Class: Chem::KEGG::KCFRXN

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

Defined Under Namespace

Classes: RXNEdge, RXNNode

Instance Method Summary collapse

Constructor Details

#initialize(reactant, product) ⇒ KCFRXN

Returns a new instance of KCFRXN.



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# File 'lib/chem/db/kcf.rb', line 147

def initialize reactant, product
  @reactant = reactant
  @product = product
  @matched_reactants = []
  @matched_products = []
  @nodes = []
end

Instance Method Details

#corresponds(from, to) ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 155

def corresponds from, to
  @matched_reactants.push(@reactant.atoms[from])
  @matched_products.push(@product.atoms[from])
  @nodes.push(RXNNode.new(@reactant.atoms[from], @product.atoms[to]))
end

#setup_bonds ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 161

def setup_bonds
  @edges = []
  @reactant.atoms.each do |atom|
    if atom && ! @matched_reactants.member?(atom)
      @nodes.push(RXNNode.new(atom, nil))
    end
  end
  @product.atoms.each do |atom|
    if atom && ! @matched_products.member?(atom)
      @nodes.push(RXNNode.new(nil, atom))
    end
  end

  @reactant.bonds.each do |bond|
    bond.e.next_atom[bond.b] = bond
    bond.b.next_atom[bond.e] = bond
  end
  @product.bonds.each do |bond|
    bond.e.next_atom[bond.b] = bond
    bond.b.next_atom[bond.e] = bond
  end
  @nodes.each_with_index do |node, index|
    index.upto(@nodes.length - 1) do |n|
      r_edge = p_edge = nil
      if @nodes[n].reactant_node && @nodes[n].reactant_node.next_atom.has_key?(node.reactant_node)
        r_edge = @nodes[n].reactant_node.next_atom[node.reactant_node]
      end
      if @nodes[n].product_node && @nodes[n].product_node.next_atom.has_key?(node.product_node)
        p_edge = @nodes[n].product_node.next_atom[node.product_node]
      end
      if r_edge || p_edge
        edge = RXNEdge.new
        edge.reactant_edge = r_edge
        edge.product_edge = p_edge
        @edges.push(edge)
      end
    end
  end
  @edges.each do |edge|
    from = edge.reactant_edge ? edge.reactant_edge.multiplicity : 0
    to = edge.product_edge ? edge.product_edge.multiplicity : 0
    puts "%3d %3d" % [from, to]
  end
end