class Bio::KEGG::GLYCAN

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source
Calls superclass method Bio::NCBIDB.new
# File lib/bio/db/kegg/glycan.rb, line 36
def initialize(entry)
  super(entry, TAGSIZE)
end

Public Instance Methods

comment() click to toggle source

COMMENT

# File lib/bio/db/kegg/glycan.rb, line 118
def comment
  field_fetch('COMMENT')
end
composition() click to toggle source

COMPOSITION

# File lib/bio/db/kegg/glycan.rb, line 51
def composition
  unless @data['COMPOSITION']
    hash = Hash.new(0)
    fetch('COMPOSITION').scan(/\((\S+)\)(\d+)/).each do |key, val|
      hash[key] = val.to_i
    end
    @data['COMPOSITION'] = hash
  end
  @data['COMPOSITION']
end
compounds() click to toggle source

COMPOUND

# File lib/bio/db/kegg/glycan.rb, line 76
def compounds
  unless @data['COMPOUND']
    @data['COMPOUND'] = fetch('COMPOUND').split(/\s+/)
  end
  @data['COMPOUND']
end
entry_id() click to toggle source

ENTRY

# File lib/bio/db/kegg/glycan.rb, line 41
def entry_id
  field_fetch('ENTRY')[/\S+/]
end
enzymes() click to toggle source

ENZYME

# File lib/bio/db/kegg/glycan.rb, line 97
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
kcf() click to toggle source

ATOM, BOND

# File lib/bio/db/kegg/glycan.rb, line 153
def kcf
  return "#{get('NODE')}#{get('EDGE')}"
end
keggclass() click to toggle source

CLASS

# File lib/bio/db/kegg/glycan.rb, line 71
def keggclass
  field_fetch('CLASS') 
end
mass() click to toggle source

MASS

# File lib/bio/db/kegg/glycan.rb, line 63
def mass
  unless @data['MASS']
    @data['MASS'] = field_fetch('MASS')[/[\d\.]+/].to_f
  end
  @data['MASS']
end
name() click to toggle source

NAME

# File lib/bio/db/kegg/glycan.rb, line 46
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/glycan.rb, line 33
def orthologs_as_hash; super; end
Also aliased as: orthologs
orthologs_as_strings() click to toggle source

ORTHOLOGY

# File lib/bio/db/kegg/glycan.rb, line 110
def orthologs_as_strings
  unless @data['ORTHOLOGY']
    @data['ORTHOLOGY'] = lines_fetch('ORTHOLOGY')
  end
  @data['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/glycan.rb, line 28
def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

PATHWAY

# File lib/bio/db/kegg/glycan.rb, line 92
def pathways_as_strings
  lines_fetch('PATHWAY') 
end
reactions() click to toggle source

REACTION

# File lib/bio/db/kegg/glycan.rb, line 84
def reactions
  unless @data['REACTION']
    @data['REACTION'] = fetch('REACTION').split(/\s+/)
  end
  @data['REACTION']
end
references() click to toggle source

REFERENCE

# File lib/bio/db/kegg/glycan.rb, line 128
def references
  unless @data['REFERENCE']
    ary = Array.new
    lines = lines_fetch('REFERENCE')
    lines.each do |line|
      if /^\d+\s+\[PMID/.match(line)
        ary << line
      else
        ary.last << " #{line.strip}"
      end
    end
    @data['REFERENCE'] = ary
  end
  @data['REFERENCE']
end
remark() click to toggle source

REMARK

# File lib/bio/db/kegg/glycan.rb, line 123
def remark
  field_fetch('REMARK')
end