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
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()
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, line 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, 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()
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, line 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, line 131
def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
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, line 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, 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

REACTION

# 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