class Bio::KEGG::COMPOUND

Description¶ ↑

Bio::KEGG::COMPOUND is a parser class for the KEGG COMPOUND database entry. KEGG COMPOUND is a chemical structure database.

`References`¶ ↑

www.genome.jp/kegg/compound/

Constants

DELIMITER
TAGSIZE

Public Class Methods

new (entry)

Source

   # File lib/bio/db/kegg/compound.rb
45 def initialize(entry)
46   super(entry, TAGSIZE)
47 end

Creates a new Bio::KEGG::COMPOUND object.

Arguments:

(required) entry: (String) single entry as a string

Returns: Bio::KEGG::COMPOUND object

Calls superclass method Bio::NCBIDB::new

Public Instance Methods

comment ()

Source

    # File lib/bio/db/kegg/compound.rb
132 def comment
133   field_fetch('COMMENT')
134 end

COMMENT

dblinks ()

Alias for: dblinks_as_hash

dblinks_as_hash ()

Source

   # File lib/bio/db/kegg/compound.rb
32 def dblinks_as_hash; super; end

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.

Calls superclass method Bio::KEGG::Common::DblinksAsHash#dblinks_as_hash

Also aliased as: dblinks

dblinks_as_strings ()

Source

    # File lib/bio/db/kegg/compound.rb
122 def dblinks_as_strings
123   lines_fetch('DBLINKS')
124 end

DBLINKS

entry_id ()

Source

   # File lib/bio/db/kegg/compound.rb
50 def entry_id
51   field_fetch('ENTRY')[/\S+/]
52 end

ENTRY

enzymes ()

Source

    # File lib/bio/db/kegg/compound.rb
109 def enzymes
110   unless @data['ENZYME']
111     field = fetch('ENZYME')
112     if /\(/.match(field)      # old version
113       @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
114     else
115       @data['ENZYME'] = field.scan(/\S+/)
116     end
117   end
118   @data['ENZYME']
119 end

ENZYME

formula ()

Source

   # File lib/bio/db/kegg/compound.rb
65 def formula
66   field_fetch('FORMULA')
67 end

FORMULA

glycans ()

Source

   # File lib/bio/db/kegg/compound.rb
80 def glycans
81   unless @data['GLYCAN']
82     @data['GLYCAN'] = fetch('GLYCAN').split(/\s+/)
83   end
84   @data['GLYCAN']
85 end

GLYCAN

kcf ()

Source

    # File lib/bio/db/kegg/compound.rb
127 def kcf
128   return "#{get('ATOM')}#{get('BOND')}"
129 end

ATOM, BOND

mass ()

Source

   # File lib/bio/db/kegg/compound.rb
70 def mass
71   field_fetch('MASS').to_f
72 end

MASS

name ()

Source

   # File lib/bio/db/kegg/compound.rb
60 def name
61   names.first
62 end

The first name recorded in the NAME field.

names ()

Source

   # File lib/bio/db/kegg/compound.rb
55 def names
56   field_fetch('NAME').split(/\s*;\s*/)
57 end

NAME

pathways ()

Alias for: pathways_as_hash

pathways_as_hash ()

Source

   # File lib/bio/db/kegg/compound.rb
37 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/compound.rb
104 def pathways_as_strings
105   lines_fetch('PATHWAY') 
106 end

PATHWAY

reactions ()

Source

   # File lib/bio/db/kegg/compound.rb
88 def reactions
89   unless @data['REACTION']
90     @data['REACTION'] = fetch('REACTION').split(/\s+/)
91   end
92   @data['REACTION']
93 end

REACTION

remark ()

Source

   # File lib/bio/db/kegg/compound.rb
75 def remark
76   field_fetch('REMARK')
77 end

REMARK

rpairs ()

Source

    # File lib/bio/db/kegg/compound.rb
 96 def rpairs
 97   unless @data['RPAIR']
 98     @data['RPAIR'] = fetch('RPAIR').split(/\s+/)
 99   end
100   @data['RPAIR']
101 end

RPAIR

class Bio::KEGG::COMPOUND

Description¶ ↑

References¶ ↑

`References`¶ ↑