Module: Chem::MDL::MdlMolParser

Included in:
KEGG::KeggCompound, MdlMolecule
Defined in:
lib/chem/db/mdl.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#filename ⇒ Object (readonly)

Returns the value of attribute filename.



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# File 'lib/chem/db/mdl.rb', line 178

def filename
  @filename
end

#mol_name ⇒ Object (readonly)

Returns the value of attribute mol_name.



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# File 'lib/chem/db/mdl.rb', line 190

def mol_name
  @mol_name
end

Instance Method Details

#date_time ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 194

def date_time
  year_last_two = @header_line2[14..15].to_i
  year = year_last_two + (year_last_two > 80 ? 1900 : 2000)
  @date ||= DateTime.new(
                         year,
                         @header_line2[10..11].to_i,
                         @header_line2[12..13].to_i,
                         @header_line2[16..17].to_i,
                         @header_line2[18..19].to_i)
end

#dimensional_codes ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 205

def dimensional_codes
  @dimensional_codes ||=  @header_line2[20..21]
end

#entry ⇒ Object Also known as: name 



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# File 'lib/chem/db/mdl.rb', line 185

def entry
  @title
end

#open(filename) ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 179

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

#parse(input) ⇒ Object

Raises:

  • (MDLException) 


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# File 'lib/chem/db/mdl.rb', line 209

def parse(input)
  @mol_name = input.readline.chop
  @header_line2 = input.readline.chop
  raise MDLException if @comment = input.readline == nil
  line = input.readline
  n_atom = line[0..2].to_i
  n_bond = line[3..5].to_i

  if 0 > n_atom or 999 < n_atom or 0 > n_bond or 999 < n_bond
    raise "counts line format error"
  end

  n_atom.times do |n|
    mol = MDLAtom.new(input.readline)
    mol.number = n + 1
    @nodes.push(mol)
  end

  n_bond.times do |n|
    line = input.readline
    b = MDLBond.new line
    b_n = line[0..2].to_i
    e_n = line[3..5].to_i
    if (b_n > n_atom || b_n < 1 || e_n > n_atom || e_n < 1)
      p line
      raise "MDL bond line format error"
    end

    @edges.push([b, @nodes[b_n - 1], @nodes[e_n - 1]])
  end
  input.each do |line|
    break if /M  END/.match(line)
  end
  self
end

#program_name ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 192

def program_name ; @program_name ||= @header_line2[2..9] end