Class: Bio::KEGG::COMPOUND

Inherits:

Bio::KEGGDB

• Object
• DB
• NCBIDB
• Bio::KEGGDB
• Bio::KEGG::COMPOUND

show all

Includes:

Bio::KEGG::Common::DblinksAsHash, Bio::KEGG::Common::PathwaysAsHash

Defined in:

lib/bio/db/kegg/compound.rb

Overview

Constant Summary

DELIMITER =

RS = "\n///\n"

TAGSIZE =

12

Instance Method Summary (collapse)

• - (Object) comment

  COMMENT.

• - (Object) dblinks_as_hash (also: #dblinks)
• - (Object) dblinks_as_strings

  DBLINKS.

• - (Object) entry_id

  ENTRY.

• - (Object) enzymes

  ENZYME.

• - (Object) formula

  FORMULA.

• - (Object) glycans

  GLYCAN.

• - (COMPOUND) initialize(entry) constructor

  Creates a new Bio::KEGG::COMPOUND object.

• - (Object) kcf

  ATOM, BOND.

• - (Object) mass

  MASS.

• - (Object) name

  The first name recorded in the NAME field.

• - (Object) names

  NAME.

• - (Object) pathways_as_hash (also: #pathways)
• - (Object) pathways_as_strings

  PATHWAY.

• - (Object) reactions

  REACTION.

• - (Object) remark

  REMARK.

• - (Object) rpairs

  RPAIR.

Methods inherited from DB

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

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# File 'lib/bio/db/kegg/compound.rb', line 45

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

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# File 'lib/bio/db/kegg/compound.rb', line 132

def comment
  field_fetch('COMMENT')
end

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# File 'lib/bio/db/kegg/compound.rb', line 32

def dblinks_as_hash; super; end

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# File 'lib/bio/db/kegg/compound.rb', line 122

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

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

def entry_id
  field_fetch('ENTRY')[/\S+/]
end

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# File 'lib/bio/db/kegg/compound.rb', line 109

def enzymes
  unless @data['ENZYME']
    field = fetch('ENZYME')
    if /\(/.match(field)	# old version
      @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
    else
      @data['ENZYME'] = field.scan(/\S+/)
    end
  end
  @data['ENZYME']
end

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# File 'lib/bio/db/kegg/compound.rb', line 65

def formula
  field_fetch('FORMULA')
end

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

def glycans
  unless @data['GLYCAN']
    @data['GLYCAN'] = fetch('GLYCAN').split(/\s+/)
  end
  @data['GLYCAN']
end

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# File 'lib/bio/db/kegg/compound.rb', line 127

def kcf
  return "#{get('ATOM')}#{get('BOND')}"
end

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

def mass
  field_fetch('MASS').to_f
end

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# File 'lib/bio/db/kegg/compound.rb', line 60

def name
  names.first
end

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# File 'lib/bio/db/kegg/compound.rb', line 55

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

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# File 'lib/bio/db/kegg/compound.rb', line 37

def pathways_as_hash; super; end

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# File 'lib/bio/db/kegg/compound.rb', line 104

def pathways_as_strings
  lines_fetch('PATHWAY') 
end

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# File 'lib/bio/db/kegg/compound.rb', line 88

def reactions
  unless @data['REACTION']
    @data['REACTION'] = fetch('REACTION').split(/\s+/)
  end
  @data['REACTION']
end

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# File 'lib/bio/db/kegg/compound.rb', line 75

def remark
  field_fetch('REMARK')
end

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# File 'lib/bio/db/kegg/compound.rb', line 96

def rpairs
  unless @data['RPAIR']
    @data['RPAIR'] = fetch('RPAIR').split(/\s+/)
  end
  @data['RPAIR']
end