chemicalml 0.1.0 → 0.2.1

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

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Line3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Line3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            attribute :units, :string
+            attribute :point3, :string
+            attribute :vector3, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "line3"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_content to: :content
+              map_attribute "units", to: :units
+              map_attribute "point3", to: :point3
+              map_attribute "vector3", to: :vector3
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Link
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Link
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :href, :string
+            attribute :rel, :string
+            attribute :title, :string
+            attribute :type, :string
+            attribute :role, :string
+
+            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"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "href", to: :href
+              map_attribute "rel", to: :rel
+              map_attribute "title", to: :title
+              map_attribute "type", to: :type
+              map_attribute "role", to: :role
+              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
+      end
+    end
+  end
+end

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

@@ -16,8 +16,9 @@ module Chemicalml
             attribute :matrices, :matrix, collection: true
             attribute :lists, :list, collection: true
 
+            attribute :type, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "list"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
@@ -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

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Map
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Map
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+            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"
+              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 "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
+      end
+    end
+  end
+end

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

@@ -17,8 +17,14 @@ 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
+              namespace Chemicalml::Cml::Namespace
               root "matrix"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
@@ -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/mechanism.rb

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

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

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

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

@@ -13,14 +13,18 @@ module Chemicalml
             attribute :convention, :string
             attribute :title, :string
 
+            attribute :dict_ref, :string
+            attribute :metadata_type, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "metadata"
               map_attribute "id", to: :id
               map_attribute "name", to: :name
               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

@@ -12,13 +12,19 @@ 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
+              namespace Chemicalml::Cml::Namespace
               root "metadataList"
               map_attribute "id", to: :id
               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

@@ -12,25 +12,51 @@ module Chemicalml
             attribute :count, :string
             attribute :formal_charge, :string
             attribute :spin_multiplicity, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :chirality, :string
             attribute :names, :name, collection: true
             attribute :identifiers, :identifier, collection: true
+            attribute :formulas, :formula, collection: true
+            attribute :properties, :property, collection: true
+            attribute :labels, :label, collection: true
             attribute :atom_array, :atomArray
             attribute :bond_array, :bondArray
             attribute :molecules, :molecule, collection: true
 
+                        attribute :crystal, :crystal
+            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
+              namespace Chemicalml::Cml::Namespace
               root "molecule"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
               map_attribute "count", to: :count
               map_attribute "formalCharge", to: :formal_charge
               map_attribute "spinMultiplicity", to: :spin_multiplicity
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "chirality", to: :chirality
               map_element "name", to: :names
               map_element "identifier", to: :identifiers
+              map_element "formula", to: :formulas
+              map_element "property", to: :properties
+              map_element "label", to: :labels
               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

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

@@ -11,12 +11,14 @@ module Chemicalml
             attribute :convention, :string
             attribute :dict_ref, :string
 
+            attribute :id, :string
             xml do
-            namespace Chemicalml::Cml::Namespace
+              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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Object
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Object
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+
+            attribute :name, :string
+            attribute :count, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "object"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              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
+      end
+    end
+  end
+end

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

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

@@ -15,8 +15,13 @@ 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
+              namespace Chemicalml::Cml::Namespace
               root "parameter"
               map_attribute "id", to: :id
               map_attribute "title", to: :title
@@ -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

@@ -12,13 +12,19 @@ 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
+              namespace Chemicalml::Cml::Namespace
               root "parameterList"
               map_attribute "id", to: :id
               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

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Particle
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Particle
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+
+            attribute :x3, :string
+            attribute :y3, :string
+            attribute :z3, :string
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "particle"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              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
+      end
+    end
+  end
+end

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

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Peak
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Peak
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :xValue, :string
+            attribute :xUnits, :string
+            attribute :xMultiplier, :string
+            attribute :yValue, :string
+            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"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "xValue", to: :xValue
+              map_attribute "xUnits", to: :xUnits
+              map_attribute "xMultiplier", to: :xMultiplier
+              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
+      end
+    end
+  end
+end