Class: Chem::KEGG::KCFCorrespondence

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input) ⇒ KCFCorrespondence

Returns a new instance of KCFCorrespondence.



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# File 'lib/chem/db/kcf.rb', line 222

def initialize input
  @name = []
  @input = input
  @compounds = []
  @correspondence = {}
  parse(input)
end

Instance Attribute Details

#compounds ⇒ Object (readonly)

Returns the value of attribute compounds.



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# File 'lib/chem/db/kcf.rb', line 220

def compounds
  @compounds
end

#correspondence ⇒ Object (readonly)

Returns the value of attribute correspondence.



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# File 'lib/chem/db/kcf.rb', line 220

def correspondence
  @correspondence
end

Instance Method Details

#make_rxn(dir) ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 230

def make_rxn dir
  reactant = KCF.open("#{dir}#{@compounds[0]}.kcf")
  product = KCF.open("#{dir}#{@compounds[1]}.kcf")
  rxn = KCFRXN.new(reactant, product)
  @correspondence.each do |k, corres|
    rxn.corresponds(corres[0][0], corres[1][0])
  end
  rxn.setup_bonds
end

#parse(input) ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 240

def parse input
  while ! /\/\/\//.match(line = input.readline)
    case line[0...12]
    when 'ENTRY       '
      @no = /(\d+)/.match(line)[1].to_i
    when 'NAME        '
      @name.push(line[12...-1])
    when 'COMPOUND    '
      @compounds.push(line[12...-1])
    when 'TYPE        '
      @type = line[12...-1]
    when 'ALIGN       '
      @align = line[12...-1].to_i
      alignment_mode = true
    else
      ary = line[12...-1].split
      @correspondence[ary[0].to_i] = ary[1..2].collect{|e| a = e.split(':'); [a[0].to_i, a[1]]}
    end
  end
end