chemicalml 0.2.0 → 0.2.1

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
               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

@@ -15,6 +15,7 @@ module Chemicalml
             attribute :elementType, :string
             attribute :spinMultiplicity, :string
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "isotope"
@@ -25,6 +26,7 @@ module Chemicalml
               map_attribute "number", to: :number
               map_attribute "elementType", to: :elementType
               map_attribute "spinMultiplicity", to: :spinMultiplicity
+              map_attribute "ref", to: :ref
             end
           end
         end

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

@@ -14,6 +14,7 @@ module Chemicalml
 
                         attribute :isotopes, :isotope, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "isotope", to: :isotopes
@@ -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/join.rb

@@ -13,6 +13,9 @@ module Chemicalml
             attribute :convention, :string
             attribute :atomRefs2, :string
 
+            attribute :ref, :string
+            attribute :molecule_refs2, :string
+            attribute :order, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "join"
@@ -21,6 +24,9 @@ module Chemicalml
               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

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

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

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

@@ -12,6 +12,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :object_class, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "label"
@@ -19,6 +20,7 @@ module Chemicalml
               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

@@ -16,6 +16,7 @@ module Chemicalml
 
                         attribute :lattice_vectors, :latticeVector, collection: true
 
+            attribute :space_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "latticeVector", to: :lattice_vectors
@@ -26,6 +27,7 @@ module Chemicalml
               map_attribute "convention", to: :convention
               map_attribute "latticeType", to: :latticeType
               map_attribute "units", to: :units
+              map_attribute "spaceType", to: :space_type
             end
           end
         end

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

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :convention, :string
             attribute :units, :string
 
+            attribute :periodic, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "latticeVector"
@@ -21,6 +22,7 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_attribute "units", to: :units
+              map_attribute "periodic", to: :periodic
             end
           end
         end

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

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

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

@@ -13,6 +13,9 @@ module Chemicalml
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
+            attribute :point3, :string
+            attribute :vector3, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "line3"
@@ -21,6 +24,9 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_content to: :content
+              map_attribute "units", to: :units
+              map_attribute "point3", to: :point3
+              map_attribute "vector3", to: :vector3
             end
           end
         end

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

@@ -17,6 +17,16 @@ module Chemicalml
             attribute :type, :string
             attribute :role, :string
 
+            attribute :from, :string
+            attribute :to, :string
+            attribute :ref, :string
+            attribute :from_type, :string
+            attribute :to_type, :string
+            attribute :from_set, :string
+            attribute :to_set, :string
+            attribute :from_context, :string
+            attribute :to_context, :string
+            attribute :link_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "link"
@@ -29,6 +39,16 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "type", to: :type
               map_attribute "role", to: :role
+              map_attribute "from", to: :from
+              map_attribute "to", to: :to
+              map_attribute "ref", to: :ref
+              map_attribute "fromType", to: :from_type
+              map_attribute "toType", to: :to_type
+              map_attribute "fromSet", to: :from_set
+              map_attribute "toSet", to: :to_set
+              map_attribute "fromContext", to: :from_context
+              map_attribute "toContext", to: :to_context
+              map_attribute "linkType", to: :link_type
             end
           end
         end

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

@@ -16,6 +16,7 @@ module Chemicalml
             attribute :matrices, :matrix, collection: true
             attribute :lists, :list, collection: true
 
+            attribute :type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "list"
@@ -27,6 +28,7 @@ module Chemicalml
               map_element "array", to: :arrays
               map_element "matrix", to: :matrices
               map_element "list", to: :lists
+              map_attribute "type", to: :type
             end
           end
         end

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

@@ -12,6 +12,12 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :ref, :string
+            attribute :from_type, :string
+            attribute :to_type, :string
+            attribute :from_context, :string
+            attribute :to_context, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "map"
@@ -19,6 +25,12 @@ 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 "fromType", to: :from_type
+              map_attribute "toType", to: :to_type
+              map_attribute "fromContext", to: :from_context
+              map_attribute "toContext", to: :to_context
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -17,6 +17,12 @@ module Chemicalml
             attribute :delimiter, :string
             attribute :content, :string
 
+            attribute :convention, :string
+            attribute :matrix_type, :string
+            attribute :error_value_array, :string
+            attribute :error_basis, :string
+            attribute :min_value_array, :string
+            attribute :max_value_array, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "matrix"
@@ -29,6 +35,12 @@ module Chemicalml
               map_attribute "columns", to: :columns
               map_attribute "delimiter", to: :delimiter
               map_content to: :content
+              map_attribute "convention", to: :convention
+              map_attribute "matrixType", to: :matrix_type
+              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
             end
           end
         end

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

@@ -13,6 +13,8 @@ module Chemicalml
             attribute :convention, :string
             attribute :title, :string
 
+            attribute :dict_ref, :string
+            attribute :metadata_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "metadata"
@@ -21,6 +23,8 @@ module Chemicalml
               map_attribute "content", to: :content
               map_attribute "convention", to: :convention
               map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "metadataType", to: :metadata_type
             end
           end
         end

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

@@ -12,6 +12,9 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :metadata, :metadata, collection: true
 
+            attribute :convention, :string
+            attribute :name, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "metadataList"
@@ -19,6 +22,9 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_element "metadata", to: :metadata
+              map_attribute "convention", to: :convention
+              map_attribute "name", to: :name
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -28,6 +28,11 @@ module Chemicalml
             attribute :spectra, :spectrum
             attribute :property_lists, :propertyList, collection: true
 
+            attribute :ref, :string
+            attribute :idgen, :string
+            attribute :process, :string
+            attribute :symmetry_oriented, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "molecule"
@@ -47,6 +52,11 @@ module Chemicalml
               map_element "atomArray", to: :atom_array
               map_element "bondArray", to: :bond_array
               map_element "molecule", to: :molecules
+              map_attribute "ref", to: :ref
+              map_attribute "idgen", to: :idgen
+              map_attribute "process", to: :process
+              map_attribute "symmetryOriented", to: :symmetry_oriented
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -14,6 +14,7 @@ module Chemicalml
 
                         attribute :molecules, :molecule, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               map_element "molecule", to: :molecules
@@ -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/name.rb

@@ -11,12 +11,14 @@ module Chemicalml
             attribute :convention, :string
             attribute :dict_ref, :string
 
+            attribute :id, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "name"
               map_content to: :content
               map_attribute "convention", to: :convention
               map_attribute "dictRef", to: :dict_ref
+              map_attribute "id", to: :id
             end
           end
         end

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

@@ -13,6 +13,8 @@ module Chemicalml
             attribute :convention, :string
             attribute :type, :string
 
+            attribute :name, :string
+            attribute :count, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "object"
@@ -21,6 +23,8 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_attribute "type", to: :type
+              map_attribute "name", to: :name
+              map_attribute "count", to: :count
             end
           end
         end

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

@@ -12,6 +12,8 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :type, :string
+            attribute :count, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "observation"
@@ -19,6 +21,8 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
+              map_attribute "type", to: :type
+              map_attribute "count", to: :count
             end
           end
         end

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

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

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

@@ -15,6 +15,11 @@ module Chemicalml
             attribute :array, :array
             attribute :matrix, :matrix
 
+            attribute :ref, :string
+            attribute :value, :string
+            attribute :constraint, :string
+            attribute :name, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "parameter"
@@ -25,6 +30,11 @@ module Chemicalml
               map_element "scalar", to: :scalar
               map_element "array", to: :array
               map_element "matrix", to: :matrix
+              map_attribute "ref", to: :ref
+              map_attribute "value", to: :value
+              map_attribute "constraint", to: :constraint
+              map_attribute "name", to: :name
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -12,6 +12,9 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :parameters, :parameter, collection: true
 
+            attribute :convention, :string
+            attribute :ref, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "parameterList"
@@ -19,6 +22,9 @@ module Chemicalml
               map_attribute "title", to: :title
               map_attribute "dictRef", to: :dict_ref
               map_element "parameter", to: :parameters
+              map_attribute "convention", to: :convention
+              map_attribute "ref", to: :ref
+              map_attribute "role", to: :role
             end
           end
         end

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

@@ -13,6 +13,9 @@ module Chemicalml
             attribute :convention, :string
             attribute :type, :string
 
+            attribute :x3, :string
+            attribute :y3, :string
+            attribute :z3, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "particle"
@@ -21,6 +24,9 @@ module Chemicalml
               map_attribute "dictRef", to: :dict_ref
               map_attribute "convention", to: :convention
               map_attribute "type", to: :type
+              map_attribute "x3", to: :x3
+              map_attribute "y3", to: :y3
+              map_attribute "z3", to: :z3
             end
           end
         end

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

@@ -18,6 +18,21 @@ module Chemicalml
             attribute :yUnits, :string
             attribute :yMultiplicity, :string
 
+            attribute :ref, :string
+            attribute :peak_height, :string
+            attribute :peak_multiplicity, :string
+            attribute :peak_shape, :string
+            attribute :integral, :string
+            attribute :peak_units, :string
+            attribute :x_min, :string
+            attribute :x_max, :string
+            attribute :x_width, :string
+            attribute :y_min, :string
+            attribute :y_max, :string
+            attribute :y_width, :string
+            attribute :atom_refs, :string
+            attribute :bond_refs, :string
+            attribute :molecule_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
               root "peak"
@@ -31,6 +46,21 @@ module Chemicalml
               map_attribute "yValue", to: :yValue
               map_attribute "yUnits", to: :yUnits
               map_attribute "yMultiplicity", to: :yMultiplicity
+              map_attribute "ref", to: :ref
+              map_attribute "peakHeight", to: :peak_height
+              map_attribute "peakMultiplicity", to: :peak_multiplicity
+              map_attribute "peakShape", to: :peak_shape
+              map_attribute "integral", to: :integral
+              map_attribute "peakUnits", to: :peak_units
+              map_attribute "xMin", to: :x_min
+              map_attribute "xMax", to: :x_max
+              map_attribute "xWidth", to: :x_width
+              map_attribute "yMin", to: :y_min
+              map_attribute "yMax", to: :y_max
+              map_attribute "yWidth", to: :y_width
+              map_attribute "atomRefs", to: :atom_refs
+              map_attribute "bondRefs", to: :bond_refs
+              map_attribute "moleculeRefs", to: :molecule_refs
             end
           end
         end