chemicalml 0.2.1 → 0.3.0

data/lib/chemicalml/cml/base/alternative.rb

@@ -7,19 +7,28 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Alternative
+
             attribute :id, :string
             attribute :convention, :string
             attribute :alternative_type, :string
+            attribute :type, :string
             attribute :content, :string
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "alternative"
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "alternativeType", to: :alternative_type
+              root 'alternative'
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'alternativeType', to: :alternative_type
+              map_attribute 'type', to: :type
               map_content to: :content
             end
+            key_value do
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'alternativeType', to: :alternative_type
+              map 'type', to: :type
+            end
           end
         end
       end

data/lib/chemicalml/cml/base/amount.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Amount
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
             attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "amount"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "units", to: :units
+              root 'amount'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'units', to: :units
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
             end
           end
         end

data/lib/chemicalml/cml/base/angle.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Angle
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -22,19 +23,33 @@ module Chemicalml
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "angle"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRefs3", to: :atomRefs3
-              map_attribute "units", to: :units
-              map_attribute "angleUnits", to: :angle_units
-              map_attribute "errorValue", to: :error_value
-              map_attribute "errorBasis", to: :error_basis
-              map_attribute "min", to: :min
-              map_attribute "max", to: :max
-              map_attribute "ref", to: :ref
+              root 'angle'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRefs3', to: :atomRefs3
+              map_attribute 'units', to: :units
+              map_attribute 'angleUnits', to: :angle_units
+              map_attribute 'errorValue', to: :error_value
+              map_attribute 'errorBasis', to: :error_basis
+              map_attribute 'min', to: :min
+              map_attribute 'max', to: :max
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRefs3', to: :atomRefs3
+              map 'units', to: :units
+              map 'angleUnits', to: :angle_units
+              map 'errorValue', to: :error_value
+              map 'errorBasis', to: :error_basis
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'ref', to: :ref
             end
           end
         end

data/lib/chemicalml/cml/base/annotation.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Annotation
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "annotation"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_element "documentation", to: :documentation
+              root 'annotation'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'documentation', to: :documentation
+            end
+            key_value do
+              map 'documentation', to: :documentation
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

data/lib/chemicalml/cml/base/any_cml.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::AnyCml
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,11 +15,17 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "anyCml"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'anyCml'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

data/lib/chemicalml/cml/base/appinfo.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Appinfo
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,13 +17,20 @@ module Chemicalml
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "appinfo"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'appinfo'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
               map_content to: :content
-              map_attribute "role", to: :role
+              map_attribute 'role', to: :role
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'role', to: :role
             end
           end
         end

data/lib/chemicalml/cml/base/arg.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Arg
+
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
@@ -21,22 +22,55 @@ module Chemicalml
             attribute :eval, :string
             attribute :content, :string
 
+            attribute :atom, :atom
+            attribute :atom_type, :atomType
+            attribute :expression, :expression
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
+            attribute :scalars, :scalar, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "arg"
-              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 "name", to: :name
-              map_attribute "dataType", to: :data_type
-              map_attribute "substitute", to: :substitute
-              map_attribute "parameterName", to: :parameter_name
-              map_attribute "parentAttribute", to: :parent_attribute
-              map_attribute "delete", to: :delete
-              map_attribute "eval", to: :eval
+              root 'arg'
+              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 'name', to: :name
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'substitute', to: :substitute
+              map_attribute 'parameterName', to: :parameter_name
+              map_attribute 'parentAttribute', to: :parent_attribute
+              map_attribute 'delete', to: :delete
+              map_attribute 'eval', to: :eval
               map_content to: :content
+              map_element 'atom', to: :atom
+              map_element 'atomType', to: :atom_type
+              map_element 'expression', to: :expression
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+              map_element 'scalar', to: :scalars
+            end
+            key_value do
+              map 'atom', to: :atom
+              map 'atomType', to: :atom_type
+              map 'expression', to: :expression
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'scalar', to: :scalars
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'ref', to: :ref
+              map 'name', to: :name
+              map 'dataType', to: :data_type
+              map 'substitute', to: :substitute
+              map 'parameterName', to: :parameter_name
+              map 'parentAttribute', to: :parent_attribute
+              map 'delete', to: :delete
+              map 'eval', to: :eval
             end
           end
         end

data/lib/chemicalml/cml/base/array.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Array
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -29,26 +30,46 @@ module Chemicalml
             attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "array"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "dataType", to: :data_type
-              map_attribute "units", to: :units
-              map_attribute "size", to: :size
-              map_attribute "delimiter", to: :delimiter
+              root 'array'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'units', to: :units
+              map_attribute 'size', to: :size
+              map_attribute 'delimiter', to: :delimiter
               map_content to: :content
-              map_attribute "convention", to: :convention
-              map_attribute "errorValueArray", to: :error_value_array
-              map_attribute "errorBasis", to: :error_basis
-              map_attribute "minValueArray", to: :min_value_array
-              map_attribute "maxValueArray", to: :max_value_array
-              map_attribute "start", to: :start
-              map_attribute "end", to: :end
-              map_attribute "ref", to: :ref
-              map_attribute "constantToSI", to: :constant_to_s_i
-              map_attribute "multiplierToSI", to: :multiplier_to_s_i
-              map_attribute "unitType", to: :unit_type
+              map_attribute 'convention', to: :convention
+              map_attribute 'errorValueArray', to: :error_value_array
+              map_attribute 'errorBasis', to: :error_basis
+              map_attribute 'minValueArray', to: :min_value_array
+              map_attribute 'maxValueArray', to: :max_value_array
+              map_attribute 'start', to: :start
+              map_attribute 'end', to: :end
+              map_attribute 'ref', to: :ref
+              map_attribute 'constantToSI', to: :constant_to_s_i
+              map_attribute 'multiplierToSI', to: :multiplier_to_s_i
+              map_attribute 'unitType', to: :unit_type
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'dataType', to: :data_type
+              map 'units', to: :units
+              map 'size', to: :size
+              map 'delimiter', to: :delimiter
+              map 'convention', to: :convention
+              map 'errorValueArray', to: :error_value_array
+              map 'errorBasis', to: :error_basis
+              map 'minValueArray', to: :min_value_array
+              map 'maxValueArray', to: :max_value_array
+              map 'start', to: :start
+              map 'end', to: :end
+              map 'ref', to: :ref
+              map 'constantToSI', to: :constant_to_s_i
+              map 'multiplierToSI', to: :multiplier_to_s_i
+              map 'unitType', to: :unit_type
             end
           end
         end

data/lib/chemicalml/cml/base/array_list.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ArrayList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
             attribute :shape, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "arrayList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "shape", to: :shape
+              root 'arrayList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'shape', to: :shape
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'shape', to: :shape
             end
           end
         end

data/lib/chemicalml/cml/base/atom.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Atom
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :element_type, :string
             attribute :count, :string
@@ -25,6 +27,13 @@ module Chemicalml
             attribute :yFract, :string
             attribute :zFract, :string
             attribute :atom_parity, :atomParity
+            attribute :atom_type, :atomType
+            attribute :electrons, :electron, collection: true
+            attribute :particles, :particle, collection: true
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
+            attribute :scalars, :scalar, collection: true
+            attribute :vectors3, :vector3, collection: true
 
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -37,34 +46,81 @@ module Chemicalml
             attribute :point_group_multiplicity, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "atom"
-              map_attribute "id", to: :id
-              map_attribute "elementType", to: :element_type
-              map_attribute "count", to: :count
-              map_attribute "formalCharge", to: :formal_charge
-              map_attribute "hydrogenCount", to: :hydrogen_count
-              map_attribute "isotope", to: :isotope
-              map_attribute "isotopeNumber", to: :isotope_number
-              map_attribute "spinMultiplicity", to: :spin_multiplicity
-              map_attribute "title", to: :title
-              map_attribute "x2", to: :x2
-              map_attribute "y2", to: :y2
-              map_attribute "x3", to: :x3
-              map_attribute "y3", to: :y3
-              map_attribute "z3", to: :z3
-              map_attribute "xFract", to: :xFract
-              map_attribute "yFract", to: :yFract
-              map_attribute "zFract", to: :zFract
-              map_element "atomParity", to: :atom_parity
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "ref", to: :ref
-              map_attribute "isotopeRef", to: :isotope_ref
-              map_attribute "isotopeListRef", to: :isotope_list_ref
-              map_attribute "occupancy", to: :occupancy
-              map_attribute "role", to: :role
-              map_attribute "spaceGroupMultiplicity", to: :space_group_multiplicity
-              map_attribute "pointGroupMultiplicity", to: :point_group_multiplicity
+              root 'atom'
+              map_attribute 'id', to: :id
+              map_attribute 'elementType', to: :element_type
+              map_attribute 'count', to: :count
+              map_attribute 'formalCharge', to: :formal_charge
+              map_attribute 'hydrogenCount', to: :hydrogen_count
+              map_attribute 'isotope', to: :isotope
+              map_attribute 'isotopeNumber', to: :isotope_number
+              map_attribute 'spinMultiplicity', to: :spin_multiplicity
+              map_attribute 'title', to: :title
+              map_attribute 'x2', to: :x2
+              map_attribute 'y2', to: :y2
+              map_attribute 'x3', to: :x3
+              map_attribute 'y3', to: :y3
+              map_attribute 'z3', to: :z3
+              map_attribute 'xFract', to: :xFract
+              map_attribute 'yFract', to: :yFract
+              map_attribute 'zFract', to: :zFract
+              map_element 'atomParity', to: :atom_parity
+              map_element 'atomType', to: :atom_type
+              map_element 'electron', to: :electrons
+              map_element 'particle', to: :particles
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+              map_element 'scalar', to: :scalars
+              map_element 'vector3', to: :vectors3
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'ref', to: :ref
+              map_attribute 'isotopeRef', to: :isotope_ref
+              map_attribute 'isotopeListRef', to: :isotope_list_ref
+              map_attribute 'occupancy', to: :occupancy
+              map_attribute 'role', to: :role
+              map_attribute 'spaceGroupMultiplicity', to: :space_group_multiplicity
+              map_attribute 'pointGroupMultiplicity', to: :point_group_multiplicity
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'atomParity', to: :atom_parity
+              map 'atomType', to: :atom_type
+              map 'electron', to: :electrons
+              map 'particle', to: :particles
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'scalar', to: :scalars
+              map 'vector3', to: :vectors3
+              map 'id', to: :id
+              map 'elementType', to: :element_type
+              map 'count', to: :count
+              map 'formalCharge', to: :formal_charge
+              map 'hydrogenCount', to: :hydrogen_count
+              map 'isotope', to: :isotope
+              map 'isotopeNumber', to: :isotope_number
+              map 'spinMultiplicity', to: :spin_multiplicity
+              map 'title', to: :title
+              map 'x2', to: :x2
+              map 'y2', to: :y2
+              map 'x3', to: :x3
+              map 'y3', to: :y3
+              map 'z3', to: :z3
+              map 'xFract', to: :xFract
+              map 'yFract', to: :yFract
+              map 'zFract', to: :zFract
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'ref', to: :ref
+              map 'isotopeRef', to: :isotope_ref
+              map 'isotopeListRef', to: :isotope_list_ref
+              map 'occupancy', to: :occupancy
+              map 'role', to: :role
+              map 'spaceGroupMultiplicity', to: :space_group_multiplicity
+              map 'pointGroupMultiplicity', to: :point_group_multiplicity
             end
           end
         end