Class: Bio::KEGG::ENZYME

Inherits:
Bio::KEGGDB show all
Includes:
Common::DblinksAsHash, Common::GenesAsHash, Common::OrthologsAsHash, Common::PathwaysAsHash
Defined in:
lib/bio/db/kegg/enzyme.rb

Constant Summary

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

Instance Method Summary (collapse)

Methods inherited from DB

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

Constructor Details

- (ENZYME) initialize(entry)

Returns a new instance of ENZYME



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# File 'lib/bio/db/kegg/enzyme.rb', line 41

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

Instance Method Details

- (Object) all_reac

ALL_REAC ';'



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# File 'lib/bio/db/kegg/enzyme.rb', line 83

def all_reac
  field_fetch('ALL_REAC')
end

- (Object) classes

CLASS



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# File 'lib/bio/db/kegg/enzyme.rb', line 68

def classes
  lines_fetch('CLASS')
end

- (Object) cofactors

COFACTOR



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# File 'lib/bio/db/kegg/enzyme.rb', line 116

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

- (Object) comment

COMMENT



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# File 'lib/bio/db/kegg/enzyme.rb', line 121

def comment
  field_fetch('COMMENT')
end


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# File 'lib/bio/db/kegg/enzyme.rb', line 23

def dblinks_as_hash; super; end

DBLINKS



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# File 'lib/bio/db/kegg/enzyme.rb', line 161

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

- (Object) diseases

DISEASE



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# File 'lib/bio/db/kegg/enzyme.rb', line 141

def diseases
  lines_fetch('DISEASE')
end

- (Object) entry

ENTRY



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# File 'lib/bio/db/kegg/enzyme.rb', line 46

def entry
  field_fetch('ENTRY')
end

- (Object) entry_id



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# File 'lib/bio/db/kegg/enzyme.rb', line 50

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

- (Object) genes_as_hash Also known as: genes



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

def genes_as_hash; super; end

- (Object) genes_as_strings

GENES



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# File 'lib/bio/db/kegg/enzyme.rb', line 136

def genes_as_strings
  lines_fetch('GENES')
end

- (Object) inhibitors

INHIBITOR



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# File 'lib/bio/db/kegg/enzyme.rb', line 111

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

- (Object) iubmb_reactions



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# File 'lib/bio/db/kegg/enzyme.rb', line 87

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

- (Object) kegg_reactions



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# 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

- (Object) motifs

MOTIF



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# File 'lib/bio/db/kegg/enzyme.rb', line 146

def motifs
  lines_fetch('MOTIF')
end

- (Object) name



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# File 'lib/bio/db/kegg/enzyme.rb', line 63

def name
  names.first
end

- (Object) names

NAME



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# File 'lib/bio/db/kegg/enzyme.rb', line 59

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

- (Boolean) obsolete?

Returns:

  • (Boolean)


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# File 'lib/bio/db/kegg/enzyme.rb', line 54

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

- (Object) orthologs_as_hash Also known as: orthologs



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

def orthologs_as_hash; super; end

- (Object) orthologs_as_strings

ORTHOLOGY



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# File 'lib/bio/db/kegg/enzyme.rb', line 131

def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end

- (Object) pathways_as_hash Also known as: pathways



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# File 'lib/bio/db/kegg/enzyme.rb', line 28

def pathways_as_hash; super; end

- (Object) pathways_as_strings

PATHWAY



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# File 'lib/bio/db/kegg/enzyme.rb', line 126

def pathways_as_strings
  lines_fetch('PATHWAY')
end

- (Object) products

PRODUCT



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# File 'lib/bio/db/kegg/enzyme.rb', line 106

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

- (Object) reaction

REACTION



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# File 'lib/bio/db/kegg/enzyme.rb', line 78

def reaction
  field_fetch('REACTION')
end

- (Object) structures

STRUCTURES



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# 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

- (Object) substrates

SUBSTRATE



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# File 'lib/bio/db/kegg/enzyme.rb', line 101

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

- (Object) sysname

SYSNAME



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# File 'lib/bio/db/kegg/enzyme.rb', line 73

def sysname
  field_fetch('SYSNAME')
end