    def initialize(seq)
+      if seq.kind_of?(String) && Bio::Sequence.guess(seq) == Bio::Sequence::AA
+        # TODO: has issue.
+        @seq = Bio::Sequence::AA.new seq
+      elsif seq.kind_of? Bio::Sequence::AA
+        @seq = seq
+      elsif seq.kind_of?(Bio::Sequence) &&
+        seq.guess.kind_of?(Bio::Sequence::AA)
+        @seq = seq.guess
+      else
+        raise ArgumentError, "sequence must be an AA sequence"
+      end
+    end
+
+    ##
+    #
+    # Return the number of negative amino acids (D and E) in an AA sequence.
+    #
+    def num_neg
+      @num_neg ||= @seq.count("DE")
+    end
+
+    ##
+    #
+    # Return the number of positive amino acids (R and K) in an AA sequence.
+    #
+    def num_pos
+      @num_neg ||= @seq.count("RK")
+    end
+
+    ##
+    #
+    # Return the number of residues in an AA sequence.
+    #
+    def amino_acid_number
+      @seq.length
+    end
+
+    ##
+    #
+    # Return the number of atoms in a sequence. If type is given, return the
+    # number of specific atoms in a sequence.
+    #
+    def total_atoms(type=nil)
+      if !type.nil?
+        type = type.to_sym
+        if /^(?:C|H|O|N|S){1}$/ !~ type.to_s
+          raise ArgumentError, "type must be C/H/O/N/S/nil(all)"
+        end
+      end
+      num_atom = {:C => 0,
+                  :H => 0,
+                  :O => 0,
+                  :N => 0,
+                  :S => 0}
+      each_aa do |aa|
+        ATOM[aa].each do |t, num|
+          num_atom[t] += num
+        end
+      end
+      num_atom[:H] = num_atom[:H] - 2 * (amino_acid_number - 1)
+      num_atom[:O] = num_atom[:O] - (amino_acid_number - 1)
+      if type.nil?
+        num_atom.values.inject(0){|prod, num| prod += num }
+      else
+        num_atom[type]
+      end
+    end
+
+    ##
+    #
+    # Return the number of carbons.
+    #
+    def num_carbon
+      @num_carbon ||= total_atoms :C
+    end
+
+    def num_hydrogen
+      @num_hydrogen ||= total_atoms :H
+    end
+
+    ##
+    #
+    # Return the number of nitrogens.
+    #
+    def num_nitro
+      @num_nitro ||= total_atoms :N
+    end
+
+    ##
+    #
+    # Return the number of oxygens.
+    #
+    def num_oxygen
+      @num_oxygen ||= total_atoms :O
+    end
+
+    ##
+    #
+    # Return the number of sulphurs.
+    #
+    def num_sulphur
+      @num_sulphur ||= total_atoms :S
+    end
+
+    ##
+    #
+    # Calculate molecular weight of an AA sequence.
+    #
+    # _Protein Mw is calculated by the addition of average isotopic masses of
+    # amino acids in the protein and the average isotopic mass of one water
+    # molecule._
+    #
+    def molecular_weight
+      @mw ||= begin
+                mass = WATER_MASS
+                each_aa do |aa|
+                  mass += AVERAGE_MASS[aa.to_sym]
+                end
+                (mass * 10).floor().to_f / 10
+              end
+    end
+
+    ##
+    #
+    # Claculate theoretical pI for an AA sequence with bisect algorithm.
+    # pK value by Bjelqist, et al. is used to calculate pI.
+    #
+    def theoretical_pI
+      charges = []
+      residue_count().each do |residue|
+        charges << charge_proc(residue[:positive],
+                               residue[:pK],
+                               residue[:num])
+      end
+      round(solve_pI(charges), 2)
+    end
+
+    ##
+    #
+    # Return estimated half_life of an AA sequence.
+    #
+    # _The half-life is a prediction of the time it takes for half of the
+    # amount of protein in a cell to disappear after its synthesis in the
+    # cell. ProtParam relies on the "N-end rule", which relates the half-life
+    # of a protein to the identity of its N-terminal residue; the prediction
+    # is given for 3 model organisms (human, yeast and E.coli)._
+    #
+    def half_life(species=nil)
+      n_end = @seq[0].chr.to_sym
+      if species
+        HALFLIFE[species][n_end]
+      else
+        {
+          :ecoli     => HALFLIFE[:ecoli][n_end],
+          :mammalian => HALFLIFE[:mammalian][n_end],
+          :yeast     => HALFLIFE[:yeast][n_end]
+        }
+      end
+    end
+
+    ##
+    #
+    # Calculate instability index of an AA sequence.
+    #
+    # _The instability index provides an estimate of the stability of your
+    # protein in a test tube. Statistical analysis of 12 unstable and 32
+    # stable proteins has revealed [7] that there are certain dipeptides, the
+    # occurence of which is significantly different in the unstable proteins
+    # compared with those in the stable ones. The authors of this method have
+    # assigned a weight value of instability to each of the 400 different
+    # dipeptides (DIWV)._
+    #
+    def instability_index
+      @instability_index ||=
+        begin
+          instability_sum = 0.0
+          i = 0
+          while @seq[i+1] != nil
+            aa, next_aa = [@seq[i].chr.to_sym, @seq[i+1].chr.to_sym]
+            if DIWV.key?(aa) && DIWV[aa].key?(next_aa)
+              instability_sum += DIWV[aa][next_aa]
+            end
+            i += 1
+          end
+          round((10.0/amino_acid_number.to_f) * instability_sum, 2)
+        end
+    end
+
+    ##
+    #
+    # Return wheter the sequence is stable or not as String (stable/unstable).
+    #
+    # _Protein whose instability index is smaller than 40 is predicted as
+    # stable, a value above 40 predicts that the protein may be unstable._
+    #
+    #
+    def stability
+      (instability_index <= 40) ? "stable" : "unstable"
+    end
+
+    ##
+    #
+    # Return true if the sequence is stable.
+    #
+    def stable?
+      (instability_index <= 40) ? true : false
+    end
+
+    ##
+    #
+    # Calculate aliphatic index of an AA sequence.
+    #
+    # _The aliphatic index of a protein is defined as the relative volume
+    # occupied by aliphatic side chains (alanine, valine, isoleucine, and
+    # leucine). It may be regarded as a positive factor for the increase of
+    # thermostability of globular proteins._
+    #
+    def aliphatic_index
+      aa_map = aa_comp_map
+      @aliphatic_index ||=  round(aa_map[:A]        +
+                                  2.9 * aa_map[:V]  +
+                                  (3.9 * (aa_map[:I] + aa_map[:L])), 2)
+    end
+
+    ##
+    #
+    # Calculate GRAVY score of an AA sequence.
+    #
+    # _The GRAVY(Grand Average of Hydropathy) value for a peptide or protein
+    # is calculated as the sum of hydropathy values [9] of all the amino acids,
+    # divided by the number of residues in the sequence._
+    #
+    def gravy
+      @gravy ||= begin
+                   hydropathy_sum = 0.0
+                   each_aa do |aa|
+                     hydropathy_sum += HYDROPATHY[aa]
+                   end
+                   round(hydropathy_sum / @seq.length.to_f, 3)
+                 end
+    end
+
+    ##
+    #
+    # Calculate the percentage composition of an AA sequence as a Hash object.
+    # It return percentage of a given amino acid if aa_code is not nil.
+    #
+    def aa_comp(aa_code=nil)
+      if aa_code.nil?
+        aa_map = {}
+        IUPAC_CODE.keys.each do |k|
+          aa_map[k] = 0.0
+        end
+        aa_map.update(aa_comp_map){|k,_,v| round(v, 1) }
+      else
+        round(aa_comp_map[aa_code], 1)
+      end
+    end
+
+    private
+
+    def aa_comp_map
+      @aa_comp_map ||=
+        begin
+          aa_map  = {}
+          aa_comp = {}
+          sum = 0
+          each_aa do |aa|
+            if aa_map.key? aa
+              aa_map[aa] += 1
+            else
+              aa_map[aa] = 1
+            end
+            sum += 1
+          end
+          aa_map.each {|aa, count| aa_comp[aa] = (Rational(count,sum) * 100).to_f }
+          aa_comp
+        end
+    end
+
+    def each_aa
+      @seq.each_byte do |x|
+        yield x.chr.to_sym
+      end
+    end
+
+    def positive? residue
+      (residue == "H" || residue == "R" || residue == "K")
+    end
+
+    #
+    # Return proc calculating charge of a residue.
+    #
+    def charge_proc positive, pK, num
+      if positive
+        lambda {|ph|
+          num.to_f / (1.0 + 10.0 ** (ph - pK))
+        }
+      else
+        lambda {|ph|
+          (-1.0 * num.to_f) / (1.0 + 10.0 ** (pK - ph))
+        }
+      end
+    end
+
+    #
+    # Transform AA sequence into residue count
+    #
+    def residue_count
+      counted = []
+      # N-terminal
+      n_term = @seq[0].chr
+      if PK[:nterm].key? n_term.to_sym
+        counted << {
+          :num => 1,
+          :residue => n_term.to_sym,
+          :pK => PK[:nterm][n_term.to_sym],
+          :positive => positive?(n_term)
+        }
+      elsif PK[:normal].key? n_term.to_sym
+        counted << {
+          :num => 1,
+          :residue => n_term.to_sym,
+          :pK => PK[:normal][n_term.to_sym],
+          :positive => positive?(n_term)
+        }
+      end
+      # Internal
+      tmp_internal = {}
+      @seq[1,(@seq.length-2)].each_byte do |x|
+        aa = x.chr.to_sym
+        if PK[:internal].key? aa
+          if tmp_internal.key? aa
+            tmp_internal[aa][:num] += 1
+          else
+            tmp_internal[aa] = {
+              :num => 1,
+              :residue => aa,
+              :pK => PK[:internal][aa],
+              :positive => positive?(aa.to_s)
+            }
+          end
+        end
+      end
+      tmp_internal.each do |aa, val|
+        counted << val
+      end
+      # C-terminal
+      c_term = @seq[-1].chr
+      if PK[:cterm].key? c_term.to_sym
+        counted << {
+          :num => 1,
+          :residue => c_term.to_sym,
+          :pK => PK[:cterm][c_term.to_sym],
+          :positive => positive?(c_term)
+        }
+      end
+      counted
+    end
+
+    #
+    # Solving pI value with bisect algorithm.
+    #
+    def solve_pI charges
+      state = {
+        :ph => 0.0,
+        :charges => charges,
+        :pI => nil,
+        :ph_prev => 0.0,
+        :ph_next => 14.0,
+        :net_charge => 0.0
+      }
+      error = false
+      # epsilon means precision [pI = pH +_ E]
+      epsilon = 0.001
+
+      loop do
+        # Reset net charge
+        state[:net_charge] = 0.0
+        # Calculate net charge
+        state[:charges].each do |charge_proc|
+          state[:net_charge] += charge_proc.call state[:ph]
+        end
+
+        # Something is wrong - pH is higher than 14
+        if state[:ph] >= 14.0
+          error = true
+          break
+        end
+
+        # Making decision
+        temp_ph = 0.0
+        if state[:net_charge] <= 0.0
+          temp_ph    = state[:ph]
+          state[:ph] = state[:ph] - ((state[:ph] - state[:ph_prev]) / 2.0)
+          state[:ph_next] = temp_ph
+        else
+          temp_ph    = state[:ph]
+          state[:ph] = state[:ph] + ((state[:ph_next] - state[:ph]) / 2.0)
+          state[:ph_prev] = temp_ph
+        end
+
+        if (state[:ph] - state[:ph_prev] < epsilon) &&
+          (state[:ph_next] - state[:ph] < epsilon)
+          state[:pI] = state[:ph]
+          break
+        end
+      end
+
+      if !state[:pI].nil? && !error
+        state[:pI]
+      else
+        raise "Failed to Calc pI: pH is higher than 14"
+      end
+    end
+
+    def round(num, ndigits=0)
+      (num * (10 ** ndigits)).round().to_f / (10 ** ndigits).to_f
+    end
+
+    # --------------------------------
+    # :section: References
+    #
+    #
+    # 1. Protein Identification and Analysis Tools on the ExPASy Server;
+    #    Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R.,
+    #    Appel R.D., Bairoch A.; (In) John M. Walker (ed): The Proteomics
+    #    Protocols Handbook, Humana Press (2005). pp. 571-607
+    # 2. Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995)
+    #    How to measure and predict the molar absorption coefficient of a
+    #    protein. Protein Sci. 11, 2411-2423.
+    # 3. Edelhoch, H. (1967) Spectroscopic determination of tryptophan and
+    #    tyrosine in proteins. Biochemistry 6, 1948-1954.
+    # 4. Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein
+    #    extinction coefficients from amino acid sequence data. Anal. Biochem.
+    #    182:319-326(1989).
+    # 5. Bachmair, A., Finley, D. and Varshavsky, A. (1986) In vivo half-life
+    #    of a protein is a function of its amino-terminal residue. Science 234,
+    #    179-186.
+    # 6. Gonda, D.K., Bachmair, A., Wunning, I., Tobias, J.W., Lane, W.S. and
+    #    Varshavsky, A. J. (1989) Universality and structure of the N-end rule.
+    #    J. Biol. Chem. 264, 16700-16712.
+    # 7. Tobias, J.W., Shrader, T.E., Rocap, G. and Varshavsky, A. (1991) The
+    #    N-end rule in bacteria. Science 254, 1374-1377.
+    # 8. Ciechanover, A. and Schwartz, A.L. (1989) How are substrates
+    #    recognized by the ubiquitin-mediated proteolytic system? Trends Biochem.
+    #    Sci. 14, 483-488.
+    # 9. Varshavsky, A. (1997) The N-end rule pathway of protein degradation.
+    #    Genes Cells 2, 13-28.
+    # 10. Guruprasad, K., Reddy, B.V.B. and Pandit, M.W. (1990) Correlation
+    #     between stability of a protein and its dipeptide composition: a novel
+    #     approach for predicting in vivo stability of a protein from its primary
+    #     sequence. Protein Eng. 4,155-161.
+    # 11. Ikai, A.J. (1980) Thermostability and aliphatic index of globular
+    #     proteins. J. Biochem. 88, 1895-1898.
+    # 12. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying
+    #     the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
+    # 13. Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
+    #     Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing positions
+    #     of polypeptides in immobilized pH gradients can be predicted from their
+    #     amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
+    #
+    # --------------------------------
+  end
+end