bio-isoelectric_point 0.1.0 → 0.1.1

data/LICENSE.txt

@@ -1,3 +1,3 @@
-Copyright (c) 2010 George Githinji
+Copyright (c) 2011 George Githinji
 
-bioruby-isoelectric_point library can be freely distributed under the same terms as Ruby.
+bioruby-isoelectric_point library can be freely distributed under the same terms as Ruby.

data/README.rdoc

@@ -2,11 +2,11 @@
 
 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 calculating the isoelectric point of a protein, based on the bioperl’s approach. It can be installed as a bioruby-plugin.
+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
 
-    * dta_select
+    * dtaselect
     * emboss
     * rodwell
     * wikipedia
@@ -29,10 +29,10 @@ You can also create a custom Pka set as shown in the example
 	protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
 
  	#what is the protein charge at ph 14?
- 	charge = protein_seq.calculate_charge_at(14)     #=>-2.999795857467562
+ 	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.calculate_iep('dtaselect', 3)   #=>8.219
+ 	#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,
@@ -45,7 +45,7 @@ You can also create a custom Pka set as shown in the example
 	            "C" => 8.33,
 	            "Y" => 9.5
 	          }
-	 iep_ph = protein_seq.calculate_iep(custom_pka_set, 3)   #=> 8.193
+	 iep_ph = protein_seq.isoelectric_point(custom_pka_set, 3)   #=> 8.193
 	
 
 == Contributing to bio-isoelectric_point
@@ -60,6 +60,6 @@ You can also create a custom Pka set as shown in the example
 
 == Copyright
 
-Copyright (c) 2010 George Githinji. See LICENSE.txt for
+Copyright (c)2011 George Githinji. See LICENSE.txt for
 further details.
 

data/Rakefile

@@ -15,8 +15,8 @@ Jeweler::Tasks.new do |gem|
   gem.name = "bio-isoelectric_point"
   gem.homepage = "http://github.com/GeorgeG/bioruby-isoelectric_point"
   gem.license = "Ruby"
-  gem.summary = %Q{A bioruby plugin for calculating the isoelectric point of a protein. It can be installed as a bioruby plugin.}
-  gem.description = %Q{The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge. }
+  gem.summary = %Q{A bioruby plugin for calculating the isoelectric point and the charge of a protein sequence.}
+  gem.description = %Q{A bioruby plugin for calculating the isoelectric point of a protein }
   gem.email = "georgkam@gmail.com"
   gem.authors = ["George Githinji","Pascal Betz"]
   # Include your dependencies below. Runtime dependencies are required when using your gem,

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bio-isoelectric_point.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-isoelectric_point}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["George Githinji", "Pascal Betz"]
-  s.date = %q{2010-12-25}
-  s.description = %q{The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge. }
+  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.extra_rdoc_files = [
     "LICENSE.txt",
@@ -36,7 +36,7 @@ Gem::Specification.new do |s|
   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 of a protein. It can be installed as a bioruby plugin.}
+  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",

data/lib/bio-isoelectric_point.rb

@@ -1,5 +1,19 @@
 require 'bio'
 
 ['pka_data', 'extensions', 'aa'].each do |name|
-  require File.join(File.dirname(__FILE__), 'isoelectric_point', name)
-end
+  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?
+# 	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
+#  
+#   puts charge
+#   puts isoelectric_point
+#
+#  

data/lib/isoelectric_point/aa.rb

@@ -12,12 +12,13 @@ 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.
-      def calculate_iep(pka_name_or_set = 'dtaselect', places = 2, loop_limit = 100)
+	#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
         step = 3.5
         begin
-          current_charge = calculate_charge_at(ph, pka_name_or_set)
+          current_charge = charge_at(ph, pka_name_or_set)
           if current_charge > 0
             ph += step
           else
@@ -32,7 +33,8 @@ 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 calculate_charge_at(ph, pka_name_or_set = 'dtaselect')
+
+      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]
         end -
@@ -67,7 +69,7 @@ module Bio
 
       #
       # 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.
+      # 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,
       # if it's a Hash then it's assumed a custom set has been supplied.
       def select_pka(pka_name_or_set = 'dtaselect')
@@ -81,4 +83,6 @@ module Bio
       end #select_pka
     end #class AA
   end #class Sequence
-end #module Bio
+end #module Bio
+#include a new class Bio::AA::Index for Pkas? suggestes by tokiashiki katayama
+

data/lib/isoelectric_point/pka_data.rb

@@ -1,5 +1,7 @@
 module Bio
   class Sequence
+
+    #It would be better to have a class for pKa, compatible with Bio::AAindex indices.Bio::AAindex
     class PkaData
       PKAS = {
         'dtaselect' => { 'N_TERMINUS' => 8.0,
@@ -55,4 +57,4 @@ module Bio
       }.freeze
     end
   end
-end
+end

data/test/aa_test.rb

@@ -1,5 +1,6 @@
 
-require 'test_helper'
+ #require 'helper'
+require File.join(File.expand_path(File.dirname(__FILE__)),'helper')
 
 # include Bio::Sequence
 class AATest < Test::Unit::TestCase
@@ -28,7 +29,7 @@ class AATest < Test::Unit::TestCase
     should 'calculate iep' do
       places = 2
       @known.each do |sequence, expected|
-        actual = Bio::Sequence::AA.new(sequence).calculate_iep('dtaselect', places)
+        actual = Bio::Sequence::AA.new(sequence).isoelectric_point('dtaselect', places)
         assert_equal expected.round_to_places(places), actual, "Expected the iep to be #{expected} but was #{actual} for #{sequence}"
       end
     end
@@ -59,10 +60,10 @@ class AATest < Test::Unit::TestCase
     end
 
     should "calculates the isolectric point to 0 places" do
-      assert_equal 11, @sequence.calculate_iep('dtaselect', 0)
+      assert_equal 11, @sequence.isoelectric_point('dtaselect', 0)
     end
     should "calculates the isolectric pointto 3 places" do
-      assert_equal 10.603, @sequence.calculate_iep('dtaselect', 3)
+      assert_equal 10.603, @sequence.isoelectric_point('dtaselect', 3)
     end
 
     context 'use a custom pka set' do
@@ -79,22 +80,22 @@ class AATest < Test::Unit::TestCase
                   }
       end
       should 'accept a custom pka set and use it for calculation' do
-        assert_equal 10.106, @sequence.calculate_iep(@custom, 3)
+        assert_equal 10.106, @sequence.isoelectric_point(@custom, 3)
       end
 
       should 'raise when no result can be found due to a invalid set' do
         @custom['K'] = 20
         assert_raises RuntimeError do
-          @sequence.calculate_iep(@custom, 3)
+          @sequence.isoelectric_point(@custom, 3)
         end
       end
     end
     context 'use another pka set' do
       should 'work with all provided sets without raising' do
         Bio::Sequence::PkaData::PKAS.keys.each do |key|
-          @sequence.calculate_iep(key, 3, 25)
+          @sequence.isoelectric_point(key, 3, 25)
         end
       end
     end
   end
-end
+end

data/test/extensions_test.rb

@@ -14,4 +14,4 @@ class ExtensionsTest < Test::Unit::TestCase
       assert_equal 1.12, @float.round_to_places(2)
     end
   end
-end
+end

data/test/test_bio-isoelectric_point.rb

@@ -1,7 +1,5 @@
 require 'helper'
 
 class TestBioIsoelectricPoint < Test::Unit::TestCase
-  should "create a real test" do
    
-  end
 end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - George Githinji
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-12-25 00:00:00 +03:00
+date: 2011-01-30 00:00:00 +03:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -89,7 +89,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: *id005
-description: "The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge. "
+description: "A bioruby plugin for calculating the isoelectric point of a protein "
 email: georgkam@gmail.com
 executables: []
 
@@ -127,7 +127,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -2384793528143520988
+      hash: -1228718005813956698
       segments: 
       - 0
       version: "0"
@@ -145,7 +145,7 @@ rubyforge_project:
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
-summary: A bioruby plugin for calculating the isoelectric point of a protein. It can be installed as a bioruby plugin.
+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