Class Bio::KEGG::ENZYME
In: lib/bio/db/kegg/enzyme.rb
Parent: KEGGDB

Methods

Constants

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

Public Class methods

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 20
20:   def initialize(entry)
21:     super(entry, TAGSIZE)
22:   end

Public Instance methods

ALL_REAC ’;’

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 62
62:   def all_reac
63:     field_fetch('ALL_REAC')
64:   end

CLASS

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 47
47:   def classes
48:     lines_fetch('CLASS')
49:   end

COFACTOR

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 95
95:   def cofactors
96:     field_fetch('COFACTOR').split(/\s*;\s*/)
97:   end

COMMENT

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 100
100:   def comment
101:     field_fetch('COMMENT')
102:   end

DBLINKS

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 140
140:   def dblinks
141:     lines_fetch('DBLINKS')
142:   end

DISEASE

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 120
120:   def diseases
121:     lines_fetch('DISEASE')
122:   end

ENTRY

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 25
25:   def entry
26:     field_fetch('ENTRY')
27:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 29
29:   def entry_id
30:     entry[/EC (\S+)/, 1]
31:   end

GENES

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 115
115:   def genes
116:     lines_fetch('GENES')
117:   end

INHIBITOR

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 90
90:   def inhibitors
91:     field_fetch('INHIBITOR').split(/\s*;\s*/)
92:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 66
66:   def iubmb_reactions
67:     all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/)
68:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 70
70:   def kegg_reactions
71:     reac = all_reac
72:     if reac[/\(other\)/]
73:       reac.sub(/.*\(other\)\s*/, '').split(/\s*;\s*/)
74:     else
75:       []
76:     end
77:   end

MOTIF

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 125
125:   def motifs
126:     lines_fetch('MOTIF')
127:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 42
42:   def name
43:     names.first
44:   end

NAME

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 38
38:   def names
39:     field_fetch('NAME').split(/\s*;\s*/)
40:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 33
33:   def obsolete?
34:     entry[/Obsolete/] ? true : false
35:   end

ORTHOLOGY

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 110
110:   def orthologs
111:     lines_fetch('ORTHOLOGY')
112:   end

PATHWAY

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 105
105:   def pathways
106:     lines_fetch('PATHWAY')
107:   end

PRODUCT

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 85
85:   def products
86:     field_fetch('PRODUCT').split(/\s*;\s*/)
87:   end

REACTION

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 57
57:   def reaction
58:     field_fetch('REACTION')
59:   end

STRUCTURES

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 130
130:   def structures
131:     unless @data['STRUCTURES']
132:       @data['STRUCTURES'] = fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
133:     end
134:     @data['STRUCTURES']
135:   end

SUBSTRATE

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 80
80:   def substrates
81:     field_fetch('SUBSTRATE').split(/\s*;\s*/)
82:   end

SYSNAME

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 52
52:   def sysname
53:     field_fetch('SYSNAME')
54:   end

[Validate]