Class: Alumina::HIN::Parser

Inherits:
Object show all
Defined in:
lib/alumina/hin/parser.rb

Overview

Class that parses HIN files to produce Molecule instances. This class is not thread-safe! You must instantiate a new parser for each thread of your program.

Constant Summary collapse

BOND_TYPES =

Mapping of HIN file bond types to their symbol values for the Atom class.

{
  's' => :single,
  'd' => :double,
  't' => :triple,
  'a' => :aromatic
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#lenient ⇒ Object

If @true@, does not raise ParseError when

  • unknown commands are encountered,

  • the bond count is incorrect, or

  • an @endmol@‘s ID does not correspond to its @mol@’s ID.



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# File 'lib/alumina/hin/parser.rb', line 23

def lenient
  @lenient
end

Instance Method Details

#parse(input) ⇒ Array<Alumina::Molecule>

Parses HIN data and returns an array of Molecules.

Parameters:

  • input (IO, String) —

    The HIN data to parse.

Returns:

Raises:

  • (ParseError) —

    If the HIN data is improperly formatted.



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# File 'lib/alumina/hin/parser.rb', line 31

def parse(input)
  @molecules = Array.new
  @current_molecule = nil
  @line_counter = 0
  @bonds = Hash.autonew

  input.each_line do |line|
    @line_counter += 1
    next if line =~ /^\s*$/
    next if line[0] == ';' # comment
    parts = line.split(/\s+/)

    command = parts.shift
    method = :"parse_#{command}"
    if respond_to?(method) then
      send(method, *parts)
    else
      if lenient then
        next
      else
        raise ParseError.new(@line_counter, "Unknown command #{command}")
      end
    end
  end
  
  @bonds.each do |molecule, firsts|
    firsts.each do |atom1, lasts|
      lasts.each do |atom2, bond_type|
        Atom.bind molecule[atom1], molecule[atom2], BOND_TYPES[bond_type]
      end
    end
  end

  return @molecules
end