chemicalml 0.1.0 → 0.2.1

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

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

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

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

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

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Float
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Float
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :units, :string
+            attribute :units_ref, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "float"
+              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_attribute "min", to: :min
+              map_attribute "max", to: :max
+              map_attribute "units", to: :units
+              map_attribute "unitsRef", to: :units_ref
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module FloatArray
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::FloatArray
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :size, :string
+            attribute :units, :string
+            attribute :units_ref, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "floatArray"
+              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_attribute "min", to: :min
+              map_attribute "max", to: :max
+              map_attribute "size", to: :size
+              map_attribute "units", to: :units
+              map_attribute "unitsRef", to: :units_ref
+              map_content to: :content
+            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 +1,41 @@
+# 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
+
+            attribute :ref, :string
+            attribute :role, :string
+            attribute :count_expression, :string
+            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
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+              map_attribute "countExpression", to: :count_expression
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,35 @@
+# 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
+
+            attribute :ref, :string
+            attribute :role, :string
+            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
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
+            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

@@ -11,12 +11,20 @@ module Chemicalml
             attribute :convention, :string
             attribute :dict_ref, :string
 
+            attribute :version, :string
+            attribute :title, :string
+            attribute :id, :string
+            attribute :tautomeric, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "identifier"
               map_attribute "value", to: :value
               map_attribute "convention", to: :convention
               map_attribute "dictRef", to: :dict_ref
+              map_attribute "version", to: :version
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "tautomeric", to: :tautomeric
             end
           end
         end

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

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Integer
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Integer
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :units, :string
+            attribute :units_ref, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "integer"
+              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_attribute "min", to: :min
+              map_attribute "max", to: :max
+              map_attribute "units", to: :units
+              map_attribute "unitsRef", to: :units_ref
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module IntegerArray
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::IntegerArray
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :size, :string
+            attribute :units, :string
+            attribute :units_ref, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "integerArray"
+              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_attribute "min", to: :min
+              map_attribute "max", to: :max
+              map_attribute "size", to: :size
+              map_attribute "units", to: :units
+              map_attribute "unitsRef", to: :units_ref
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,36 @@
+# 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
+
+            attribute :ref, :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
+              map_attribute "ref", to: :ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,33 @@
+# 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
+
+            attribute :ref, :string
+            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
+              map_attribute "ref", to: :ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,36 @@
+# 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
+
+            attribute :ref, :string
+            attribute :molecule_refs2, :string
+            attribute :order, :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
+              map_attribute "ref", to: :ref
+              map_attribute "moleculeRefs2", to: :molecule_refs2
+              map_attribute "order", to: :order
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,34 @@
+# 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
+
+            attribute :label, :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
+              map_attribute "label", to: :label
+            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

@@ -12,13 +12,15 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :object_class, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "label"
               map_attribute "id", to: :id
               map_attribute "value", to: :value
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "objectClass", to: :object_class
             end
           end
         end

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

@@ -0,0 +1,37 @@
+# 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
+
+            attribute :space_type, :string
+            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
+              map_attribute "spaceType", to: :space_type
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,32 @@
+# 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
+
+            attribute :periodic, :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
+              map_attribute "periodic", to: :periodic
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+# 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
+
+            attribute :error_value, :string
+            attribute :error_basis, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :ref, :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
+              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
+            end
+          end
+        end
+      end
+    end
+  end
+end