isoelectric_point 0.0.5 → 0.0.6

data/README.rdoc

@@ -1,32 +1,39 @@
 = isoelectric_point
-A ruby class for calculating the isoelectric point of a protein. It's based on bioperl.
-It's currently beeing refactored to fit into bioruby.
+The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge.
 
-== PKA Sets
-The available pka sets are:
+This library is a ruby implementation for calculating the iep of a protein, based on bioperl's approach.
+It can be installed as a gem. It is currently been refactored to fit as a bioruby plugin. 
+
+
+== Supported PKA sets
+Support for the following Pka sets is available
 * dta_select
 * emboss
 * rodwell
 * wikipedia
 * sillero
 
+You can also create a custom Pka set as shown in the example
+
 == Installation
- gem install isoelectric_point
+ gem install 'bio'
+ gem install 'isoelectric_point'
 
 == Usage
+ require 'bio'
  require 'isoelectric_point'
- # Either prefix or include namespace
- include Bio::Sequence
- aa = AA.new("KKGFTCGELA")
+		
+ protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
 
  #what is the protein charge at ph 14?
- charge = aa.calculate_charge_at(14)
+ charge = protein_seq.calculate_charge_at(14)     #=>-2.999795857467562
+
+ #calculate the ph using dtaselect pka set and round off to 3 decimal places
 
- #calculate the ph using dtaselect and round off to 3 decimal places
- ph = aa.calculate_iep('dtaselect', 3)
+ isoelectric_point = protein_seq.calculate_iep('dtaselect', 3)   #=>8.219
 
- # calculate the ph with a custom set
- custom = { "N_TERMINUS" => 8.1,
+ # calculate the iep ph with a custom set
+ custom_pka_set = { "N_TERMINUS" => 8.1,
             "K" => 10.1,
             "R" => 12.1,
             "H" => 6.4,
@@ -36,4 +43,11 @@ The available pka sets are:
             "C" => 8.33,
             "Y" => 9.5
           }
- ph = aa.calculate_iep(custom, 3)
+ iep_ph = protein_seq.calculate_iep(custom, 3)        #=> 8.193 
+
+
+== Authors
+ George Githinji -- KEMRI-Wellcome Trust Research program (georgkam@gmail.com)
+ Pascal Betz     -- Simplificator GmbH 
+
+Copyright (C) 2010 George Githinji

data/lib/isoelectric_point.rb

@@ -1,3 +1,5 @@
+require 'bio'
+
 ['pka_data', 'extensions', 'aa'].each do |name|
   require File.join(File.dirname(__FILE__), 'isoelectric_point', name)
 end

data/lib/isoelectric_point/aa.rb

@@ -1,6 +1,6 @@
 module Bio
-  module Sequence
-    class AA < String
+  class Sequence
+    class AA
       CHARGED_GROUPS = ['K', 'R', 'H', 'D', 'E', 'C', 'Y']
 
       def initialize(sequence)
@@ -74,11 +74,11 @@ module Bio
         if pka_name_or_set.is_a?(Hash)
           pka_name_or_set
         else
-          set = PkaData::PKAS[pka_name_or_set]
+          set = Bio::Sequence::PkaData::PKAS[pka_name_or_set]
           raise ArgumentError.new("Set '#{pka_name_or_set}' is unknown. Please specify one of #{PkaData::PKAS.keys.join(', ')} or pass a custom set") unless set
           set
-        end
-      end
-    end
-  end
-end
+        end #if
+      end #select_pka
+    end #class AA
+  end #class Sequence
+end #module Bio

data/lib/isoelectric_point/pka_data.rb

@@ -1,6 +1,6 @@
 module Bio
-  module Sequence
-    module PkaData
+  class Sequence
+    class PkaData
       PKAS = {
         'dtaselect' => { 'N_TERMINUS' => 8.0,
                           'K' => 10.0,

data/test/aa_test.rb

@@ -1,5 +1,6 @@
 require 'test_helper'
-include Bio::Sequence
+
+# include Bio::Sequence
 class AATest < Test::Unit::TestCase
 
   context 'some known sequences' do
@@ -26,7 +27,7 @@ class AATest < Test::Unit::TestCase
     should 'calculate iep' do
       places = 2
       @known.each do |sequence, expected|
-        actual = AA.new(sequence).calculate_iep('dtaselect', places)
+        actual = Bio::Sequence::AA.new(sequence).calculate_iep('dtaselect', places)
         assert_equal expected.round_to_places(places), actual, "Expected the iep to be #{expected} but was #{actual} for #{sequence}"
       end
     end
@@ -34,26 +35,26 @@ class AATest < Test::Unit::TestCase
 
   should "Raise if not sequence given" do
     assert_raise ArgumentError do
-      AA.new(nil)
+      Bio::Sequence::AA.new(nil)
     end
   end
 
   should "Raise if empty sequence given" do
     assert_raise ArgumentError do
-      AA.new(' ')
+      Bio::Sequence::AA.new(' ')
     end
   end
 
 
   should "Raise if unknown pks used" do
     assert_raise ArgumentError do
-      AA.new('PG', 'youdontknowme')
+      Bio::Sequence::AA.new('PG', 'youdontknowme')
     end
   end
 
   context "a Sequence" do
     setup do
-      @sequence = AA.new("PGAKAAAKKPKKAAG")
+      @sequence = Bio::Sequence::AA.new("PGAKAAAKKPKKAAG")
     end
 
     should "calculates the isolectric point to 0 places" do

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: isoelectric_point
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 19
   prerelease: false
   segments: 
   - 0
   - 0
-  - 5
-  version: 0.0.5
+  - 6
+  version: 0.0.6
 platform: ruby
 authors: 
 - GeorgeG
@@ -48,7 +48,9 @@ dependencies:
   type: :development
   version_requirements: *id002
 description: Calculate the Isoelectric point
-email: info@simplificator.com
+email: 
+- info@simplificator.com
+- georgkam@gmail.com
 executables: []
 
 extensions: []
@@ -99,7 +101,7 @@ rubyforge_project:
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
-summary: Calculate isoelectric point.
+summary: Calculate the iso-electric point of a protein sequence.
 test_files: 
 - test/aa_test.rb
 - test/extensions_test.rb