class Bio::KEGG::REACTION

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source

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


Arguments:

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

Returns

Bio::KEGG::REACTION object

Calls superclass method Bio::NCBIDB.new
# File lib/bio/db/kegg/reaction.rb, line 38
def initialize(entry)
  super(entry, TAGSIZE)
end

Public Instance Methods

definition() click to toggle source

Definition of the reaction, described in the DEFINITION line.


Returns

String

# File lib/bio/db/kegg/reaction.rb, line 59
def definition
  field_fetch('DEFINITION')
end
entry_id() click to toggle source

ID of the entry, described in the ENTRY line.


Returns

String

# File lib/bio/db/kegg/reaction.rb, line 45
def entry_id
  field_fetch('ENTRY')[/\S+/]
end
enzymes() click to toggle source

Enzymes described in the ENZYME line.


Returns

Array containing String

# File lib/bio/db/kegg/reaction.rb, line 117
def enzymes
  unless @data['ENZYME']
    @data['ENZYME'] = fetch('ENZYME').scan(/\S+/)
  end
  @data['ENZYME']
end
equation() click to toggle source

Chemical equation, described in the EQUATION line.


Returns

String

# File lib/bio/db/kegg/reaction.rb, line 66
def equation
  field_fetch('EQUATION')
end
name() click to toggle source

Name of the reaction, described in the NAME line.


Returns

String

# File lib/bio/db/kegg/reaction.rb, line 52
def name
  field_fetch('NAME')
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/reaction.rb, line 30
def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings() click to toggle source

Orthologs described in the ORTHOLOGY lines.


Returns

Array containing String

# File lib/bio/db/kegg/reaction.rb, line 127
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/reaction.rb, line 25
def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathway information, described in the PATHWAY lines.


Returns

Array containing String

# File lib/bio/db/kegg/reaction.rb, line 110
def pathways_as_strings
  lines_fetch('PATHWAY')
end
rpairs()
Alias for: rpairs_as_hash
rpairs_as_hash() click to toggle source

KEGG RPAIR (ReactantPair) information, described in the RPAIR lines. Returns a hash of RPair IDs and [ name, type ] informations, for example,

{ "RP12733" => [ "C00022_C00900", "trans" ],
  "RP05698" => [ "C00011_C00022", "leave" ],
  "RP00440" => [ "C00022_C00900", "main" ]
}

Returns

Hash

# File lib/bio/db/kegg/reaction.rb, line 85
def rpairs_as_hash
  unless defined? @rpairs_as_hash
    rps = {}
    rpairs_as_strings.each do |line|
      _, entry_id, name, rptype = line.split(/\s+/)
      rps[entry_id] = [ name, rptype ]
    end
    @rpairs_as_hash = rps
  end
  @rpairs_as_hash
end
Also aliased as: rpairs
rpairs_as_strings() click to toggle source

KEGG RPAIR (ReactantPair) information, described in the RPAIR lines.


Returns

Array containing String

# File lib/bio/db/kegg/reaction.rb, line 73
def rpairs_as_strings
  lines_fetch('RPAIR')
end
rpairs_as_tokens() click to toggle source

Returns the content of the RPAIR entry as tokens (RPair signature, RPair ID, , RPair type).


Returns

Array containing String

# File lib/bio/db/kegg/reaction.rb, line 103
def rpairs_as_tokens
  fetch('RPAIR').split(/\s+/)
end