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
38 def initialize(entry)
39   super(entry, TAGSIZE)
40 end

Public Instance Methods

definition() click to toggle source

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
entry_id() click to toggle source

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() click to toggle source

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
equation() click to toggle source

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() click to toggle source

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
orthologs()
Alias for: orthologs_as_hash
orthologs_as_hash() click to toggle source

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

   # File lib/bio/db/kegg/reaction.rb
30 def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings() click to toggle source

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
pathways()
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Returns a Hash of the pathway ID and name in PATHWAY field.

   # File lib/bio/db/kegg/reaction.rb
25 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathway information, described in the PATHWAY lines.


Returns

Array containing String

    # File lib/bio/db/kegg/reaction.rb
110 def pathways_as_strings
111   lines_fetch('PATHWAY')
112 end
rpairs()
Alias for: rpairs_as_hash
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

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
Also aliased as: rpairs
rpairs_as_strings() click to toggle source

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
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
103 def rpairs_as_tokens
104   fetch('RPAIR').split(/\s+/)
105 end