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, line 41 def initialize(entry) super(entry, TAGSIZE) end
Public Instance Methods
all_reac()
click to toggle source
ALL_REAC ';'
# File lib/bio/db/kegg/enzyme.rb, line 83 def all_reac field_fetch('ALL_REAC') end
classes()
click to toggle source
CLASS
# File lib/bio/db/kegg/enzyme.rb, line 68 def classes lines_fetch('CLASS') end
cofactors()
click to toggle source
COFACTOR
# File lib/bio/db/kegg/enzyme.rb, line 116 def cofactors field_fetch('COFACTOR').split(/\s*;\s*/) end
comment()
click to toggle source
COMMENT
# File lib/bio/db/kegg/enzyme.rb, line 121 def comment field_fetch('COMMENT') end
dblinks_as_hash()
click to toggle source
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, line 23 def dblinks_as_hash; super; end
Also aliased as: dblinks
dblinks_as_strings()
click to toggle source
DBLINKS
# File lib/bio/db/kegg/enzyme.rb, line 161 def dblinks_as_strings lines_fetch('DBLINKS') end
diseases()
click to toggle source
DISEASE
# File lib/bio/db/kegg/enzyme.rb, line 141 def diseases lines_fetch('DISEASE') end
entry()
click to toggle source
ENTRY
# File lib/bio/db/kegg/enzyme.rb, line 46 def entry field_fetch('ENTRY') end
entry_id()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 50 def entry_id entry[/EC (\S+)/, 1] end
genes_as_hash()
click to toggle source
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, line 38 def genes_as_hash; super; end
Also aliased as: genes
genes_as_strings()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 136 def genes_as_strings lines_fetch('GENES') end
inhibitors()
click to toggle source
INHIBITOR
# File lib/bio/db/kegg/enzyme.rb, line 111 def inhibitors field_fetch('INHIBITOR').split(/\s*;\s*/) end
iubmb_reactions()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 87 def iubmb_reactions all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/) end
kegg_reactions()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 91 def kegg_reactions reac = all_reac if reac[/\(other\)/] reac.sub(/.*\(other\)\s*/, '').split(/\s*;\s*/) else [] end end
motifs()
click to toggle source
MOTIF
# File lib/bio/db/kegg/enzyme.rb, line 146 def motifs lines_fetch('MOTIF') end
name()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 63 def name names.first end
names()
click to toggle source
NAME
# File lib/bio/db/kegg/enzyme.rb, line 59 def names field_fetch('NAME').split(/\s*;\s*/) end
obsolete?()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 54 def obsolete? entry[/Obsolete/] ? true : false end
orthologs_as_hash()
click to toggle source
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, line 33 def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 131 def orthologs_as_strings lines_fetch('ORTHOLOGY') end
pathways_as_hash()
click to toggle source
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, line 28 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 126 def pathways_as_strings lines_fetch('PATHWAY') end
products()
click to toggle source
PRODUCT
# File lib/bio/db/kegg/enzyme.rb, line 106 def products field_fetch('PRODUCT').split(/\s*;\s*/) end
reaction()
click to toggle source
# File lib/bio/db/kegg/enzyme.rb, line 78 def reaction field_fetch('REACTION') end
structures()
click to toggle source
STRUCTURES
# File lib/bio/db/kegg/enzyme.rb, line 151 def structures unless @data['STRUCTURES'] @data['STRUCTURES'] = fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/) end @data['STRUCTURES'] end
substrates()
click to toggle source
SUBSTRATE
# File lib/bio/db/kegg/enzyme.rb, line 101 def substrates field_fetch('SUBSTRATE').split(/\s*;\s*/) end
sysname()
click to toggle source
SYSNAME
# File lib/bio/db/kegg/enzyme.rb, line 73 def sysname field_fetch('SYSNAME') end