chemicalml 0.1.0 → 0.2.0

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

@@ -0,0 +1,34 @@
+# 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
+
+            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
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,36 @@
+# 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
+
+            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
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -18,7 +18,7 @@ module Chemicalml
             attribute :atom_array, :atomArray
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "formula"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Fragment
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Fragment
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :molecule, :molecule
+            attribute :atom_array, :atomArray
+            attribute :bond_array, :bondArray
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "molecule", to: :molecule
+              map_element "atomArray", to: :atom_array
+              map_element "bondArray", to: :bond_array
+              root "fragment"
+              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/fragment_list.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module FragmentList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::FragmentList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :fragments, :fragment, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "fragment", to: :fragments
+              root "fragmentList"
+              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/gradient.rb

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

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

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

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

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

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module IsotopeList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::IsotopeList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :isotopes, :isotope, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "isotope", to: :isotopes
+              root "isotopeList"
+              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/join.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Join
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Join
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRefs2, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "join"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "atomRefs2", to: :atomRefs2
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module KpointList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::KpointList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :kpoints, :kpoint, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "kpoint", to: :kpoints
+              root "kpointList"
+              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/label.rb

@@ -13,7 +13,7 @@ module Chemicalml
             attribute :convention, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "label"
               map_attribute "id", to: :id
               map_attribute "value", to: :value

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Lattice
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Lattice
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :latticeType, :string
+            attribute :units, :string
+
+                        attribute :lattice_vectors, :latticeVector, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "latticeVector", to: :lattice_vectors
+              root "lattice"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "latticeType", to: :latticeType
+              map_attribute "units", to: :units
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Length
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Length
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRefs2, :string
+            attribute :units, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "length"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "atomRefs2", to: :atomRefs2
+              map_attribute "units", to: :units
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base/line3.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Line3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Line3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "line3"
+              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/link.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Link
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Link
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :href, :string
+            attribute :rel, :string
+            attribute :title, :string
+            attribute :type, :string
+            attribute :role, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "link"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "href", to: :href
+              map_attribute "rel", to: :rel
+              map_attribute "title", to: :title
+              map_attribute "type", to: :type
+              map_attribute "role", to: :role
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -17,7 +17,7 @@ module Chemicalml
             attribute :lists, :list, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "list"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Map
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Map
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "map"
+              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/matrix.rb

@@ -18,7 +18,7 @@ module Chemicalml
             attribute :content, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "matrix"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Mechanism
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Mechanism
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :mechanism_components, :mechanismComponent, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "mechanismComponent", to: :mechanism_components
+              root "mechanism"
+              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/mechanism_component.rb

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

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

@@ -14,7 +14,7 @@ module Chemicalml
             attribute :title, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "metadata"
               map_attribute "id", to: :id
               map_attribute "name", to: :name

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

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