class Bio::KEGG::REACTION

Constants

DELIMITER
TAGSIZE

Public Class Methods

Source

   # File lib/bio/db/kegg/reaction.rb
38 def initialize(entry)
39   super(entry, TAGSIZE)
40 end

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

Public Instance Methods

definition ()

Source

   # File lib/bio/db/kegg/reaction.rb
59 def definition
60   field_fetch('DEFINITION')
61 end

Definition of the reaction, described in the DEFINITION line.

Returns: String

entry_id ()

Source

   # File lib/bio/db/kegg/reaction.rb
45 def entry_id
46   field_fetch('ENTRY')[/\S+/]
47 end

ID of the entry, described in the ENTRY line.

Returns: String

enzymes ()

Source

    # 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

Enzymes described in the ENZYME line.

Returns: Array containing String

equation ()

Source

   # File lib/bio/db/kegg/reaction.rb
66 def equation
67   field_fetch('EQUATION')
68 end

Chemical equation, described in the EQUATION line.

Returns: String

name ()

Source

   # File lib/bio/db/kegg/reaction.rb
52 def name
53   field_fetch('NAME')
54 end

Name of the reaction, described in the NAME line.

Returns: String

orthologs ()

Alias for: orthologs_as_hash

orthologs_as_hash ()

Source

   # File lib/bio/db/kegg/reaction.rb
30 def orthologs_as_hash; super; end

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

Calls superclass method Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash

Also aliased as: orthologs

orthologs_as_strings ()

Source

    # File lib/bio/db/kegg/reaction.rb
127 def orthologs_as_strings
128   lines_fetch('ORTHOLOGY')
129 end

Orthologs described in the ORTHOLOGY lines.

Returns: Array containing String

pathways ()

Alias for: pathways_as_hash

pathways_as_hash ()

Source

   # File lib/bio/db/kegg/reaction.rb
25 def pathways_as_hash; super; end

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

Calls superclass method Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash

Also aliased as: pathways

pathways_as_strings ()

Source

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

Pathway information, described in the PATHWAY lines.

Returns: Array containing String

rpairs ()

Alias for: rpairs_as_hash

rpairs_as_hash ()

Source

   # 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 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

Also aliased as: rpairs

rpairs_as_strings ()

Source

   # File lib/bio/db/kegg/reaction.rb
73 def rpairs_as_strings
74   lines_fetch('RPAIR')
75 end

KEGG RPAIR (ReactantPair) information, described in the RPAIR lines.

Returns: Array containing String

rpairs_as_tokens ()

Source

    # File lib/bio/db/kegg/reaction.rb
103 def rpairs_as_tokens
104   fetch('RPAIR').split(/\s+/)
105 end

Returns the content of the RPAIR entry as tokens (RPair signature, RPair ID, , RPair type).

Returns: Array containing String