chemicalml 0.1.0

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

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

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

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

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

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Molecule
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Molecule
+            attribute :id, :string
+            attribute :title, :string
+            attribute :count, :string
+            attribute :formal_charge, :string
+            attribute :spin_multiplicity, :string
+            attribute :names, :name, collection: true
+            attribute :identifiers, :identifier, collection: true
+            attribute :atom_array, :atomArray
+            attribute :bond_array, :bondArray
+            attribute :molecules, :molecule, collection: true
+
+            xml do
+            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_element "name", to: :names
+              map_element "identifier", to: :identifiers
+              map_element "atomArray", to: :atom_array
+              map_element "bondArray", to: :bond_array
+              map_element "molecule", to: :molecules
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Name
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Name
+            attribute :content, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "name"
+              map_content to: :content
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Parameter
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Parameter
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :scalar, :scalar
+            attribute :array, :array
+            attribute :matrix, :matrix
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "parameter"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_element "scalar", to: :scalar
+              map_element "array", to: :array
+              map_element "matrix", to: :matrix
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Product
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Product
+            attribute :substance, :substance
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "product"
+              map_element "substance", to: :substance
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ProductList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ProductList
+            attribute :products, :product, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "productList"
+              map_element "product", to: :products
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Property
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Property
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :scalar, :scalar
+            attribute :array, :array
+            attribute :matrix, :matrix
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "property"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_element "scalar", to: :scalar
+              map_element "array", to: :array
+              map_element "matrix", to: :matrix
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Reactant
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Reactant
+            attribute :substance, :substance
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "reactant"
+              map_element "substance", to: :substance
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ReactantList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ReactantList
+            attribute :reactants, :reactant, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "reactantList"
+              map_element "reactant", to: :reactants
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Reaction
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Reaction
+            attribute :id, :string
+            attribute :title, :string
+            attribute :type, :string
+            attribute :state, :string
+            attribute :reactant_list, :reactantList
+            attribute :product_list, :productList
+
+            xml do
+            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_element "reactantList", to: :reactant_list
+              map_element "productList", to: :product_list
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ReactionList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ReactionList
+            attribute :reactions, :reaction, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "reactionList"
+              map_element "reaction", to: :reactions
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Substance
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Substance
+            attribute :title, :string
+            attribute :role, :string
+            attribute :molecule, :molecule
+            attribute :names, :name, collection: true
+            attribute :identifiers, :identifier, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "substance"
+              map_attribute "title", to: :title
+              map_attribute "role", to: :role
+              map_element "molecule", to: :molecule
+              map_element "name", to: :names
+              map_element "identifier", to: :identifiers
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Unit
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Unit
+            attribute :id, :string
+            attribute :title, :string
+            attribute :symbol, :string
+            attribute :parent_si, :string
+            attribute :multiplier_to_si, :string
+            attribute :constant_to_si, :string
+            attribute :unit_type, :string
+            attribute :definition, :string
+            attribute :description, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "unit"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "symbol", to: :symbol
+              map_attribute "parentSI", to: :parent_si
+              map_attribute "multiplierToSI", to: :multiplier_to_si
+              map_attribute "constantToSI", to: :constant_to_si
+              map_attribute "unitType", to: :unit_type
+              map_element "definition", to: :definition
+              map_element "description", to: :description
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module UnitList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::UnitList
+            attribute :title, :string
+            attribute :namespace, :string
+            attribute :convention, :string
+            attribute :description, :string
+            attribute :units, :unit, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "unitList"
+              map_attribute "title", to: :title
+              map_attribute "namespace", to: :namespace
+              map_attribute "convention", to: :convention
+              map_element "description", to: :description
+              map_element "unit", to: :units
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module UnitType
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::UnitType
+            attribute :id, :string
+            attribute :name, :string
+            attribute :definition, :string
+            attribute :description, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "unitType"
+              map_attribute "id", to: :id
+              map_attribute "name", to: :name
+              map_element "definition", to: :definition
+              map_element "description", to: :description
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module UnitTypeList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::UnitTypeList
+            attribute :title, :string
+            attribute :namespace, :string
+            attribute :convention, :string
+            attribute :description, :string
+            attribute :unit_types, :unitType, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "unitTypeList"
+              map_attribute "title", to: :title
+              map_attribute "namespace", to: :namespace
+              map_attribute "convention", to: :convention
+              map_element "description", to: :description
+              map_element "unitType", to: :unit_types
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base.rb

@@ -0,0 +1,51 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    # Shared attribute + xml-mapping declarations for every CML element.
+    #
+    # Each module here is mixed into the corresponding `Schema3::*` and
+    # `Schema24::*` wire class. Schema-version-specific deviations live
+    # in `Base::Schema3Only::*` / `Base::Schema24Only::*` and are
+    # included only by the relevant version's classes — keeping the
+    # shared declarations open for extension, closed for modification.
+    module Base
+      autoload :Array,            "chemicalml/cml/base/array"
+      autoload :Atom,             "chemicalml/cml/base/atom"
+      autoload :AtomArray,        "chemicalml/cml/base/atom_array"
+      autoload :AtomParity,       "chemicalml/cml/base/atom_parity"
+      autoload :Bond,             "chemicalml/cml/base/bond"
+      autoload :BondArray,        "chemicalml/cml/base/bond_array"
+      autoload :BondStereo,       "chemicalml/cml/base/bond_stereo"
+      autoload :Dictionary,       "chemicalml/cml/base/dictionary"
+      autoload :DictionaryEntry,  "chemicalml/cml/base/dictionary_entry"
+      autoload :Document,         "chemicalml/cml/base/document"
+      autoload :Formula,          "chemicalml/cml/base/formula"
+      autoload :Identifier,       "chemicalml/cml/base/identifier"
+      autoload :Label,            "chemicalml/cml/base/label"
+      autoload :List,             "chemicalml/cml/base/list"
+      autoload :Matrix,           "chemicalml/cml/base/matrix"
+      autoload :Metadata,         "chemicalml/cml/base/metadata"
+      autoload :MetadataList,     "chemicalml/cml/base/metadata_list"
+      autoload :Module,           "chemicalml/cml/base/cml_module"
+      autoload :Molecule,         "chemicalml/cml/base/molecule"
+      autoload :Name,             "chemicalml/cml/base/name"
+      autoload :Parameter,        "chemicalml/cml/base/parameter"
+      autoload :ParameterList,    "chemicalml/cml/base/parameter_list"
+      autoload :Product,          "chemicalml/cml/base/product"
+      autoload :ProductList,      "chemicalml/cml/base/product_list"
+      autoload :Property,         "chemicalml/cml/base/property"
+      autoload :PropertyList,     "chemicalml/cml/base/property_list"
+      autoload :Reaction,         "chemicalml/cml/base/reaction"
+      autoload :ReactionList,     "chemicalml/cml/base/reaction_list"
+      autoload :Reactant,         "chemicalml/cml/base/reactant"
+      autoload :ReactantList,     "chemicalml/cml/base/reactant_list"
+      autoload :Scalar,           "chemicalml/cml/base/scalar"
+      autoload :Substance,        "chemicalml/cml/base/substance"
+      autoload :Unit,             "chemicalml/cml/base/unit"
+      autoload :UnitList,         "chemicalml/cml/base/unit_list"
+      autoload :UnitType,         "chemicalml/cml/base/unit_type"
+      autoload :UnitTypeList,     "chemicalml/cml/base/unit_type_list"
+    end
+  end
+end

data/lib/chemicalml/cml/bond.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Bond.
+module Chemicalml
+  module Cml
+    remove_const(:Bond) if const_defined?(:Bond, false)
+    const_set(:Bond, Chemicalml::Cml::Schema3::Bond)
+  end
+end

data/lib/chemicalml/cml/bond_array.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::BondArray.
+module Chemicalml
+  module Cml
+    remove_const(:BondArray) if const_defined?(:BondArray, false)
+    const_set(:BondArray, Chemicalml::Cml::Schema3::BondArray)
+  end
+end