Class: Bio::KEGG::ENZYME

Inherits:
Bio::KEGGDB show all
Defined in:
lib/bio/db/kegg/enzyme.rb

Constant Summary collapse

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

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(entry) ⇒ ENZYME

Returns a new instance of ENZYME.



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# File 'lib/bio/db/kegg/enzyme.rb', line 20

def initialize(entry)
  super(entry, TAGSIZE)
end

Instance Method Details

#all_reac ⇒ Object

ALL_REAC ‘;’



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# File 'lib/bio/db/kegg/enzyme.rb', line 62

def all_reac
  field_fetch('ALL_REAC')
end

#classes ⇒ Object

CLASS



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# File 'lib/bio/db/kegg/enzyme.rb', line 47

def classes
  lines_fetch('CLASS')
end

#cofactors ⇒ Object

COFACTOR



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# File 'lib/bio/db/kegg/enzyme.rb', line 95

def cofactors
  field_fetch('COFACTOR').split(/\s*;\s*/)
end

#comment ⇒ Object

COMMENT



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# File 'lib/bio/db/kegg/enzyme.rb', line 100

def comment
  field_fetch('COMMENT')
end

#dblinks ⇒ Object

DBLINKS



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# File 'lib/bio/db/kegg/enzyme.rb', line 140

def dblinks
  lines_fetch('DBLINKS')
end

#diseases ⇒ Object

DISEASE



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# File 'lib/bio/db/kegg/enzyme.rb', line 120

def diseases
  lines_fetch('DISEASE')
end

#entry ⇒ Object

ENTRY



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# File 'lib/bio/db/kegg/enzyme.rb', line 25

def entry
  field_fetch('ENTRY')
end

#entry_id ⇒ Object 



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# File 'lib/bio/db/kegg/enzyme.rb', line 29

def entry_id
  entry[/EC (\S+)/, 1]
end

#genes ⇒ Object

GENES



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# File 'lib/bio/db/kegg/enzyme.rb', line 115

def genes
  lines_fetch('GENES')
end

#inhibitors ⇒ Object

INHIBITOR



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# File 'lib/bio/db/kegg/enzyme.rb', line 90

def inhibitors
  field_fetch('INHIBITOR').split(/\s*;\s*/)
end

#iubmb_reactions ⇒ Object 



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# File 'lib/bio/db/kegg/enzyme.rb', line 66

def iubmb_reactions
  all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/)
end

#kegg_reactions ⇒ Object 



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# File 'lib/bio/db/kegg/enzyme.rb', line 70

def kegg_reactions
  reac = all_reac
  if reac[/\(other\)/]
    reac.sub(/.*\(other\)\s*/, '').split(/\s*;\s*/)
  else
    []
  end
end

#motifs ⇒ Object

MOTIF



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# File 'lib/bio/db/kegg/enzyme.rb', line 125

def motifs
  lines_fetch('MOTIF')
end

#name ⇒ Object 



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# File 'lib/bio/db/kegg/enzyme.rb', line 42

def name
  names.first
end

#names ⇒ Object

NAME



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# File 'lib/bio/db/kegg/enzyme.rb', line 38

def names
  field_fetch('NAME').split(/\s*;\s*/)
end

#obsolete? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/db/kegg/enzyme.rb', line 33

def obsolete?
  entry[/Obsolete/] ? true : false
end

#orthologs ⇒ Object

ORTHOLOGY



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# File 'lib/bio/db/kegg/enzyme.rb', line 110

def orthologs
  lines_fetch('ORTHOLOGY')
end

#pathways ⇒ Object

PATHWAY



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# File 'lib/bio/db/kegg/enzyme.rb', line 105

def pathways
  lines_fetch('PATHWAY')
end

#products ⇒ Object

PRODUCT



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# File 'lib/bio/db/kegg/enzyme.rb', line 85

def products
  field_fetch('PRODUCT').split(/\s*;\s*/)
end

#reaction ⇒ Object

REACTION



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# File 'lib/bio/db/kegg/enzyme.rb', line 57

def reaction
  field_fetch('REACTION')
end

#structures ⇒ Object

STRUCTURES



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# File 'lib/bio/db/kegg/enzyme.rb', line 130

def structures
  unless @data['STRUCTURES']
    @data['STRUCTURES'] = fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
  end
  @data['STRUCTURES']
end

#substrates ⇒ Object

SUBSTRATE



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# File 'lib/bio/db/kegg/enzyme.rb', line 80

def substrates
  field_fetch('SUBSTRATE').split(/\s*;\s*/)
end

#sysname ⇒ Object

SYSNAME



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# File 'lib/bio/db/kegg/enzyme.rb', line 52

def sysname
  field_fetch('SYSNAME')
end