chemicalml 0.1.0 → 0.2.0

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ReactionStepList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ReactionStepList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :reaction_steps, :reactionStep, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "reactionStep", to: :reaction_steps
+              root "reactionStepList"
+              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/reactive_centre.rb

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

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

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

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

@@ -15,7 +15,7 @@ module Chemicalml
             attribute :content, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "scalar"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module SpectatorList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::SpectatorList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :spectators, :spectator, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "spectator", to: :spectators
+              root "spectatorList"
+              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/spectrum.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Spectrum
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Spectrum
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :format, :string
+            attribute :condition, :string
+
+                        attribute :xaxis, :xaxis
+            attribute :yaxis, :yaxis
+            attribute :peak_list, :peakList
+            attribute :condition_list, :conditionList
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "xaxis", to: :xaxis
+              map_element "yaxis", to: :yaxis
+              map_element "peakList", to: :peak_list
+              map_element "conditionList", to: :condition_list
+              root "spectrum"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "format", to: :format
+              map_attribute "condition", to: :condition
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module SpectrumData
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::SpectrumData
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :xaxis, :xaxis
+            attribute :yaxis, :yaxis
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "xaxis", to: :xaxis
+              map_element "yaxis", to: :yaxis
+              root "spectrumData"
+              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/spectrum_list.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module SpectrumList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::SpectrumList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :spectra, :spectrum
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "spectrum", to: :spectra
+              root "spectrumList"
+              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/sphere3.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Sphere3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Sphere3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "sphere3"
+              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
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

@@ -14,7 +14,7 @@ module Chemicalml
             attribute :identifiers, :identifier, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "substance"
               map_attribute "title", to: :title
               map_attribute "role", to: :role

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module SubstanceList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::SubstanceList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :substances, :substance, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "substance", to: :substances
+              root "substanceList"
+              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/symmetry.rb

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

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

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Table
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Table
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :table_content, :tableContent
+            attribute :table_header, :tableHeader
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "tableContent", to: :table_content
+              map_element "tableHeader", to: :table_header
+              root "table"
+              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/table_cell.rb

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

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

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module TableContent
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::TableContent
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :table_rows, :tableRow, collection: true
+            attribute :table_row_lists, :tableRowList, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "tableRow", to: :table_rows
+              map_element "tableRowList", to: :table_row_lists
+              root "tableContent"
+              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/table_header.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module TableHeader
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::TableHeader
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :table_header_cells, :tableHeaderCell, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "tableHeaderCell", to: :table_header_cells
+              root "tableHeader"
+              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/table_header_cell.rb

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

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

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