class Bio::KEGG::ENZYME
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
new(entry)
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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()
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ALL_REAC ‘;’
# File lib/bio/db/kegg/enzyme.rb 83 def all_reac 84 field_fetch('ALL_REAC') 85 end
classes()
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CLASS
# File lib/bio/db/kegg/enzyme.rb 68 def classes 69 lines_fetch('CLASS') 70 end
cofactors()
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COFACTOR
# File lib/bio/db/kegg/enzyme.rb 116 def cofactors 117 field_fetch('COFACTOR').split(/\s*;\s*/) 118 end
comment()
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COMMENT
# File lib/bio/db/kegg/enzyme.rb 121 def comment 122 field_fetch('COMMENT') 123 end
dblinks_as_hash()
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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
# File lib/bio/db/kegg/enzyme.rb 23 def dblinks_as_hash; super; end
Also aliased as: dblinks
dblinks_as_strings()
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DBLINKS
# File lib/bio/db/kegg/enzyme.rb 161 def dblinks_as_strings 162 lines_fetch('DBLINKS') 163 end
diseases()
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DISEASE
# File lib/bio/db/kegg/enzyme.rb 141 def diseases 142 lines_fetch('DISEASE') 143 end
entry()
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ENTRY
# File lib/bio/db/kegg/enzyme.rb 46 def entry 47 field_fetch('ENTRY') 48 end
entry_id()
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# File lib/bio/db/kegg/enzyme.rb 50 def entry_id 51 entry[/EC (\S+)/, 1] 52 end
genes_as_hash()
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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
# File lib/bio/db/kegg/enzyme.rb 38 def genes_as_hash; super; end
Also aliased as: genes
genes_as_strings()
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# File lib/bio/db/kegg/enzyme.rb 136 def genes_as_strings 137 lines_fetch('GENES') 138 end
inhibitors()
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INHIBITOR
# File lib/bio/db/kegg/enzyme.rb 111 def inhibitors 112 field_fetch('INHIBITOR').split(/\s*;\s*/) 113 end
iubmb_reactions()
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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
kegg_reactions()
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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
motifs()
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MOTIF
# File lib/bio/db/kegg/enzyme.rb 146 def motifs 147 lines_fetch('MOTIF') 148 end
name()
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# File lib/bio/db/kegg/enzyme.rb 63 def name 64 names.first 65 end
names()
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NAME
# File lib/bio/db/kegg/enzyme.rb 59 def names 60 field_fetch('NAME').split(/\s*;\s*/) 61 end
obsolete?()
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# File lib/bio/db/kegg/enzyme.rb 54 def obsolete? 55 entry[/Obsolete/] ? true : false 56 end
orthologs_as_hash()
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Returns a Hash of the orthology ID and definition in ORTHOLOGY
field.
Calls superclass method
Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash
# File lib/bio/db/kegg/enzyme.rb 33 def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings()
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# File lib/bio/db/kegg/enzyme.rb 131 def orthologs_as_strings 132 lines_fetch('ORTHOLOGY') 133 end
pathways_as_hash()
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Returns a Hash of the pathway ID and name in PATHWAY
field.
Calls superclass method
Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash
# File lib/bio/db/kegg/enzyme.rb 28 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings()
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# File lib/bio/db/kegg/enzyme.rb 126 def pathways_as_strings 127 lines_fetch('PATHWAY') 128 end
products()
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PRODUCT
# File lib/bio/db/kegg/enzyme.rb 106 def products 107 field_fetch('PRODUCT').split(/\s*;\s*/) 108 end
reaction()
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# File lib/bio/db/kegg/enzyme.rb 78 def reaction 79 field_fetch('REACTION') 80 end
structures()
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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()
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SUBSTRATE
# File lib/bio/db/kegg/enzyme.rb 101 def substrates 102 field_fetch('SUBSTRATE').split(/\s*;\s*/) 103 end
sysname()
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SYSNAME
# File lib/bio/db/kegg/enzyme.rb 73 def sysname 74 field_fetch('SYSNAME') 75 end