chemicalml 0.1.0 → 0.2.0

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

@@ -12,22 +12,38 @@ module Chemicalml
             attribute :count, :string
             attribute :formal_charge, :string
             attribute :spin_multiplicity, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :chirality, :string
             attribute :names, :name, collection: true
             attribute :identifiers, :identifier, collection: true
+            attribute :formulas, :formula, collection: true
+            attribute :properties, :property, collection: true
+            attribute :labels, :label, collection: true
             attribute :atom_array, :atomArray
             attribute :bond_array, :bondArray
             attribute :molecules, :molecule, collection: true
 
+                        attribute :crystal, :crystal
+            attribute :spectra, :spectrum
+            attribute :property_lists, :propertyList, collection: true
+
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "molecule"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
               map_attribute "count", to: :count
               map_attribute "formalCharge", to: :formal_charge
               map_attribute "spinMultiplicity", to: :spin_multiplicity
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "chirality", to: :chirality
               map_element "name", to: :names
               map_element "identifier", to: :identifiers
+              map_element "formula", to: :formulas
+              map_element "property", to: :properties
+              map_element "label", to: :labels
               map_element "atomArray", to: :atom_array
               map_element "bondArray", to: :bond_array
               map_element "molecule", to: :molecules

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module MoleculeList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::MoleculeList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :molecules, :molecule, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "molecule", to: :molecules
+              root "moleculeList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -12,7 +12,7 @@ module Chemicalml
             attribute :dict_ref, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "name"
               map_content to: :content
               map_attribute "convention", to: :convention

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Object
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Object
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "object"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "type", to: :type
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Observation
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Observation
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "observation"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -16,7 +16,7 @@ module Chemicalml
             attribute :matrix, :matrix
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "parameter"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -13,7 +13,7 @@ module Chemicalml
             attribute :parameters, :parameter, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "parameterList"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Particle
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Particle
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "particle"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "type", to: :type
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Peak
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Peak
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :xValue, :string
+            attribute :xUnits, :string
+            attribute :xMultiplier, :string
+            attribute :yValue, :string
+            attribute :yUnits, :string
+            attribute :yMultiplicity, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "peak"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "xValue", to: :xValue
+              map_attribute "xUnits", to: :xUnits
+              map_attribute "xMultiplier", to: :xMultiplier
+              map_attribute "yValue", to: :yValue
+              map_attribute "yUnits", to: :yUnits
+              map_attribute "yMultiplicity", to: :yMultiplicity
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module PeakGroup
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::PeakGroup
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :peaks, :peak, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "peak", to: :peaks
+              root "peakGroup"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module PeakList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::PeakList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :peaks, :peak, collection: true
+            attribute :peak_groups, :peakGroup, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "peak", to: :peaks
+              map_element "peakGroup", to: :peak_groups
+              root "peakList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module PeakStructure
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::PeakStructure
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :peakShape, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "peakStructure"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "peakShape", to: :peakShape
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Plane3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Plane3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "plane3"
+              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
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Point3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Point3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "point3"
+              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
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Potential
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Potential
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :formRef, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "potential"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "formRef", to: :formRef
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module PotentialForm
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::PotentialForm
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "potentialForm"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "type", to: :type
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module PotentialList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::PotentialList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :potentials, :potential, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "potential", to: :potentials
+              root "potentialList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -10,7 +10,7 @@ module Chemicalml
             attribute :substance, :substance
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "product"
               map_element "substance", to: :substance
             end

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

@@ -10,7 +10,7 @@ module Chemicalml
             attribute :products, :product, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "productList"
               map_element "product", to: :products
             end

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

@@ -16,7 +16,7 @@ module Chemicalml
             attribute :matrix, :matrix
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "property"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -13,7 +13,7 @@ module Chemicalml
             attribute :properties, :property, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "propertyList"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -10,7 +10,7 @@ module Chemicalml
             attribute :substance, :substance
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "reactant"
               map_element "substance", to: :substance
             end

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

@@ -10,7 +10,7 @@ module Chemicalml
             attribute :reactants, :reactant, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "reactantList"
               map_element "reactant", to: :reactants
             end

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

@@ -11,16 +11,24 @@ module Chemicalml
             attribute :title, :string
             attribute :type, :string
             attribute :state, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
             attribute :reactant_list, :reactantList
             attribute :product_list, :productList
 
+                        attribute :spectator_list, :spectatorList
+            attribute :condition_list, :conditionList
+            attribute :metadata_lists, :metadataList, collection: true
+
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "reaction"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
               map_attribute "type", to: :type
               map_attribute "state", to: :state
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
               map_element "reactantList", to: :reactant_list
               map_element "productList", to: :product_list
             end

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

@@ -10,7 +10,7 @@ module Chemicalml
             attribute :reactions, :reaction, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "reactionList"
               map_element "reaction", to: :reactions
             end

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ReactionScheme
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ReactionScheme
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :reaction_step_lists, :reactionStepList, collection: true
+            attribute :reactions, :reaction, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "reactionStepList", to: :reaction_step_lists
+              map_element "reaction", to: :reactions
+              root "reactionScheme"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ReactionStep
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ReactionStep
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :reaction, :reaction
+            attribute :reactant_list, :reactantList
+            attribute :product_list, :productList
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "reaction", to: :reaction
+              map_element "reactantList", to: :reactant_list
+              map_element "productList", to: :product_list
+              root "reactionStep"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end