chemicalml 0.2.1 → 0.4.0

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

@@ -7,27 +7,46 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::SubstanceList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :substances, :substance, collection: true
+            attribute :substances, :substance, collection: true
 
             attribute :substance_list_type, :string
             attribute :role, :string
             attribute :ref, :string
+            attribute :type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "substance", to: :substances
-              root "substanceList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "substanceListType", to: :substance_list_type
-              map_attribute "role", to: :role
-              map_attribute "ref", to: :ref
+              map_element 'substance', to: :substances
+              root 'substanceList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'substanceListType', to: :substance_list_type
+              map_attribute 'type', to: :type
+              map_attribute 'role', to: :role
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'substance', to: :substances
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'substanceListType', to: :substance_list_type
+              map 'type', to: :type
+              map 'role', to: :role
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Symmetry
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,17 +18,37 @@ module Chemicalml
 
             attribute :irreducible_representation, :string
             attribute :number, :string
+            attribute :matrices, :matrix, collection: true
+            attribute :transform3s, :transform3, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "symmetry"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "pointGroup", to: :pointGroup
-              map_attribute "spaceGroup", to: :spaceGroup
-              map_attribute "irreducibleRepresentation", to: :irreducible_representation
-              map_attribute "number", to: :number
+              root 'symmetry'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'pointGroup', to: :pointGroup
+              map_attribute 'spaceGroup', to: :spaceGroup
+              map_attribute 'irreducibleRepresentation', to: :irreducible_representation
+              map_attribute 'number', to: :number
+              map_element 'matrix', to: :matrices
+              map_element 'transform3', to: :transform3s
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'matrix', to: :matrices
+              map 'transform3', to: :transform3s
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'pointGroup', to: :pointGroup
+              map 'spaceGroup', to: :spaceGroup
+              map 'irreducibleRepresentation', to: :irreducible_representation
+              map 'number', to: :number
             end
           end
         end

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

@@ -7,27 +7,38 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::System
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :atom_array, :atomArray
+            attribute :atom_array, :atomArray
             attribute :molecules, :molecule, collection: true
 
             attribute :dimensionality, :string
             attribute :periodicity, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "atomArray", to: :atom_array
-              map_element "molecule", to: :molecules
-              root "system"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "dimensionality", to: :dimensionality
-              map_attribute "periodicity", to: :periodicity
+              map_element 'atomArray', to: :atom_array
+              map_element 'molecule', to: :molecules
+              root 'system'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'dimensionality', to: :dimensionality
+              map_attribute 'periodicity', to: :periodicity
+            end
+            key_value do
+              map 'atomArray', to: :atom_array
+              map 'molecule', to: :molecules
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'dimensionality', to: :dimensionality
+              map 'periodicity', to: :periodicity
             end
           end
         end

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

@@ -7,13 +7,17 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Table
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_content, :tableContent
+            attribute :table_content, :tableContent
             attribute :table_header, :tableHeader
+            attribute :array_lists, :arrayList, collection: true
+            attribute :table_row_lists, :tableRowList, collection: true
 
             attribute :rows, :string
             attribute :columns, :string
@@ -22,18 +26,39 @@ module Chemicalml
             attribute :data_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableContent", to: :table_content
-              map_element "tableHeader", to: :table_header
-              root "table"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "rows", to: :rows
-              map_attribute "columns", to: :columns
-              map_attribute "units", to: :units
-              map_attribute "tableType", to: :table_type
-              map_attribute "dataType", to: :data_type
+              map_element 'tableContent', to: :table_content
+              map_element 'tableHeader', to: :table_header
+              map_element 'arrayList', to: :array_lists
+              map_element 'tableRowList', to: :table_row_lists
+              root 'table'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'rows', to: :rows
+              map_attribute 'columns', to: :columns
+              map_attribute 'units', to: :units
+              map_attribute 'tableType', to: :table_type
+              map_attribute 'dataType', to: :data_type
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'tableContent', to: :table_content
+              map 'tableHeader', to: :table_header
+              map 'arrayList', to: :array_lists
+              map 'tableRowList', to: :table_row_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'rows', to: :rows
+              map 'columns', to: :columns
+              map 'units', to: :units
+              map 'tableType', to: :table_type
+              map 'dataType', to: :data_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableCell
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,13 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tableCell"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'tableCell'
+              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
             end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+            end
           end
         end
       end

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

@@ -7,25 +7,35 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableContent
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_rows, :tableRow, collection: true
+            attribute :table_rows, :tableRow, collection: true
             attribute :table_row_lists, :tableRowList, collection: true
 
             attribute :delimiter, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableRow", to: :table_rows
-              map_element "tableRowList", to: :table_row_lists
-              root "tableContent"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "delimiter", to: :delimiter
+              map_element 'tableRow', to: :table_rows
+              map_element 'tableRowList', to: :table_row_lists
+              root 'tableContent'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'delimiter', to: :delimiter
+            end
+            key_value do
+              map 'tableRow', to: :table_rows
+              map 'tableRowList', to: :table_row_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'delimiter', to: :delimiter
             end
           end
         end

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

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableHeader
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_header_cells, :tableHeaderCell, collection: true
+            attribute :table_header_cells, :tableHeaderCell, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableHeaderCell", to: :table_header_cells
-              root "tableHeader"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableHeaderCell', to: :table_header_cells
+              root 'tableHeader'
+              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 'tableHeaderCell', to: :table_header_cells
+              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/table_header_cell.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableHeaderCell
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -20,17 +21,28 @@ module Chemicalml
             attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tableHeaderCell"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'tableHeaderCell'
+              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 "dataType", to: :data_type
-              map_attribute "units", to: :units
-              map_attribute "constantToSI", to: :constant_to_s_i
-              map_attribute "multiplierToSI", to: :multiplier_to_s_i
-              map_attribute "unitType", to: :unit_type
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'units', to: :units
+              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 'convention', to: :convention
+              map 'dataType', to: :data_type
+              map 'units', to: :units
+              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/table_row.rb

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableRow
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_cells, :tableCell, collection: true
+            attribute :table_cells, :tableCell, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableCell", to: :table_cells
-              root "tableRow"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableCell', to: :table_cells
+              root 'tableRow'
+              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 'tableCell', to: :table_cells
+              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/table_row_list.rb

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableRowList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_rows, :tableRow, collection: true
+            attribute :table_rows, :tableRow, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableRow", to: :table_rows
-              root "tableRowList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableRow', to: :table_rows
+              root 'tableRowList'
+              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 'tableRow', to: :table_rows
+              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/tcell.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Tcell
+
             attribute :units, :string
             attribute :data_type, :string
             attribute :title, :string
@@ -17,15 +18,23 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tcell"
-              map_attribute "units", to: :units
-              map_attribute "dataType", to: :data_type
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
+              root 'tcell'
+              map_attribute 'units', to: :units
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
               map_content to: :content
             end
+            key_value do
+              map 'units', to: :units
+              map 'dataType', to: :data_type
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+            end
           end
         end
       end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Torsion
+
             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 "torsion"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRefs4", to: :atomRefs4
-              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 'torsion'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRefs4', to: :atomRefs4
+              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 'atomRefs4', to: :atomRefs4
+              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/transform3.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Transform3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,13 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "transform3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'transform3'
+              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
             end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+            end
           end
         end
       end

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

@@ -7,18 +7,36 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TransitionState
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
+            attribute :molecule, :molecule
+            attribute :property_lists, :propertyList, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "transitionState"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'transitionState'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'molecule', to: :molecule
+              map_element 'propertyList', to: :property_lists
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'molecule', to: :molecule
+              map 'propertyList', to: :property_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end