chemicalml 0.2.0 → 0.2.1

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
               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
               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

@@ -12,6 +12,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :size, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "atomSet"
@@ -19,6 +20,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "size", to: :size
             end
           end
         end

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

@@ -14,6 +14,8 @@ module Chemicalml
             attribute :elementType, :string
             attribute :ref, :string
 
+            attribute :name, :string
+            attribute :atom_ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "atomType"
@@ -23,6 +25,8 @@ module Chemicalml
               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

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

@@ -14,6 +14,7 @@ module Chemicalml
 
                         attribute :atom_types, :atomType, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "atomType", to: :atom_types
@@ -22,6 +23,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -18,6 +18,8 @@ module Chemicalml
             attribute :ms, :string
             attribute :type, :string
 
+            attribute :symbol, :string
+            attribute :lm, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "atomicBasisFunction"
@@ -31,6 +33,8 @@ module Chemicalml
               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

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

@@ -14,6 +14,7 @@ module Chemicalml
             attribute :kpointRef, :string
             attribute :weight, :string
 
+            attribute :label, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "band"
@@ -23,6 +24,7 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_attribute "kpointRef", to: :kpointRef
               map_attribute "weight", to: :weight
+              map_attribute "label", to: :label
             end
           end
         end

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

@@ -14,6 +14,8 @@ module Chemicalml
 
                         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
@@ -22,6 +24,8 @@ module Chemicalml
               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

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

@@ -14,6 +14,9 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :bond_stereo, :bondStereo
 
+            attribute :convention, :string
+            attribute :ref, :string
+            attribute :bond_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "bond"
@@ -23,6 +26,9 @@ module Chemicalml
               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
               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

@@ -12,6 +12,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :size, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "bondSet"
@@ -19,6 +20,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "size", to: :size
             end
           end
         end

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

@@ -12,6 +12,11 @@ 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
               root "bondStereo"
@@ -19,6 +24,11 @@ module Chemicalml
               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

@@ -14,6 +14,7 @@ module Chemicalml
             attribute :order, :string
             attribute :ref, :string
 
+            attribute :name, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "bondType"
@@ -23,6 +24,7 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_attribute "order", to: :order
               map_attribute "ref", to: :ref
+              map_attribute "name", to: :name
             end
           end
         end

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

@@ -14,6 +14,7 @@ module Chemicalml
 
                         attribute :bond_types, :bondType, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "bondType", to: :bond_types
@@ -22,6 +23,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -15,6 +15,8 @@ module Chemicalml
             attribute :parameterType, :string
             attribute :units, :string
 
+            attribute :cell_parameter_type, :string
+            attribute :cell_parameter_error, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "cellParameter"
@@ -25,6 +27,8 @@ module Chemicalml
               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

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

@@ -15,6 +15,8 @@ module Chemicalml
                         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
@@ -24,6 +26,8 @@ module Chemicalml
               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

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

@@ -16,6 +16,7 @@ module Chemicalml
             attribute :lattice, :lattice
             attribute :symmetry, :symmetry
 
+            attribute :z, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "scalar", to: :scalars
@@ -26,6 +27,7 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "z", to: :z
             end
           end
         end

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

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :object_class, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "description"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_content to: :content
+              map_attribute "objectClass", to: :object_class
             end
           end
         end

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

@@ -14,6 +14,9 @@ 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
               root "dictionary"
@@ -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/dimension.rb

@@ -14,6 +14,11 @@ module Chemicalml
             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"
@@ -23,6 +28,11 @@ module Chemicalml
               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

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

@@ -15,6 +15,7 @@ module Chemicalml
             attribute :type, :string
             attribute :content, :string
 
+            attribute :eigen_orientation, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "eigen"
@@ -25,6 +26,7 @@ module Chemicalml
               map_attribute "units", to: :units
               map_attribute "type", to: :type
               map_content to: :content
+              map_attribute "eigenOrientation", to: :eigen_orientation
             end
           end
         end

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

@@ -16,6 +16,9 @@ module Chemicalml
             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"
@@ -27,6 +30,9 @@ module Chemicalml
               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

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/fragment.rb

@@ -16,6 +16,9 @@ module Chemicalml
             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
@@ -26,6 +29,9 @@ module Chemicalml
               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

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

@@ -14,6 +14,8 @@ module Chemicalml
 
                         attribute :fragments, :fragment, collection: true
 
+            attribute :ref, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "fragment", to: :fragments
@@ -22,6 +24,8 @@ module Chemicalml
               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