Class: Bio::KEGG::COMPOUND

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

Overview

Description

Bio::KEGG::COMPOUND is a parser class for the KEGG COMPOUND database entry. KEGG COMPOUND is a chemical structure database.

References

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) ⇒ COMPOUND

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

Arguments:

  • (required) entry: (String) single entry as a string

Returns

Bio::KEGG::COMPOUND object



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

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

Instance Method Details

#comment ⇒ Object

COMMENT



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

def comment
  field_fetch('COMMENT')
end

#dblinks_as_hash ⇒ Object Also known as: dblinks

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.



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

def dblinks_as_hash; super; end

#dblinks_as_strings ⇒ Object

DBLINKS



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

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

#entry_id ⇒ Object

ENTRY



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

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

#enzymes ⇒ Object

ENZYME



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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

#formula ⇒ Object

FORMULA



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

def formula
  field_fetch('FORMULA')
end

#glycans ⇒ Object

GLYCAN



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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

#kcf ⇒ Object

ATOM, BOND



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

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

#mass ⇒ Object

MASS



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

def mass
  field_fetch('MASS').to_f
end

#name ⇒ Object

The first name recorded in the NAME field.



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

def name
  names.first
end

#names ⇒ Object

NAME



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

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

#pathways_as_hash ⇒ Object Also known as: pathways

Returns a Hash of the pathway ID and name in PATHWAY field.



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

def pathways_as_hash; super; end

#pathways_as_strings ⇒ Object

PATHWAY



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

def pathways_as_strings
  lines_fetch('PATHWAY') 
end

#reactions ⇒ Object

REACTION



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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

#remark ⇒ Object

REMARK



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

def remark
  field_fetch('REMARK')
end

#rpairs ⇒ Object

RPAIR



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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