class Bio::KEGG::ENZYME
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
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# File lib/bio/db/kegg/enzyme.rb 41 def initialize(entry) 42 super(entry, TAGSIZE) 43 end
Calls superclass method
Bio::NCBIDB::new
Public Instance Methods
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# File lib/bio/db/kegg/enzyme.rb 83 def all_reac 84 field_fetch('ALL_REAC') 85 end
ALL_REAC ‘;’
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# File lib/bio/db/kegg/enzyme.rb 68 def classes 69 lines_fetch('CLASS') 70 end
CLASS
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# File lib/bio/db/kegg/enzyme.rb 116 def cofactors 117 field_fetch('COFACTOR').split(/\s*;\s*/) 118 end
COFACTOR
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# File lib/bio/db/kegg/enzyme.rb 121 def comment 122 field_fetch('COMMENT') 123 end
COMMENT
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# File lib/bio/db/kegg/enzyme.rb 23 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
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# File lib/bio/db/kegg/enzyme.rb 161 def dblinks_as_strings 162 lines_fetch('DBLINKS') 163 end
DBLINKS
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# File lib/bio/db/kegg/enzyme.rb 141 def diseases 142 lines_fetch('DISEASE') 143 end
DISEASE
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# File lib/bio/db/kegg/enzyme.rb 38 def genes_as_hash; super; end
Returns a Hash of the organism ID and an Array of entry IDs in GENES
field.
Calls superclass method
Bio::KEGG::Common::GenesAsHash#genes_as_hash
Also aliased as: genes
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# File lib/bio/db/kegg/enzyme.rb 136 def genes_as_strings 137 lines_fetch('GENES') 138 end
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# File lib/bio/db/kegg/enzyme.rb 111 def inhibitors 112 field_fetch('INHIBITOR').split(/\s*;\s*/) 113 end
INHIBITOR
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# File lib/bio/db/kegg/enzyme.rb 87 def iubmb_reactions 88 all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/) 89 end
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# 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
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# File lib/bio/db/kegg/enzyme.rb 146 def motifs 147 lines_fetch('MOTIF') 148 end
MOTIF
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# File lib/bio/db/kegg/enzyme.rb 59 def names 60 field_fetch('NAME').split(/\s*;\s*/) 61 end
NAME
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# File lib/bio/db/kegg/enzyme.rb 54 def obsolete? 55 entry[/Obsolete/] ? true : false 56 end
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# File lib/bio/db/kegg/enzyme.rb 33 def orthologs_as_hash; super; end
Returns a Hash of the orthology ID and definition in ORTHOLOGY
field.
Calls superclass method
Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash
Also aliased as: orthologs
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# File lib/bio/db/kegg/enzyme.rb 131 def orthologs_as_strings 132 lines_fetch('ORTHOLOGY') 133 end
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# File lib/bio/db/kegg/enzyme.rb 28 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
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# File lib/bio/db/kegg/enzyme.rb 126 def pathways_as_strings 127 lines_fetch('PATHWAY') 128 end
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# File lib/bio/db/kegg/enzyme.rb 106 def products 107 field_fetch('PRODUCT').split(/\s*;\s*/) 108 end
PRODUCT
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# File lib/bio/db/kegg/enzyme.rb 78 def reaction 79 field_fetch('REACTION') 80 end
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# 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
STRUCTURES
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# File lib/bio/db/kegg/enzyme.rb 101 def substrates 102 field_fetch('SUBSTRATE').split(/\s*;\s*/) 103 end
SUBSTRATE
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# File lib/bio/db/kegg/enzyme.rb 73 def sysname 74 field_fetch('SYSNAME') 75 end
SYSNAME