[BioRuby-cvs] bioruby/lib/bio/db/kegg enzyme.rb,0.8,0.9

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv31768/lib/bio/db/kegg

Modified Files:
	enzyme.rb 
Log Message:
* license is changed from LGPL to Ruby's


Index: enzyme.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/enzyme.rb,v
retrieving revision 0.8
retrieving revision 0.9
diff -C2 -d -r0.8 -r0.9
*** enzyme.rb	8 Sep 2005 01:22:11 -0000	0.8
--- enzyme.rb	19 Sep 2006 05:52:05 -0000	0.9
***************
*** 1,22 ****
  #
! # bio/db/kegg/enzyme.rb - KEGG/ENZYME database class
! #
! #   Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k at bioruby.org>
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
  #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
--- 1,9 ----
  #
! # = bio/db/kegg/enzyme.rb - KEGG/ENZYME database class
  #
! # Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k at bioruby.org>
! # License::    Ruby's
  #
! # $Id$
  #
  
***************
*** 24,125 ****
  
  module Bio
  
!   class KEGG
! 
!     class ENZYME < KEGGDB
! 
!       DELIMITER	= RS = "\n///\n"
!       TAGSIZE	= 12
! 
!       def initialize(entry)
!         super(entry, TAGSIZE)
!       end
  
!       # ENTRY
!       def entry_id
!         field_fetch('ENTRY')
!       end
  
!       # NAME
!       def names
!         lines_fetch('NAME')
!       end
!       def name
!         names[0]
!       end
  
!       # CLASS
!       def classes
!         lines_fetch('CLASS')
!       end
  
!       # SYSNAME
!       def sysname
!         field_fetch('SYSNAME')
!       end
  
!       # REACTION ';'
!       def reaction
!         field_fetch('REACTION')
!       end
!       
!       # SUBSTRATE
!       def substrates
!         lines_fetch('SUBSTRATE')
!       end
  
!       # PRODUCT
!       def products
!         lines_fetch('PRODUCT')
!       end
  
!       # COFACTOR
!       def cofactors
!         lines_fetch('COFACTOR')
!       end
  
!       # COMMENT
!       def comment
!         field_fetch('COMMENT')
!       end
  
!       # PATHWAY
!       def pathways
!         lines_fetch('PATHWAY')
!       end
  
!       # GENES
!       def genes
!         lines_fetch('GENES')
!       end
  
!       # DISEASE
!       def diseases
!         lines_fetch('DISEASE')
!       end
  
!       # MOTIF
!       def motifs
!         lines_fetch('MOTIF')
!       end
  
!       # STRUCTURES
!       def structures
!         unless @data['STRUCTURES']
!           @data['STRUCTURES'] =
!             fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
!         end
!         @data['STRUCTURES']
!       end
  
!       # DBLINKS
!       def dblinks
!         lines_fetch('DBLINKS')
!       end
  
      end
  
    end
  
! end
  
--- 11,110 ----
  
  module Bio
+ class KEGG
  
! class ENZYME < KEGGDB
  
!   DELIMITER	= RS = "\n///\n"
!   TAGSIZE	= 12
  
!   def initialize(entry)
!     super(entry, TAGSIZE)
!   end
  
!   # ENTRY
!   def entry_id
!     field_fetch('ENTRY')
!   end
  
!   # NAME
!   def names
!     lines_fetch('NAME')
!   end
!   def name
!     names[0]
!   end
  
!   # CLASS
!   def classes
!     lines_fetch('CLASS')
!   end
  
!   # SYSNAME
!   def sysname
!     field_fetch('SYSNAME')
!   end
  
!   # REACTION ';'
!   def reaction
!     field_fetch('REACTION')
!   end
!   
!   # SUBSTRATE
!   def substrates
!     lines_fetch('SUBSTRATE')
!   end
  
!   # PRODUCT
!   def products
!     lines_fetch('PRODUCT')
!   end
  
!   # COFACTOR
!   def cofactors
!     lines_fetch('COFACTOR')
!   end
  
!   # COMMENT
!   def comment
!     field_fetch('COMMENT')
!   end
  
!   # PATHWAY
!   def pathways
!     lines_fetch('PATHWAY')
!   end
  
!   # GENES
!   def genes
!     lines_fetch('GENES')
!   end
  
!   # DISEASE
!   def diseases
!     lines_fetch('DISEASE')
!   end
  
!   # MOTIF
!   def motifs
!     lines_fetch('MOTIF')
!   end
  
+   # STRUCTURES
+   def structures
+     unless @data['STRUCTURES']
+       @data['STRUCTURES'] =
+         fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
      end
+     @data['STRUCTURES']
+   end
  
+   # DBLINKS
+   def dblinks
+     lines_fetch('DBLINKS')
    end
  
! end # ENZYME
! 
! end # KEGG
! end # Bio