bio-isoelectric_point 0.1.1 → 0.1.2

data/Gemfile

@@ -1,14 +1,9 @@
 source "http://rubygems.org"
-# Add dependencies required to use the gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
 
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
+#development dependencies
 group :development do
-  gem "shoulda", ">= 0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.1"
-  gem "rcov", ">= 0"
-  gem "bio", ">= 1.4.1"
+  gem "shoulda", "~> 2.11.3"
+  gem "bundler", "~> 1.1.rc.7"
+  gem "jeweler","~> 1.8.3"
+  gem "bio", ">= 1.4.2"
 end

data/README.rdoc

@@ -2,17 +2,15 @@
 
 The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge.
 
-This library is a ruby implementation for estimating the isoelectric point of a protein, based on the bioperl’s approach. It can be installed as a bioruby-plugin.
-
-Support for the following Pka sets is available
+This library is a Ruby implementation for estimating the isoelectric point of a protein.
 
+The following Pka sets are supported
     * dtaselect
     * emboss
     * rodwell
     * wikipedia
     * sillero
-
-You can also create a custom Pka set as shown in the example
+    *Custom Pka sets are also supported
 
 == Installation
 
@@ -23,43 +21,40 @@ You can also create a custom Pka set as shown in the example
  gem uninstall bio-isoelectric_point
  
 == Usage
-
-	require 'bio-isoelectric_point'
-
-	protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
-
- 	#what is the protein charge at ph 14?
- 	charge = protein_seq.charge_at(14)     #=>-2.999795857467562
-
- 	#calculate the pH using dtaselect pka set and round off to 3 decimal places
- 	isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3)   #=>8.219
-
-	 # calculate the iep ph with a custom set
-	 custom_pka_set = { "N_TERMINUS" => 8.1,
-	            "K" => 10.1,
-	            "R" => 12.1,
-	            "H" => 6.4,
-	            "C_TERMINUS" => 3.15,
-	            "D" => 4.34,
-	            "E" => 4.33,
-	            "C" => 8.33,
-	            "Y" => 9.5
-	          }
-	 iep_ph = protein_seq.isoelectric_point(custom_pka_set, 3)   #=> 8.193
-	
+ require 'bio-isoelectric_point'
+
+ #create  a protein sequence amino acid object
+ protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
+
+ #what is the protein charge at ph 14?
+ charge = protein_seq.charge_at(14)     #=>-2.999795857467562
+
+ #calculate the pH using dtaselect pka set and round off to 3 decimal places
+ isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3) #=>8.219
+
+ #calculate the iep ph with a custom set
+ custom_pka_set = { "N_TERMINUS" => 8.1,
+                    "C_TERMINUS" => 3.15,
+                             "K" => 10.1,
+                             "R" => 12.1,
+                             "H" => 6.4,
+                             "D" => 4.34,
+                             "E" => 4.33,
+                             "C" => 8.33,
+                             "Y" => 9.5
+                  }
+ iep_ph = protein_seq.isoelectric_point(custom_pka_set, 3) #=> 8.193
 
 == Contributing to bio-isoelectric_point
  
 * 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
 * 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)2011 George Githinji. See LICENSE.txt for
-further details.
+Copyright (c)2011 George Githinji.
+See LICENSE.txt for more details.
 

data/Rakefile

@@ -29,20 +29,20 @@ Jeweler::RubygemsDotOrgTasks.new
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
+  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
-end
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |test|
+  #test.libs << 'test'
+  #test.pattern = 'test/**/test_*.rb'
+  #test.verbose = true
+#end
 
 task :default => :test
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bio-isoelectric_point.gemspec

@@ -4,14 +4,14 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-isoelectric_point}
-  s.version = "0.1.1"
+  s.name = "bio-isoelectric_point"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["George Githinji", "Pascal Betz"]
-  s.date = %q{2011-01-30}
-  s.description = %q{A bioruby plugin for calculating the isoelectric point of a protein }
-  s.email = %q{georgkam@gmail.com}
+  s.date = "2012-02-25"
+  s.description = "A bioruby plugin for calculating the isoelectric point of a protein "
+  s.email = "georgkam@gmail.com"
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -32,41 +32,31 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/test_bio-isoelectric_point.rb"
   ]
-  s.homepage = %q{http://github.com/GeorgeG/bioruby-isoelectric_point}
+  s.homepage = "http://github.com/GeorgeG/bioruby-isoelectric_point"
   s.licenses = ["Ruby"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
-  s.summary = %q{A bioruby plugin for calculating the isoelectric point and the charge of a protein sequence.}
-  s.test_files = [
-    "test/aa_test.rb",
-    "test/extensions_test.rb",
-    "test/helper.rb",
-    "test/test_bio-isoelectric_point.rb"
-  ]
+  s.rubygems_version = "1.8.17"
+  s.summary = "A bioruby plugin for calculating the isoelectric point and the charge of a protein sequence."
 
   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<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.1"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_development_dependency(%q<shoulda>, ["~> 2.11.3"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.1.rc.7"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
     else
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<shoulda>, ["~> 2.11.3"])
+      s.add_dependency(%q<bundler>, ["~> 1.1.rc.7"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
     end
   else
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<shoulda>, ["~> 2.11.3"])
+    s.add_dependency(%q<bundler>, ["~> 1.1.rc.7"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
   end
 end
 

data/lib/bio-isoelectric_point.rb

@@ -1,10 +1,8 @@
 require 'bio'
-
 ['pka_data', 'extensions', 'aa'].each do |name|
   require File.join(File.expand_path(File.dirname(__FILE__)), 'isoelectric_point',"#{name}")
 end
 
-
 #   protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
 #
 # 	#what is the protein charge at ph 14?
@@ -12,8 +10,6 @@ end
 #
 # 	#calculate the pH using dtaselect pka set and round off to 3 decimal places
 # 	isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3)   #=>8.219
-#  
-#   puts charge
-#   puts isoelectric_point
 #
-#  
+#   puts charge
+#   puts isoelectric_point:

data/lib/isoelectric_point/aa.rb

@@ -12,7 +12,6 @@ module Bio
       # pka_name_or_set: the name of a PKA set or a custom PKA set
       # places: specify the number of decimal places the value should be rounded to.
       # loop_limit: how many iterations should be made to find the point. You should not need to tweak this.
-	#TODO to be renamed to isoelectric_point to preserve clarity
       def isoelectric_point(pka_name_or_set = 'dtaselect', places = 2, loop_limit = 100)
         loops = 0
         ph = 7.5
@@ -33,7 +32,6 @@ module Bio
 
       # Calculate the charge of the sequence at a given ph
       # As a second argument you can pass the name of the PKA set or a custom PKA set
-
       def charge_at(ph, pka_name_or_set = 'dtaselect')
         ['K', 'R', 'H'].inject(partial_charge(select_pka(pka_name_or_set)['N_TERMINUS'], ph)) do |memo, item|
           memo += partial_charge(select_pka(pka_name_or_set)[item], ph) * charged_residue_frequencies[item]
@@ -67,7 +65,6 @@ module Bio
         end
       end
 
-      #
       # Select a PKA set according to the name or supply a custom set.
       # Raises ArgumentError if the name can not be mapped to a Pka set.
       # If the argument is a String it is used as a key to lookup the set,
@@ -84,5 +81,3 @@ module Bio
     end #class AA
   end #class Sequence
 end #module Bio
-#include a new class Bio::AA::Index for Pkas? suggestes by tokiashiki katayama
-

data/lib/isoelectric_point/pka_data.rb

@@ -1,6 +1,5 @@
 module Bio
   class Sequence
-
     #It would be better to have a class for pKa, compatible with Bio::AAindex indices.Bio::AAindex
     class PkaData
       PKAS = {
@@ -58,3 +57,5 @@ module Bio
     end
   end
 end
+#Refactor this to a class Bio::AA::Index for Pkas? suggestion by Toshiaki Katayama
+

data/test/aa_test.rb

@@ -1,10 +1,6 @@
-
- #require 'helper'
 require File.join(File.expand_path(File.dirname(__FILE__)),'helper')
 
-# include Bio::Sequence
 class AATest < Test::Unit::TestCase
-
   context 'some known sequences' do
     setup do
       # Values are taken from http://isoelectric.ovh.org/

data/test/extensions_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require File.join(File.expand_path(File.dirname(__FILE__)),'helper')
 class ExtensionsTest < Test::Unit::TestCase
   context 'float' do
     setup do

data/test/helper.rb

@@ -1,4 +1,4 @@
-require 'rubygems'
+#require 'rubygems'
 require 'bundler'
 begin
   Bundler.setup(:default, :development)
@@ -13,6 +13,3 @@ require 'shoulda'
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-isoelectric_point'
-
-class Test::Unit::TestCase
-end

data/test/test_bio-isoelectric_point.rb

@@ -1,4 +1,4 @@
-require 'helper'
+require File.join(File.expand_path(File.dirname(__FILE__)),'helper')
 
 class TestBioIsoelectricPoint < Test::Unit::TestCase
    

metadata

@@ -1,104 +1,69 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-isoelectric_point
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 1
-  version: 0.1.1
+version: !ruby/object:Gem::Version
+  version: 0.1.2
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - George Githinji
 - Pascal Betz
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-01-30 00:00:00 +03:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-02-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &2156641380 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.11.3
   type: :development
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2156641380
+- !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &2156640700 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
+      - !ruby/object:Gem::Version
+        version: 1.1.rc.7
   type: :development
   prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2156640700
+- !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &2156640180 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 5
-        - 1
-        version: 1.5.1
-  type: :development
-  prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
+      - !ruby/object:Gem::Version
+        version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2156640180
+- !ruby/object:Gem::Dependency
   name: bio
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &2156639700 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 4
-        - 1
-        version: 1.4.1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *id005
-description: "A bioruby plugin for calculating the isoelectric point of a protein "
+  version_requirements: *2156639700
+description: ! 'A bioruby plugin for calculating the isoelectric point of a protein '
 email: georgkam@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - Gemfile
 - LICENSE.txt
 - README.rdoc
@@ -113,41 +78,33 @@ files:
 - test/extensions_test.rb
 - test/helper.rb
 - test/test_bio-isoelectric_point.rb
-has_rdoc: true
 homepage: http://github.com/GeorgeG/bioruby-isoelectric_point
-licenses: 
+licenses:
 - Ruby
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: -1228718005813956698
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -602066681349865312
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.8.17
 signing_key: 
 specification_version: 3
-summary: A bioruby plugin for calculating the isoelectric point and the charge of a protein sequence.
-test_files: 
-- test/aa_test.rb
-- test/extensions_test.rb
-- test/helper.rb
-- test/test_bio-isoelectric_point.rb
+summary: A bioruby plugin for calculating the isoelectric point and the charge of
+  a protein sequence.
+test_files: []