chemicalml 0.1.0 → 0.2.1

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BasisSet
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BasisSet
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :atomic_basis_functions, :atomicBasisFunction, collection: true
+
+            attribute :ref, :string
+            attribute :role, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "atomicBasisFunction", to: :atomic_basis_functions
+              root "basisSet"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -11,14 +11,24 @@ module Chemicalml
             attribute :atom_refs2, :string
             attribute :order, :string
             attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :bond_stereo, :bondStereo
 
+            attribute :convention, :string
+            attribute :ref, :string
+            attribute :bond_refs, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "bond"
               map_attribute "id", to: :id
               map_attribute "atomRefs2", to: :atom_refs2
               map_attribute "order", to: :order
               map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_element "bondStereo", to: :bond_stereo
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "bondRefs", to: :bond_refs
             end
           end
         end

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

@@ -9,10 +9,26 @@ module Chemicalml
             include Chemicalml::Cml::Role::BondArray
             attribute :bonds, :bond, collection: true
 
+            attribute :title, :string
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :bond_i_d_array, :string
+            attribute :atom_ref1_array, :string
+            attribute :atom_ref2_array, :string
+            attribute :order_array, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "bondArray"
               map_element "bond", to: :bonds
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "bondIDArray", to: :bond_i_d_array
+              map_attribute "atomRef1Array", to: :atom_ref1_array
+              map_attribute "atomRef2Array", to: :atom_ref2_array
+              map_attribute "orderArray", to: :order_array
             end
           end
         end

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

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

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

@@ -12,13 +12,23 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :content, :string
 
+            attribute :atom_ref_array, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :convention_value, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "bondStereo"
               map_attribute "atomRefs2", to: :atom_refs2
               map_attribute "atomRefs4", to: :atom_refs4
               map_attribute "dictRef", to: :dict_ref
               map_content to: :content
+              map_attribute "atomRefArray", to: :atom_ref_array
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "conventionValue", to: :convention_value
             end
           end
         end

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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BondType
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BondType
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :order, :string
+            attribute :ref, :string
+
+            attribute :name, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "bondType"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "order", to: :order
+              map_attribute "ref", to: :ref
+              map_attribute "name", to: :name
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BondTypeList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BondTypeList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :bond_types, :bondType, collection: true
+
+            attribute :ref, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "bondType", to: :bond_types
+              root "bondTypeList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module CellParameter
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::CellParameter
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :cellType, :string
+            attribute :parameterType, :string
+            attribute :units, :string
+
+            attribute :cell_parameter_type, :string
+            attribute :cell_parameter_error, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "cellParameter"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "cellType", to: :cellType
+              map_attribute "parameterType", to: :parameterType
+              map_attribute "units", to: :units
+              map_attribute "cellParameterType", to: :cell_parameter_type
+              map_attribute "cellParameterError", to: :cell_parameter_error
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -19,7 +19,7 @@ module Chemicalml
             attribute :lists, :list, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "module"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

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

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

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ConditionList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ConditionList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :scalars, :scalar, collection: true
+            attribute :metadata, :metadata
+
+            attribute :ref, :string
+            attribute :role, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "scalar", to: :scalars
+              map_element "metadata", to: :metadata
+              root "conditionList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Crystal
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Crystal
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :scalars, :scalar, collection: true
+            attribute :lattice, :lattice
+            attribute :symmetry, :symmetry
+
+            attribute :z, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "scalar", to: :scalars
+              map_element "lattice", to: :lattice
+              map_element "symmetry", to: :symmetry
+              root "crystal"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "z", to: :z
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

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

@@ -14,8 +14,11 @@ module Chemicalml
             attribute :description, :string
             attribute :entries, :entry, collection: true
 
+            attribute :id, :string
+            attribute :dict_ref, :string
+            attribute :href, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "dictionary"
               map_attribute "title", to: :title
               map_attribute "namespace", to: :namespace
@@ -23,6 +26,9 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_element "description", to: :description
               map_element "entry", to: :entries
+              map_attribute "id", to: :id
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "href", to: :href
             end
           end
         end

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

@@ -16,7 +16,7 @@ module Chemicalml
             attribute :description, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "entry"
               map_attribute "id", to: :id
               map_attribute "term", to: :term

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Dimension
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Dimension
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :dataType, :string
+            attribute :units, :string
+
+            attribute :dimension_basis, :string
+            attribute :name, :string
+            attribute :power, :string
+            attribute :preserve, :string
+            attribute :unit_type, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "dimension"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "dataType", to: :dataType
+              map_attribute "units", to: :units
+              map_attribute "dimensionBasis", to: :dimension_basis
+              map_attribute "name", to: :name
+              map_attribute "power", to: :power
+              map_attribute "preserve", to: :preserve
+              map_attribute "unitType", to: :unit_type
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -7,13 +7,21 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Document
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
             attribute :molecules, :molecule, collection: true
             attribute :reaction_lists, :reactionList, collection: true
             attribute :reactions, :reaction, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "cml"
+              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: :molecules
               map_element "reactionList", to: :reaction_lists
               map_element "reaction", to: :reactions

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

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

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Eigen
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Eigen
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :units, :string
+            attribute :type, :string
+            attribute :content, :string
+
+            attribute :eigen_orientation, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "eigen"
+              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
+              map_attribute "type", to: :type
+              map_content to: :content
+              map_attribute "eigenOrientation", to: :eigen_orientation
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Electron
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Electron
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRef, :string
+            attribute :bondRef, :string
+            attribute :count, :string
+            attribute :spinMultiplicity, :string
+
+            attribute :atom_refs, :string
+            attribute :bond_refs, :string
+            attribute :ref, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "electron"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "atomRef", to: :atomRef
+              map_attribute "bondRef", to: :bondRef
+              map_attribute "count", to: :count
+              map_attribute "spinMultiplicity", to: :spinMultiplicity
+              map_attribute "atomRefs", to: :atom_refs
+              map_attribute "bondRefs", to: :bond_refs
+              map_attribute "ref", to: :ref
+            end
+          end
+        end
+      end
+    end
+  end
+end