Class: Chem::KEGG::KeggReactionParser

Inherits:
Object
  • Object
show all
Includes:
KeggFormat, Enumerable
Defined in:
lib/chem/db/kegg.rb

Instance Method Summary collapse

Methods included from KeggFormat

#compound_folder=, #each_entry

Constructor Details

#initialize(filename) ⇒ KeggReactionParser

Returns a new instance of KeggReactionParser.



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# File 'lib/chem/db/kegg.rb', line 268

def initialize filename
  @input = File.open(filename)
end

Instance Method Details

#each ⇒ Object 



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# File 'lib/chem/db/kegg.rb', line 290

def each
  reaction = nil
  each_entry do |str, state|
    case state
    when "ENTRY"
#          reaction = Reaction.find(:first, :conditions => ["entry = ?", str.split[0]])
#            if reaction == nil
      reaction = KEGGReaction.new
      reaction.entry = str.split[0]
#          end
    when "NAME"
      reaction.name = str
    when "DEFINITION"
      #@definition = str
    when "EQUATION"
      c = str.split("<=>")
      reaction.compounds << parse_compounds(c[0])
      reaction.compounds << parse_compounds(c[1])
    when "RPAIR"
      # @rpair = str
    when "ENZYME"
      str.split.each do |e|
        ec = KeggEc.new
        ec.entry = "EC" + e
        sp = e.split(".")
        ec.number = sp.collect{|i| i.to_i}
        reaction.ecs << ec
      end
    when "///"
      #          reaction.save
      yield reaction
    when "PATHWAY"
    when "COMMENT"
    when "REFERENCE"
    else
      p state
    end
  end
end

#parse_compounds(species) ⇒ Object 



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# File 'lib/chem/db/kegg.rb', line 272

def parse_compounds species
  ary = []
  species.split(" + ").each do |mol|
    stoichiometry = 1
    if m = /(\d+) *[CG]/.match(mol)
      stoichiometry = m[1].to_i
    end
    compound_entry = ""
    if m = /(C\d+)/.match(mol)
      compound_entry = m[1]
    elsif m = /(G\d+)/.match(mol)
      compound_entry = m[1]
    end
    ary.push([compound_entry, stoichiometry])
  end
  ary
end