class Bio::KEGG::ENZYME

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source
Calls superclass method Bio::NCBIDB::new
   # File lib/bio/db/kegg/enzyme.rb
41 def initialize(entry)
42   super(entry, TAGSIZE)
43 end

Public Instance Methods

all_reac() click to toggle source

ALL_REAC ';'

   # File lib/bio/db/kegg/enzyme.rb
83 def all_reac
84   field_fetch('ALL_REAC')
85 end
classes() click to toggle source

CLASS

   # File lib/bio/db/kegg/enzyme.rb
68 def classes
69   lines_fetch('CLASS')
70 end
cofactors() click to toggle source

COFACTOR

    # File lib/bio/db/kegg/enzyme.rb
116 def cofactors
117   field_fetch('COFACTOR').split(/\s*;\s*/)
118 end
comment() click to toggle source

COMMENT

    # File lib/bio/db/kegg/enzyme.rb
121 def comment
122   field_fetch('COMMENT')
123 end
diseases() click to toggle source

DISEASE

    # File lib/bio/db/kegg/enzyme.rb
141 def diseases
142   lines_fetch('DISEASE')
143 end
entry() click to toggle source

ENTRY

   # File lib/bio/db/kegg/enzyme.rb
46 def entry
47   field_fetch('ENTRY')
48 end
entry_id() click to toggle source
   # File lib/bio/db/kegg/enzyme.rb
50 def entry_id
51   entry[/EC (\S+)/, 1]
52 end
genes()
Alias for: genes_as_hash
genes_as_hash() click to toggle source

Returns a Hash of the organism ID and an Array of entry IDs in GENES field.

   # File lib/bio/db/kegg/enzyme.rb
38 def genes_as_hash; super; end
Also aliased as: genes
genes_as_strings() click to toggle source

GENES

    # File lib/bio/db/kegg/enzyme.rb
136 def genes_as_strings
137   lines_fetch('GENES')
138 end
inhibitors() click to toggle source

INHIBITOR

    # File lib/bio/db/kegg/enzyme.rb
111 def inhibitors
112   field_fetch('INHIBITOR').split(/\s*;\s*/)
113 end
iubmb_reactions() click to toggle source
   # File lib/bio/db/kegg/enzyme.rb
87 def iubmb_reactions
88   all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/)
89 end
kegg_reactions() click to toggle source
   # File lib/bio/db/kegg/enzyme.rb
91 def kegg_reactions
92   reac = all_reac
93   if reac[/\(other\)/]
94     reac.sub(/.*\(other\)\s*/, '').split(/\s*;\s*/)
95   else
96     []
97   end
98 end
motifs() click to toggle source

MOTIF

    # File lib/bio/db/kegg/enzyme.rb
146 def motifs
147   lines_fetch('MOTIF')
148 end
name() click to toggle source
   # File lib/bio/db/kegg/enzyme.rb
63 def name
64   names.first
65 end
names() click to toggle source

NAME

   # File lib/bio/db/kegg/enzyme.rb
59 def names
60   field_fetch('NAME').split(/\s*;\s*/)
61 end
obsolete?() click to toggle source
   # File lib/bio/db/kegg/enzyme.rb
54 def obsolete?
55   entry[/Obsolete/] ? true : false
56 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/enzyme.rb
33 def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings() click to toggle source

ORTHOLOGY

    # File lib/bio/db/kegg/enzyme.rb
131 def orthologs_as_strings
132   lines_fetch('ORTHOLOGY')
133 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/enzyme.rb
28 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

PATHWAY

    # File lib/bio/db/kegg/enzyme.rb
126 def pathways_as_strings
127   lines_fetch('PATHWAY')
128 end
products() click to toggle source

PRODUCT

    # File lib/bio/db/kegg/enzyme.rb
106 def products
107   field_fetch('PRODUCT').split(/\s*;\s*/)
108 end
reaction() click to toggle source

REACTION

   # File lib/bio/db/kegg/enzyme.rb
78 def reaction
79   field_fetch('REACTION')
80 end
structures() click to toggle source

STRUCTURES

    # File lib/bio/db/kegg/enzyme.rb
151 def structures
152   unless @data['STRUCTURES']
153     @data['STRUCTURES'] = fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
154   end
155   @data['STRUCTURES']
156 end
substrates() click to toggle source

SUBSTRATE

    # File lib/bio/db/kegg/enzyme.rb
101 def substrates
102   field_fetch('SUBSTRATE').split(/\s*;\s*/)
103 end
sysname() click to toggle source

SYSNAME

   # File lib/bio/db/kegg/enzyme.rb
73 def sysname
74   field_fetch('SYSNAME')
75 end