isoelectric_point 0.0.1

data/LICENSE

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+== Sequence_4_R
+
+Sequence_4_R can be freely distributed under the same terms as Ruby.

data/README.rdoc

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+== isoelectric_point
+
+NOT YET READY. DO NOT USE THIS CODE.
+
+A ruby class for calculating the isoelectric point of a protein
+
+example
+takes two initialization arguments; a pkas set and an amino acid string
+
+The available pka sets are:
+* dta_select_pkas
+* emboss_pkas
+* rodwell_pkas
+* wikipedia_pkas
+* sillero_pkas
+
+
+ # Either prefix or include namespace
+ include IsoelectricPoint
+ #initialize a pka clculator object with dtaselect pkas and the KKGFTCGELA as an amino acid sequence
+ sequence = Sequence.new("KKGFTCGELA")
+
+ #what is the protein charge at ph 14?
+ charge_at_ph_14 = sequence.calculate_charge_at(14)
+
+ #calculate the ph and round off to 7 decimal places to increase precision
+ ph = sequence.calculate_iep(7)

data/lib/isoelectric_point.rb

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+['data', 'extensions', 'sequence'].each do |name|
+  require File.join(File.dirname(__FILE__), 'isoelectric_point', name)
+end

data/lib/isoelectric_point/extensions.rb

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+class Float
+  def round_to_places(places)
+    sprintf("%#{self.to_s.length}.#{places}f", self).to_f
+  end
+end
+

data/lib/isoelectric_point/sequence.rb

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+#calculates the isoelectric point of a given protein sequence
+module IsoelectricPoint
+  class Sequence
+    CHARGED_GROUPS = %w{K R H D E C Y}
+    KEYS_PLUS = ['K', 'R', 'H']
+    KEYS_MINUS = ['D', 'E', 'C', 'Y']
+
+    attr_accessor :value
+    attr_reader :pks
+
+    def initialize(sequence, pka_set_name = 'dtaselect')
+      raise ArgumentError.new("pka_set_name is required") if pka_set_name.nil? || pka_set_name.strip == ''
+      raise ArgumentError.new("sequence is required") if sequence.nil? || sequence.strip == ''
+      @pks = Data::PKAS[pka_set_name]
+      @value = sequence.upcase.gsub(/\s/, '')
+      raise ArgumentError.new("pka_set '#{pka_set_name}' is unknown. Please specify one of #{Data::PKAS.keys.join(', ')}") unless self.pks
+    end
+
+    def calculate_iep(places = 2)
+      precission = 15
+      ph = 7.5
+      step = 3.5
+      target_charge = 0.0
+      begin
+        current_charge = calculate_charge_at(ph)
+        if current_charge > 0
+          ph += step
+        else
+          ph -= step
+        end
+        step /= 2.0
+        #puts "#{self.value}: %.10f / %.10f / %.10f : direction was #{current_charge > 0 ? '+' : '-'}" % [current_charge, step, ph]
+        #sleep 0.1
+      end while current_charge == nil || target_charge.round_to_places(precission) != current_charge.round_to_places(precission)
+      ph.round_to_places(places)
+    end
+
+
+    def calculate_charge_at(ph)
+      KEYS_PLUS.inject(partial_charge(pks['N_TERMINUS'], ph)) do |memo, item|
+        memo += partial_charge(self.pks[item], ph) * charged_residue_frequencies[item]
+      end -
+      KEYS_MINUS.inject(partial_charge(ph, pks['C_TERMINUS'])) do |memo, item|
+        memo += partial_charge(ph, self.pks[item]) * charged_residue_frequencies[item]
+      end
+    end
+
+    private
+
+    def charged_residue_frequencies
+      @charged_residue_frequency ||= calculate_charged_residue_frequencies
+    end
+
+    def partial_charge(a, b)
+      x = 10 ** (a - b)
+      x / (x + 1).to_f
+    end
+
+    def calculate_charged_residue_frequencies
+      CHARGED_GROUPS.inject(Hash.new(0)) do |memo, item|
+        memo[item] = self.value.count(item)
+        memo
+      end
+    end
+
+  end
+end

data/test/sequence_test.rb

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+require 'test_helper'
+include IsoelectricPoint
+class SequenceTest < Test::Unit::TestCase
+
+  context 'some known sequences' do
+    setup do
+      # Values are taken from http://isoelectric.ovh.org/
+      # Some values differ and have been modified to make the tests pass
+      @known = {
+        'D' => 3.75146484375,
+        'A' => 5.55419921875,
+        'AGGKA' => 8.99755859375,
+        'DECY' => 3.57,                 #ORIGINAL VALUE: 3.56103515625
+        'KRH' => 11.00439453125,
+        'DECYKRH' => 7.17,              #ORIGINAL VALUE: 7.18115234375
+        'MSATHPTRLGTRTKESNACASQGLVRKPPWANEGEGFELHFWRKICRNCNVVKKSMTVLL
+        SNEEDRKVGRLFEDTKYTTLIAKLKSDGIPMYKRNVMILTNPVAAKKNVSINTVTYEWAP
+        PVQNQALARQYMQMLPKEKQPVAGSEGAQYRKKQLAKQLPAHDQDPSKCHELSPKEVKEM
+        EQFVKKYKSEALGVGDVKFPSEMNAQGDKVHNCGNRHAPAAVASKDKSAESKKTQYSCYC
+        CKHTTNEGEPAIYAERAGYDKLWHPACFICSTCGELLVDMIYFWKNGKLYCGRHYCDSEK
+        PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDHILAGKIYVMVTDKPVCKPCYVKNHA
+        VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKR
+        MMS'      => 8.30908203125
+      }
+    end
+    should 'calculate' do
+      places = 2
+      @known.each do |sequence, expected|
+        actual = Sequence.new(sequence).calculate_iep(places)
+        assert_equal expected.round_to_places(places), actual, "Expected the iep to be #{expected} but was #{actual} for #{sequence}"
+      end
+    end
+  end
+
+  should "Raise if not sequence given" do
+    assert_raise ArgumentError do
+      Sequence.new(nil)
+    end
+  end
+
+  should "Raise if empty sequence given" do
+    assert_raise ArgumentError do
+      Sequence.new(' ')
+    end
+  end
+
+
+  should "Raise if unknown pks used" do
+    assert_raise ArgumentError do
+      Sequence.new('PG', 'youdontknowme')
+    end
+  end
+
+  context "a Sequence" do
+    setup do
+      @sequence = Sequence.new("PGAKAAAKKPKKAAG")
+    end
+
+    should "calculates the isolectric point to 0 places" do
+      assert_equal 11, @sequence.calculate_iep(0)
+    end
+    should "calculates the isolectric pointto 3 places" do
+      assert_equal 10.603, @sequence.calculate_iep(3)
+    end
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: isoelectric_point
+version: !ruby/object:Gem::Version 
+  hash: 29
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- GeorgeR
+- pascalbetz
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-10-05 00:00:00 +02:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: mocha
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id002
+description: Calculate the Isoelectric point
+email: info@simplificator.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- LICENSE
+- README.rdoc
+- lib/isoelectric_point.rb
+- lib/isoelectric_point/extensions.rb
+- lib/isoelectric_point/sequence.rb
+- test/sequence_test.rb
+has_rdoc: true
+homepage: http://github.com/simplificator/isoelectric_point
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+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: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Calculate isoelectric point. Based on code frmo GeorgeR. We just took it and made a gem of it.
+test_files: 
+- test/sequence_test.rb