Class Bio::KEGG::COMPOUND
In: lib/bio/db/kegg/compound.rb
Parent: KEGGDB

Description

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

References

Methods

Included Modules

Common::DblinksAsHash Common::PathwaysAsHash

Constants

DELIMITER = RS = "\n///\n"
TAGSIZE = 12

Public Class methods

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


Arguments:

  • (required) entry: (String) single entry as a string
Returns:Bio::KEGG::COMPOUND object

[Source]

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

Public Instance methods

COMMENT

[Source]

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

Alias for dblinks_as_hash

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

[Source]

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

DBLINKS

[Source]

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

ENTRY

[Source]

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

ENZYME

[Source]

     # File lib/bio/db/kegg/compound.rb, line 109
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

FORMULA

[Source]

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

GLYCAN

[Source]

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

ATOM, BOND

[Source]

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

MASS

[Source]

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

The first name recorded in the NAME field.

[Source]

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

NAME

[Source]

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

Alias for pathways_as_hash

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

[Source]

    # File lib/bio/db/kegg/compound.rb, line 37
37:   def pathways_as_hash; super; end

PATHWAY

[Source]

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

REACTION

[Source]

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

REMARK

[Source]

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

RPAIR

[Source]

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

[Validate]