[BioRuby-cvs] bioruby/lib/bio/data na.rb,0.15,0.16

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/data
In directory pub.open-bio.org:/tmp/cvs-serv25615/lib/bio/data

Modified Files:
	na.rb 
Log Message:
* Updates and correction by Trevor Wennblom


Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v
retrieving revision 0.15
retrieving revision 0.16
diff -C2 -d -r0.15 -r0.16
*** na.rb	4 Nov 2005 17:49:10 -0000	0.15
--- na.rb	14 Nov 2005 01:52:19 -0000	0.16
***************
*** 4,11 ****
  # Copyright::	Copyright (C) 2001, 2005
  #		Toshiaki Katayama <k at bioruby.org>
! # Lisence::	LGPL
  #
  # $Id$
  #
  #--
  #
--- 4,42 ----
  # Copyright::	Copyright (C) 2001, 2005
  #		Toshiaki Katayama <k at bioruby.org>
! # License::	LGPL
  #
  # $Id$
  #
+ # == Synopsis
+ #
+ # Bio::NucleicAcid class contains data related to nucleic acids.
+ #
+ # == Usage
+ #
+ # Examples:
+ #
+ #   require 'bio'
+ #
+ #   puts "### na = Bio::NucleicAcid.new"
+ #   na = Bio::NucleicAcid.new
+ #
+ #   puts "# na.to_re('yrwskmbdhvnatgc')"
+ #   p na.to_re('yrwskmbdhvnatgc')
+ #
+ #   puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
+ #   p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
+ #
+ #   puts "# na.weight('A')"
+ #   p na.weight('A')
+ #
+ #   puts "# Bio::NucleicAcid.weight('A')"
+ #   p Bio::NucleicAcid.weight('A')
+ #
+ #   puts "# na.weight('atgc')"
+ #   p na.weight('atgc')
+ #
+ #   puts "# Bio::NucleicAcid.weight('atgc')"
+ #   p Bio::NucleicAcid.weight('atgc')
+ #
  #--
  #
***************
*** 44,48 ****
        's'	=> '[gc]',	# Strong
        'k'	=> '[tg]',	# Keto
!       'm'	=> '[ac]',	# aMino
  
        'b'	=> '[tgc]',	# not A
--- 75,79 ----
        's'	=> '[gc]',	# Strong
        'k'	=> '[tg]',	# Keto
!       'm'	=> '[ac]',	# aroMatic
  
        'b'	=> '[tgc]',	# not A
***************
*** 81,91 ****
        :guanine	=> 151.15,
        :cytosine	=> 111.12,
!       :uracil		=> 112.10,
  
        :deoxyribose_phosphate	=> 196.11,
!       :ribose_phosphate	=> 212.11,
  
        :hydrogen	=> 1.00794,
!       :water		=> 18.015,
  
      }
--- 112,122 ----
        :guanine	=> 151.15,
        :cytosine	=> 111.12,
!       :uracil	=> 112.10,
  
        :deoxyribose_phosphate	=> 196.11,
!       :ribose_phosphate		=> 212.11,
  
        :hydrogen	=> 1.00794,
!       :water	=> 18.015,
  
      }
***************
*** 158,166 ****
    extend Data
  
- 
    # backward compatibility
    Names = Data::Names
    Weight = Data::Weight
- 
  
  end
--- 189,195 ----