class Bio::KEGG::REACTION
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
new(entry)
click to toggle source
Creates a new Bio::KEGG::REACTION object.
Arguments:
-
(required) entry: (String) single entry as a string
- Returns
-
Bio::KEGG::REACTION object
Calls superclass method
Bio::NCBIDB.new
# File lib/bio/db/kegg/reaction.rb, line 38 def initialize(entry) super(entry, TAGSIZE) end
Public Instance Methods
definition()
click to toggle source
Definition of the reaction, described in the DEFINITION line.
- Returns
# File lib/bio/db/kegg/reaction.rb, line 59 def definition field_fetch('DEFINITION') end
entry_id()
click to toggle source
ID of the entry, described in the ENTRY line.
- Returns
# File lib/bio/db/kegg/reaction.rb, line 45 def entry_id field_fetch('ENTRY')[/\S+/] end
enzymes()
click to toggle source
equation()
click to toggle source
Chemical equation, described in the EQUATION line.
- Returns
# File lib/bio/db/kegg/reaction.rb, line 66 def equation field_fetch('EQUATION') end
name()
click to toggle source
Name of the reaction, described in the NAME line.
- Returns
# File lib/bio/db/kegg/reaction.rb, line 52 def name field_fetch('NAME') end
orthologs_as_hash()
click to toggle source
Returns a Hash of the orthology ID and definition in ORTHOLOGY field.
Calls superclass method
Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash
# File lib/bio/db/kegg/reaction.rb, line 30 def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings()
click to toggle source
pathways_as_hash()
click to toggle source
Returns a Hash of the pathway ID and name in PATHWAY field.
Calls superclass method
Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash
# File lib/bio/db/kegg/reaction.rb, line 25 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings()
click to toggle source
rpairs_as_hash()
click to toggle source
KEGG RPAIR (ReactantPair) information, described in the RPAIR lines. Returns a hash of RPair IDs and [ name, type ] informations, for example,
{ "RP12733" => [ "C00022_C00900", "trans" ], "RP05698" => [ "C00011_C00022", "leave" ], "RP00440" => [ "C00022_C00900", "main" ] }
- Returns
# File lib/bio/db/kegg/reaction.rb, line 85 def rpairs_as_hash unless defined? @rpairs_as_hash rps = {} rpairs_as_strings.each do |line| namespace, entry_id, name, rptype = line.split(/\s+/) rps[entry_id] = [ name, rptype ] end @rpairs_as_hash = rps end @rpairs_as_hash end
Also aliased as: rpairs
rpairs_as_strings()
click to toggle source
rpairs_as_tokens()
click to toggle source
Returns the content of the RPAIR entry as tokens (RPair signature, RPair ID, , RPair type).
- Returns
-
Array containing String
# File lib/bio/db/kegg/reaction.rb, line 103 def rpairs_as_tokens fetch('RPAIR').split(/\s+/) end