chemicalml 0.2.0 → 0.2.1

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

@@ -14,6 +14,25 @@ module Chemicalml
 
                         attribute :peaks, :peak, collection: true
 
+            attribute :ref, :string
+            attribute :peak_height, :string
+            attribute :peak_multiplicity, :string
+            attribute :peak_shape, :string
+            attribute :integral, :string
+            attribute :peak_units, :string
+            attribute :x_min, :string
+            attribute :x_max, :string
+            attribute :x_value, :string
+            attribute :x_width, :string
+            attribute :x_units, :string
+            attribute :y_min, :string
+            attribute :y_max, :string
+            attribute :y_value, :string
+            attribute :y_width, :string
+            attribute :y_units, :string
+            attribute :atom_refs, :string
+            attribute :bond_refs, :string
+            attribute :molecule_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "peak", to: :peaks
@@ -22,6 +41,25 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "peakHeight", to: :peak_height
+              map_attribute "peakMultiplicity", to: :peak_multiplicity
+              map_attribute "peakShape", to: :peak_shape
+              map_attribute "integral", to: :integral
+              map_attribute "peakUnits", to: :peak_units
+              map_attribute "xMin", to: :x_min
+              map_attribute "xMax", to: :x_max
+              map_attribute "xValue", to: :x_value
+              map_attribute "xWidth", to: :x_width
+              map_attribute "xUnits", to: :x_units
+              map_attribute "yMin", to: :y_min
+              map_attribute "yMax", to: :y_max
+              map_attribute "yValue", to: :y_value
+              map_attribute "yWidth", to: :y_width
+              map_attribute "yUnits", to: :y_units
+              map_attribute "atomRefs", to: :atom_refs
+              map_attribute "bondRefs", to: :bond_refs
+              map_attribute "moleculeRefs", to: :molecule_refs
             end
           end
         end

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

@@ -15,6 +15,7 @@ module Chemicalml
                         attribute :peaks, :peak, collection: true
             attribute :peak_groups, :peakGroup, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "peak", to: :peaks
@@ -24,6 +25,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -13,6 +13,13 @@ module Chemicalml
             attribute :convention, :string
             attribute :peakShape, :string
 
+            attribute :ref, :string
+            attribute :peak_multiplicity, :string
+            attribute :peak_structure_type, :string
+            attribute :value, :string
+            attribute :units, :string
+            attribute :atom_refs, :string
+            attribute :bond_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "peakStructure"
@@ -21,6 +28,13 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_attribute "peakShape", to: :peakShape
+              map_attribute "ref", to: :ref
+              map_attribute "peakMultiplicity", to: :peak_multiplicity
+              map_attribute "peakStructureType", to: :peak_structure_type
+              map_attribute "value", to: :value
+              map_attribute "units", to: :units
+              map_attribute "atomRefs", to: :atom_refs
+              map_attribute "bondRefs", to: :bond_refs
             end
           end
         end

data/lib/chemicalml/cml/base/plane3.rb

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "plane3"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_content to: :content
+              map_attribute "units", to: :units
             end
           end
         end

data/lib/chemicalml/cml/base/point3.rb

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "point3"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_content to: :content
+              map_attribute "units", to: :units
             end
           end
         end

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

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :type, :string
 
+            attribute :name, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "potentialForm"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_attribute "type", to: :type
+              map_attribute "name", to: :name
             end
           end
         end

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

@@ -9,10 +9,26 @@ module Chemicalml
             include Chemicalml::Cml::Role::Product
             attribute :substance, :substance
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :count, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "product"
               map_element "substance", to: :substance
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "count", to: :count
+              map_attribute "state", to: :state
             end
           end
         end

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

@@ -9,10 +9,24 @@ module Chemicalml
             include Chemicalml::Cml::Role::ProductList
             attribute :products, :product, collection: true
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :count, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "productList"
               map_element "product", to: :products
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "count", to: :count
             end
           end
         end

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

@@ -15,6 +15,9 @@ module Chemicalml
             attribute :array, :array
             attribute :matrix, :matrix
 
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "property"
@@ -25,6 +28,9 @@ module Chemicalml
               map_element "scalar", to: :scalar
               map_element "array", to: :array
               map_element "matrix", to: :matrix
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "state", to: :state
             end
           end
         end

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

@@ -12,6 +12,9 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :properties, :property, collection: true
 
+            attribute :convention, :string
+            attribute :ref, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "propertyList"
@@ -19,6 +22,9 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_element "property", to: :properties
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -9,10 +9,26 @@ module Chemicalml
             include Chemicalml::Cml::Role::Reactant
             attribute :substance, :substance
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :count, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "reactant"
               map_element "substance", to: :substance
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "count", to: :count
+              map_attribute "state", to: :state
             end
           end
         end

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

@@ -9,10 +9,24 @@ module Chemicalml
             include Chemicalml::Cml::Role::ReactantList
             attribute :reactants, :reactant, collection: true
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :count, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "reactantList"
               map_element "reactant", to: :reactants
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "count", to: :count
             end
           end
         end

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

@@ -20,6 +20,14 @@ module Chemicalml
             attribute :condition_list, :conditionList
             attribute :metadata_lists, :metadataList, collection: true
 
+            attribute :reaction_format, :string
+            attribute :ref, :string
+            attribute :reaction_role, :string
+            attribute :reaction_type, :string
+            attribute :atom_map, :string
+            attribute :electron_map, :string
+            attribute :bond_map, :string
+            attribute :yield, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "reaction"
@@ -31,6 +39,14 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_element "reactantList", to: :reactant_list
               map_element "productList", to: :product_list
+              map_attribute "reactionFormat", to: :reaction_format
+              map_attribute "ref", to: :ref
+              map_attribute "reactionRole", to: :reaction_role
+              map_attribute "reactionType", to: :reaction_type
+              map_attribute "atomMap", to: :atom_map
+              map_attribute "electronMap", to: :electron_map
+              map_attribute "bondMap", to: :bond_map
+              map_attribute "yield", to: :yield
             end
           end
         end

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

@@ -9,10 +9,22 @@ module Chemicalml
             include Chemicalml::Cml::Role::ReactionList
             attribute :reactions, :reaction, collection: true
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :name, :string
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "reactionList"
               map_element "reaction", to: :reactions
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "name", to: :name
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -15,6 +15,11 @@ module Chemicalml
                         attribute :reaction_step_lists, :reactionStepList, collection: true
             attribute :reactions, :reaction, collection: true
 
+            attribute :ref, :string
+            attribute :reaction_role, :string
+            attribute :reaction_type, :string
+            attribute :state, :string
+            attribute :reaction_format, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "reactionStepList", to: :reaction_step_lists
@@ -24,6 +29,11 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "reactionRole", to: :reaction_role
+              map_attribute "reactionType", to: :reaction_type
+              map_attribute "state", to: :state
+              map_attribute "reactionFormat", to: :reaction_format
             end
           end
         end

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

@@ -16,6 +16,9 @@ module Chemicalml
             attribute :reactant_list, :reactantList
             attribute :product_list, :productList
 
+            attribute :ref, :string
+            attribute :yield, :string
+            attribute :ratio, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "reaction", to: :reaction
@@ -26,6 +29,9 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "yield", to: :yield
+              map_attribute "ratio", to: :ratio
             end
           end
         end

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

@@ -14,6 +14,10 @@ module Chemicalml
 
                         attribute :reaction_steps, :reactionStep, collection: true
 
+            attribute :ref, :string
+            attribute :reaction_step_list_type, :string
+            attribute :reaction_format, :string
+            attribute :type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "reactionStep", to: :reaction_steps
@@ -22,6 +26,10 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "reactionStepListType", to: :reaction_step_list_type
+              map_attribute "reactionFormat", to: :reaction_format
+              map_attribute "type", to: :type
             end
           end
         end

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

@@ -12,6 +12,10 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :sphere3, :string
+            attribute :box3, :string
+            attribute :atom_set_ref, :string
+            attribute :region_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "region"
@@ -19,6 +23,10 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "sphere3", to: :sphere3
+              map_attribute "box3", to: :box3
+              map_attribute "atomSetRef", to: :atom_set_ref
+              map_attribute "regionRefs", to: :region_refs
             end
           end
         end

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

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module RelatedEntry
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::RelatedEntry
+            attribute :related_entry_type, :string
+            attribute :href, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "relatedEntry"
+              map_attribute "relatedEntryType", to: :related_entry_type
+              map_attribute "href", to: :href
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -12,6 +12,8 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :ref, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "sample"
@@ -19,6 +21,8 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "state", to: :state
             end
           end
         end

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

@@ -14,6 +14,15 @@ module Chemicalml
             attribute :units, :string
             attribute :content, :string
 
+            attribute :convention, :string
+            attribute :error_value, :string
+            attribute :error_basis, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :ref, :string
+            attribute :constant_to_s_i, :string
+            attribute :multiplier_to_s_i, :string
+            attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "scalar"
@@ -23,6 +32,15 @@ module Chemicalml
               map_attribute "dataType", to: :data_type
               map_attribute "units", to: :units
               map_content to: :content
+              map_attribute "convention", to: :convention
+              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
+              map_attribute "constantToSI", to: :constant_to_s_i
+              map_attribute "multiplierToSI", to: :multiplier_to_s_i
+              map_attribute "unitType", to: :unit_type
             end
           end
         end

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

@@ -12,6 +12,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "spectator"
@@ -19,6 +20,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -19,6 +19,12 @@ module Chemicalml
             attribute :peak_list, :peakList
             attribute :condition_list, :conditionList
 
+            attribute :ref, :string
+            attribute :molecule_ref, :string
+            attribute :spectrum_type, :string
+            attribute :measurement, :string
+            attribute :ft, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "xaxis", to: :xaxis
@@ -32,6 +38,12 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_attribute "format", to: :format
               map_attribute "condition", to: :condition
+              map_attribute "ref", to: :ref
+              map_attribute "moleculeRef", to: :molecule_ref
+              map_attribute "spectrumType", to: :spectrum_type
+              map_attribute "measurement", to: :measurement
+              map_attribute "ft", to: :ft
+              map_attribute "state", to: :state
             end
           end
         end

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

@@ -15,6 +15,7 @@ module Chemicalml
                         attribute :xaxis, :xaxis
             attribute :yaxis, :yaxis
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "xaxis", to: :xaxis
@@ -24,6 +25,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -14,6 +14,8 @@ module Chemicalml
 
                         attribute :spectra, :spectrum
 
+            attribute :ref, :string
+            attribute :molecule_ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "spectrum", to: :spectra
@@ -22,6 +24,8 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "moleculeRef", to: :molecule_ref
             end
           end
         end

data/lib/chemicalml/cml/base/sphere3.rb

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "sphere3"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_content to: :content
+              map_attribute "units", to: :units
             end
           end
         end

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module String
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::String
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "string"
+              map_attribute "builtin", to: :builtin
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end