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removed empty lines and comments

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1 parent ad9794e commit 7514fe6e2644885078e2586b3c19069eed54607c @georgeG committed Sep 27, 2011
Showing with 1 addition and 11 deletions.
  1. +0 −2 lib/bio-isoelectric_point.rb
  2. +1 −4 lib/isoelectric_point/aa.rb
  3. +0 −1 lib/isoelectric_point/pka_data.rb
  4. +0 −4 test/aa_test.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?
@@ -12,7 +12,6 @@ def initialize(sequence)
# 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 @@ def isoelectric_point(pka_name_or_set = 'dtaselect', places = 2, loop_limit = 10
# 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 @@ def calculate_charged_residue_frequencies
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 +81,5 @@ def select_pka(pka_name_or_set = 'dtaselect')
end #class AA
end #class Sequence
end #module Bio
-#include a new class Bio::AA::Index for Pkas? suggestes by tokiashiki katayama
+#include a new class Bio::AA::Index for Pkas? suggestion by tokiashiki katayama
@@ -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 = {
View
@@ -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/

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