Module: Chemicalml::Cml::Base::AtomArray

Included in:
Schema24::AtomArray, Schema3::AtomArray
Defined in:
lib/chemicalml/cml/base/atom_array.rb

Overview

Container for a list of atoms. Two equivalent serialisations:

<atomArray><atom id="a1" elementType="C"/></atomArray>

The parallel-array form uses the same XML attribute names as the singular <atom> (e.g. elementType, x3), NOT names like elementTypeArray. The XSD names the attribute groups elementTypeArray etc., but the wire attribute is elementType.

Class Method Summary collapse

Class Method Details

.included(klass) ⇒ Object 



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# File 'lib/chemicalml/cml/base/atom_array.rb', line 17

def self.included(klass)
  klass.class_eval do
    include Chemicalml::Cml::Role::AtomArray

    attribute :atoms, :atom, collection: true

    attribute :title, :string
    attribute :id, :string
    attribute :convention, :string
    attribute :dict_ref, :string
    attribute :ref, :string

    # Parallel-array attributes. Wire names match the singular
    # <atom> attributes; the Ruby names use _array suffix for
    # clarity at the call site.
    attribute :atom_id_array, :string
    attribute :count_array, :string
    attribute :element_type_array, :string
    attribute :formal_charge_array, :string
    attribute :hydrogen_count_array, :string
    attribute :occupancy_array, :string
    attribute :x2_array, :string
    attribute :y2_array, :string
    attribute :x3_array, :string
    attribute :y3_array, :string
    attribute :z3_array, :string
    attribute :x_fract_array, :string
    attribute :y_fract_array, :string
    attribute :z_fract_array, :string
    xml do
      namespace Chemicalml::Cml::Namespace
      root 'atomArray'
      map_element 'atom', to: :atoms
      map_attribute 'title', to: :title
      map_attribute 'id', to: :id
      map_attribute 'convention', to: :convention
      map_attribute 'dictRef', to: :dict_ref
      map_attribute 'ref', to: :ref
      map_attribute 'atomID', to: :atom_id_array
      map_attribute 'count', to: :count_array
      map_attribute 'elementType', to: :element_type_array
      map_attribute 'formalCharge', to: :formal_charge_array
      map_attribute 'hydrogenCount', to: :hydrogen_count_array
      map_attribute 'occupancy', to: :occupancy_array
      map_attribute 'x2', to: :x2_array
      map_attribute 'y2', to: :y2_array
      map_attribute 'x3', to: :x3_array
      map_attribute 'y3', to: :y3_array
      map_attribute 'z3', to: :z3_array
      map_attribute 'xFract', to: :x_fract_array
      map_attribute 'yFract', to: :y_fract_array
      map_attribute 'zFract', to: :z_fract_array
    end
    key_value do
      map 'atom', to: :atoms
      map 'title', to: :title
      map 'id', to: :id
      map 'convention', to: :convention
      map 'dictRef', to: :dict_ref
      map 'ref', to: :ref
      map 'atomID', to: :atom_id_array
      map 'count', to: :count_array
      map 'elementType', to: :element_type_array
      map 'formalCharge', to: :formal_charge_array
      map 'hydrogenCount', to: :hydrogen_count_array
      map 'occupancy', to: :occupancy_array
      map 'x2', to: :x2_array
      map 'y2', to: :y2_array
      map 'x3', to: :x3_array
      map 'y3', to: :y3_array
      map 'z3', to: :z3_array
      map 'xFract', to: :x_fract_array
      map 'yFract', to: :y_fract_array
      map 'zFract', to: :z_fract_array
    end
  end
end