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

Methods

Included Modules

Common::DblinksAsHash Common::PathwaysAsHash Common::OrthologsAsHash Common::GenesAsHash

Constants

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

Public Class methods

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 41
41:   def initialize(entry)
42:     super(entry, TAGSIZE)
43:   end

Public Instance methods

ALL_REAC ’;’

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 83
83:   def all_reac
84:     field_fetch('ALL_REAC')
85:   end

CLASS

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 68
68:   def classes
69:     lines_fetch('CLASS')
70:   end

COFACTOR

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 116
116:   def cofactors
117:     field_fetch('COFACTOR').split(/\s*;\s*/)
118:   end

COMMENT

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 121
121:   def comment
122:     field_fetch('COMMENT')
123:   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/enzyme.rb, line 23
23:   def dblinks_as_hash; super; end

DBLINKS

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 161
161:   def dblinks_as_strings
162:     lines_fetch('DBLINKS')
163:   end

DISEASE

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 141
141:   def diseases
142:     lines_fetch('DISEASE')
143:   end

ENTRY

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 46
46:   def entry
47:     field_fetch('ENTRY')
48:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 50
50:   def entry_id
51:     entry[/EC (\S+)/, 1]
52:   end
genes()

Alias for genes_as_hash

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

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 38
38:   def genes_as_hash; super; end

GENES

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 136
136:   def genes_as_strings
137:     lines_fetch('GENES')
138:   end

INHIBITOR

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 111
111:   def inhibitors
112:     field_fetch('INHIBITOR').split(/\s*;\s*/)
113:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 87
87:   def iubmb_reactions
88:     all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/)
89:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 91
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

MOTIF

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 146
146:   def motifs
147:     lines_fetch('MOTIF')
148:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 63
63:   def name
64:     names.first
65:   end

NAME

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 59
59:   def names
60:     field_fetch('NAME').split(/\s*;\s*/)
61:   end

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 54
54:   def obsolete?
55:     entry[/Obsolete/] ? true : false
56:   end
orthologs()

Alias for orthologs_as_hash

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

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 33
33:   def orthologs_as_hash; super; end

ORTHOLOGY

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 131
131:   def orthologs_as_strings
132:     lines_fetch('ORTHOLOGY')
133:   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/enzyme.rb, line 28
28:   def pathways_as_hash; super; end

PATHWAY

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 126
126:   def pathways_as_strings
127:     lines_fetch('PATHWAY')
128:   end

PRODUCT

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 106
106:   def products
107:     field_fetch('PRODUCT').split(/\s*;\s*/)
108:   end

REACTION

[Source]

    # File lib/bio/db/kegg/enzyme.rb, line 78
78:   def reaction
79:     field_fetch('REACTION')
80:   end

STRUCTURES

[Source]

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

SUBSTRATE

[Source]

     # File lib/bio/db/kegg/enzyme.rb, line 101
101:   def substrates
102:     field_fetch('SUBSTRATE').split(/\s*;\s*/)
103:   end

SYSNAME

[Source]

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

[Validate]