Class: Chem::GSpan

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

Constant Summary collapse

FIRST_NODE = 
/\((\d+)\)/
REG_NODE = 
/\s*(\d+)\s*\((\d*)(f|b)(\d+)\)/

Class Method Summary collapse

Class Method Details

.parse(str, name = "") ⇒ Object

Parse one-lined gSpan formatted string and return molecule object.



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# File 'lib/chem/db/gspan.rb', line 22

def self.parse str, name = ""
  mol = GSpanMolecule.new
  mol.name = name

  first_atom = GSpanAtom.new(FIRST_NODE.match(str)[1].to_i)
  mol.nodes.push(first_atom)

  str.scan(REG_NODE) do |s|
    bond = GSpanBond.new( s[0].to_i )
    if s[2] == 'f'
      from_atom = mol.nodes[ s[1].to_i ]
      to_atom = GSpanAtom.new( s[3].to_i )
      mol.nodes.push(to_atom)
    else # s[2] == 'b'
      from_atom = mol.nodes[ mol.nodes.size-1 ]
      to_atom = mol.nodes[ s[3].to_i ]
    end
    mol.edges.push([bond, from_atom, to_atom ])
  end

  mol
end

.save(mols, filename, params = {}) ⇒ Object

Save molecule as gSpan formatted file. Example :

Chem::GSpan.save(mols , "filename") # mols : an array of molecules



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# File 'lib/chem/db/gspan.rb', line 48

def self.save mols, filename, params = {}
  open(filename, "w") do |out|
    mols.each_with_index do |mol, mol_idx|
      out.puts "t # #{mol_idx} -1 #{mol.name}"
      mol.nodes.each_with_index do |node, idx|
        out.puts "v %d %d" % [idx, node.atomic_number]
      end
      mol.edges.each_with_index do |(bond, node1, node2), idx|
        out.puts "e %d %d %d" % [mol.nodes.index(node1), mol.nodes.index(node2), bond.v]
      end
      out.puts
    end
    
  end
end