class Bio::KEGG::REACTION
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
Creates a new Bio::KEGG::REACTION
object.
Arguments:
-
(required) entry: (String) single entry as a string
- Returns
-
Bio::KEGG::REACTION
object
Bio::NCBIDB::new
# File lib/bio/db/kegg/reaction.rb 38 def initialize(entry) 39 super(entry, TAGSIZE) 40 end
Public Instance Methods
Definition of the reaction, described in the DEFINITION line.
- Returns
-
String
# File lib/bio/db/kegg/reaction.rb 59 def definition 60 field_fetch('DEFINITION') 61 end
ID of the entry, described in the ENTRY line.
- Returns
-
String
# File lib/bio/db/kegg/reaction.rb 45 def entry_id 46 field_fetch('ENTRY')[/\S+/] 47 end
Enzymes described in the ENZYME
line.
- Returns
-
Array containing String
# File lib/bio/db/kegg/reaction.rb 117 def enzymes 118 unless @data['ENZYME'] 119 @data['ENZYME'] = fetch('ENZYME').scan(/\S+/) 120 end 121 @data['ENZYME'] 122 end
Chemical equation, described in the EQUATION line.
- Returns
-
String
# File lib/bio/db/kegg/reaction.rb 66 def equation 67 field_fetch('EQUATION') 68 end
Name of the reaction, described in the NAME line.
- Returns
-
String
# File lib/bio/db/kegg/reaction.rb 52 def name 53 field_fetch('NAME') 54 end
Returns a Hash of the orthology ID and definition in ORTHOLOGY
field.
Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash
# File lib/bio/db/kegg/reaction.rb 30 def orthologs_as_hash; super; end
Orthologs described in the ORTHOLOGY
lines.
- Returns
-
Array containing String
# File lib/bio/db/kegg/reaction.rb 127 def orthologs_as_strings 128 lines_fetch('ORTHOLOGY') 129 end
Returns a Hash of the pathway ID and name in PATHWAY
field.
Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash
# File lib/bio/db/kegg/reaction.rb 25 def pathways_as_hash; super; end
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
-
Hash
# File lib/bio/db/kegg/reaction.rb 85 def rpairs_as_hash 86 unless defined? @rpairs_as_hash 87 rps = {} 88 rpairs_as_strings.each do |line| 89 _, entry_id, name, rptype = line.split(/\s+/) 90 rps[entry_id] = [ name, rptype ] 91 end 92 @rpairs_as_hash = rps 93 end 94 @rpairs_as_hash 95 end
KEGG
RPAIR (ReactantPair) information, described in the RPAIR lines.
- Returns
-
Array containing String
# File lib/bio/db/kegg/reaction.rb 73 def rpairs_as_strings 74 lines_fetch('RPAIR') 75 end
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 103 def rpairs_as_tokens 104 fetch('RPAIR').split(/\s+/) 105 end