Class: Chem::KEGG::KeggReaction

Inherits:
Object
  • Object
show all
Defined in:
lib/chem/db/kcf.rb

Defined Under Namespace

Classes: ReactionEntry

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input) ⇒ KeggReaction 



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# File 'lib/chem/db/kcf.rb', line 101

def initialize input
  @input = input
end

Class Method Details

.open(filename) ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 105

def KeggReaction.open filename
  KeggReaction.new(File.open(filename))
end

Instance Method Details

#each ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 109

def each
  while ! @input.eof?
    entry = ReactionEntry.new
    state = :INITIAL
    while ! /\/\/\//.match(line = @input.readline)
      #case line[0...12]
      type = line[0...12]
      if 'ENTRY       ' == type
        entry.entry = line[12...-1]
      elsif 'NAME        ' == type || state == :NAME
        state = :NAME
        entry.name = line[12...-1]
      elsif 'DEFINITION  '  == type || state == :DEFINITION
        state = :DEFINITION
        entry.definition.push(line[12...-1])
      elsif 'EQUATION    ' == type
        ary = line[12...-1].split('<=>')
        entry.reactants = ary[0].split('+').collect{|mol| mol.strip}
        entry.products = ary[1].split('+').collect{|mol| mol.strip}
      elsif 'RPAIR       ' == type
        entry.rpair = line[12...-1]
      elsif 'ENZYME      ' == type
        entry.ec = line[12...-1].split('.').collect{|n| n.to_i}
      elsif 'COMMENT     ' == type || state == :COMMENT
        state = :COMMENT
        entry.comment.push(line[12...-1])
      elsif 'PATHWAY     ' == type || state == :PATHWAY
        state = :PATHWAY
      else
        puts "Error Unknown line : %s" % line
      end
    end
    yield entry
  end
end