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#
# = bio/db/kegg/compound.rb - KEGG COMPOUND database class
#
# Copyright:: Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
require 'bio/db'
require 'bio/db/kegg/common'
module Bio
class KEGG
# == Description
#
# Bio::KEGG::COMPOUND is a parser class for the KEGG COMPOUND database entry.
# KEGG COMPOUND is a chemical structure database.
#
# == References
#
# * http://www.genome.jp/kegg/compound/
#
class COMPOUND < KEGGDB
DELIMITER = RS = "\n///\n"
TAGSIZE = 12
include Common::DblinksAsHash
# Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.
def dblinks_as_hash; super; end if false #dummy for RDoc
alias dblinks dblinks_as_hash
include Common::PathwaysAsHash
# Returns a Hash of the pathway ID and name in PATHWAY field.
def pathways_as_hash; super; end if false #dummy for RDoc
alias pathways pathways_as_hash
# Creates a new Bio::KEGG::COMPOUND object.
# ---
# *Arguments*:
# * (required) _entry_: (String) single entry as a string
# *Returns*:: Bio::KEGG::COMPOUND object
def initialize(entry)
super(entry, TAGSIZE)
end
# ENTRY
def entry_id
field_fetch('ENTRY')[/\S+/]
end
# NAME
def names
field_fetch('NAME').split(/\s*;\s*/)
end
# The first name recorded in the NAME field.
def name
names.first
end
# FORMULA
def formula
field_fetch('FORMULA')
end
# MASS
def mass
field_fetch('MASS').to_f
end
# REMARK
def remark
field_fetch('REMARK')
end
# GLYCAN
def glycans
unless @data['GLYCAN']
@data['GLYCAN'] = fetch('GLYCAN').split(/\s+/)
end
@data['GLYCAN']
end
# REACTION
def reactions
unless @data['REACTION']
@data['REACTION'] = fetch('REACTION').split(/\s+/)
end
@data['REACTION']
end
# RPAIR
def rpairs
unless @data['RPAIR']
@data['RPAIR'] = fetch('RPAIR').split(/\s+/)
end
@data['RPAIR']
end
# PATHWAY
def pathways_as_strings
lines_fetch('PATHWAY')
end
# ENZYME
def enzymes
unless @data['ENZYME']
field = fetch('ENZYME')
if /\(/.match(field) # old version
@data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
else
@data['ENZYME'] = field.scan(/\S+/)
end
end
@data['ENZYME']
end
# DBLINKS
def dblinks_as_strings
lines_fetch('DBLINKS')
end
# ATOM, BOND
def kcf
return "#{get('ATOM')}#{get('BOND')}"
end
# COMMENT
def comment
field_fetch('COMMENT')
end
end # COMPOUND
end # KEGG
end # Bio
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