chemicalml 0.1.0 → 0.2.1

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Alternative
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Alternative
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :alternative_type, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "alternative"
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "alternativeType", to: :alternative_type
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Angle
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Angle
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRefs3, :string
+            attribute :units, :string
+
+            attribute :angle_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 "angle"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "atomRefs3", to: :atomRefs3
+              map_attribute "units", to: :units
+              map_attribute "angleUnits", to: :angle_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

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

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

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

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

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

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

@@ -0,0 +1,46 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Arg
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Arg
+            attribute :title, :string
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :ref, :string
+            attribute :name, :string
+            attribute :data_type, :string
+            attribute :substitute, :string
+            attribute :parameter_name, :string
+            attribute :parent_attribute, :string
+            attribute :delete, :string
+            attribute :eval, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "arg"
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "ref", to: :ref
+              map_attribute "name", to: :name
+              map_attribute "dataType", to: :data_type
+              map_attribute "substitute", to: :substitute
+              map_attribute "parameterName", to: :parameter_name
+              map_attribute "parentAttribute", to: :parent_attribute
+              map_attribute "delete", to: :delete
+              map_attribute "eval", to: :eval
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -16,8 +16,19 @@ module Chemicalml
             attribute :delimiter, :string
             attribute :content, :string
 
+            attribute :convention, :string
+            attribute :error_value_array, :string
+            attribute :error_basis, :string
+            attribute :min_value_array, :string
+            attribute :max_value_array, :string
+            attribute :start, :string
+            attribute :end, :string
+            attribute :ref, :string
+            attribute :constant_to_s_i, :string
+            attribute :multiplier_to_s_i, :string
+            attribute :unit_type, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "array"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
@@ -27,6 +38,17 @@ module Chemicalml
               map_attribute "size", to: :size
               map_attribute "delimiter", to: :delimiter
               map_content to: :content
+              map_attribute "convention", to: :convention
+              map_attribute "errorValueArray", to: :error_value_array
+              map_attribute "errorBasis", to: :error_basis
+              map_attribute "minValueArray", to: :min_value_array
+              map_attribute "maxValueArray", to: :max_value_array
+              map_attribute "start", to: :start
+              map_attribute "end", to: :end
+              map_attribute "ref", to: :ref
+              map_attribute "constantToSI", to: :constant_to_s_i
+              map_attribute "multiplierToSI", to: :multiplier_to_s_i
+              map_attribute "unitType", to: :unit_type
             end
           end
         end

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

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

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

@@ -16,9 +16,27 @@ module Chemicalml
             attribute :isotope_number, :string
             attribute :spin_multiplicity, :string
             attribute :title, :string
+            attribute :x2, :string
+            attribute :y2, :string
+            attribute :x3, :string
+            attribute :y3, :string
+            attribute :z3, :string
+            attribute :xFract, :string
+            attribute :yFract, :string
+            attribute :zFract, :string
+            attribute :atom_parity, :atomParity
 
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :ref, :string
+            attribute :isotope_ref, :string
+            attribute :isotope_list_ref, :string
+            attribute :occupancy, :string
+            attribute :role, :string
+            attribute :space_group_multiplicity, :string
+            attribute :point_group_multiplicity, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "atom"
               map_attribute "id", to: :id
               map_attribute "elementType", to: :element_type
@@ -29,6 +47,24 @@ module Chemicalml
               map_attribute "isotopeNumber", to: :isotope_number
               map_attribute "spinMultiplicity", to: :spin_multiplicity
               map_attribute "title", to: :title
+              map_attribute "x2", to: :x2
+              map_attribute "y2", to: :y2
+              map_attribute "x3", to: :x3
+              map_attribute "y3", to: :y3
+              map_attribute "z3", to: :z3
+              map_attribute "xFract", to: :xFract
+              map_attribute "yFract", to: :yFract
+              map_attribute "zFract", to: :zFract
+              map_element "atomParity", to: :atom_parity
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "ref", to: :ref
+              map_attribute "isotopeRef", to: :isotope_ref
+              map_attribute "isotopeListRef", to: :isotope_list_ref
+              map_attribute "occupancy", to: :occupancy
+              map_attribute "role", to: :role
+              map_attribute "spaceGroupMultiplicity", to: :space_group_multiplicity
+              map_attribute "pointGroupMultiplicity", to: :point_group_multiplicity
             end
           end
         end

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

@@ -9,10 +9,48 @@ module Chemicalml
             include Chemicalml::Cml::Role::AtomArray
             attribute :atoms, :atom, collection: true
 
+            attribute :title, :string
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :ref, :string
+            attribute :element_type_array, :string
+            attribute :count_array, :string
+            attribute :formal_charge_array, :string
+            attribute :hydrogen_count_array, :string
+            attribute :occupancy_array, :string
+            attribute :x2_array, :string
+            attribute :y2_array, :string
+            attribute :x3_array, :string
+            attribute :y3_array, :string
+            attribute :z3_array, :string
+            attribute :x_fract_array, :string
+            attribute :y_fract_array, :string
+            attribute :z_fract_array, :string
+            attribute :atom_i_d_array, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "atomArray"
               map_element "atom", to: :atoms
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "ref", to: :ref
+              map_attribute "elementTypeArray", to: :element_type_array
+              map_attribute "countArray", to: :count_array
+              map_attribute "formalChargeArray", to: :formal_charge_array
+              map_attribute "hydrogenCountArray", to: :hydrogen_count_array
+              map_attribute "occupancyArray", to: :occupancy_array
+              map_attribute "x2Array", to: :x2_array
+              map_attribute "y2Array", to: :y2_array
+              map_attribute "x3Array", to: :x3_array
+              map_attribute "y3Array", to: :y3_array
+              map_attribute "z3Array", to: :z3_array
+              map_attribute "xFractArray", to: :x_fract_array
+              map_attribute "yFractArray", to: :y_fract_array
+              map_attribute "zFractArray", to: :z_fract_array
+              map_attribute "atomIDArray", to: :atom_i_d_array
             end
           end
         end

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

@@ -10,11 +10,19 @@ module Chemicalml
             attribute :atom_refs4, :string
             attribute :content, :string
 
+            attribute :title, :string
+            attribute :id, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "atomParity"
               map_attribute "atomRefs4", to: :atom_refs4
               map_content to: :content
+              map_attribute "title", to: :title
+              map_attribute "id", to: :id
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
             end
           end
         end

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

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

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module AtomType
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::AtomType
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :elementType, :string
+            attribute :ref, :string
+
+            attribute :name, :string
+            attribute :atom_ref, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "atomType"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "elementType", to: :elementType
+              map_attribute "ref", to: :ref
+              map_attribute "name", to: :name
+              map_attribute "atomRef", to: :atom_ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module AtomTypeList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::AtomTypeList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :atom_types, :atomType, collection: true
+
+            attribute :ref, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "atomType", to: :atom_types
+              root "atomTypeList"
+              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/atomic_basis_function.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module AtomicBasisFunction
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::AtomicBasisFunction
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRef, :string
+            attribute :n, :string
+            attribute :l, :string
+            attribute :m, :string
+            attribute :ms, :string
+            attribute :type, :string
+
+            attribute :symbol, :string
+            attribute :lm, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "atomicBasisFunction"
+              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 "n", to: :n
+              map_attribute "l", to: :l
+              map_attribute "m", to: :m
+              map_attribute "ms", to: :ms
+              map_attribute "type", to: :type
+              map_attribute "symbol", to: :symbol
+              map_attribute "lm", to: :lm
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BandList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BandList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :bands, :band, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "band", to: :bands
+              root "bandList"
+              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