chemicalml 0.2.0 → 0.3.0

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Formula
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :concise, :string
@@ -17,18 +19,37 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :atom_array, :atomArray
 
+            attribute :formulas_inner, :formula, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "formula"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "concise", to: :concise
-              map_attribute "inline", to: :inline
-              map_attribute "formalCharge", to: :formal_charge
-              map_attribute "count", to: :count
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_element "atomArray", to: :atom_array
+              root 'formula'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'concise', to: :concise
+              map_attribute 'inline', to: :inline
+              map_attribute 'formalCharge', to: :formal_charge
+              map_attribute 'count', to: :count
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'atomArray', to: :atom_array
+              map_element 'formula', to: :formulas_inner
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'atomArray', to: :atom_array
+              map 'formula', to: :formulas_inner
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'concise', to: :concise
+              map 'inline', to: :inline
+              map 'formalCharge', to: :formal_charge
+              map 'count', to: :count
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
             end
           end
         end

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

@@ -7,25 +7,49 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Fragment
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :molecule, :molecule
+            attribute :molecule, :molecule
             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
-              map_element "atomArray", to: :atom_array
-              map_element "bondArray", to: :bond_array
-              root "fragment"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'molecule', to: :molecule
+              map_element 'atomArray', to: :atom_array
+              map_element 'bondArray', to: :bond_array
+              root 'fragment'
+              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 'role', to: :role
+              map_attribute 'countExpression', to: :count_expression
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'molecule', to: :molecule
+              map 'atomArray', to: :atom_array
+              map 'bondArray', to: :bond_array
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'role', to: :role
+              map 'countExpression', to: :count_expression
             end
           end
         end

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

@@ -7,21 +7,40 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::FragmentList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :fragments, :fragment, collection: true
+            attribute :fragments, :fragment, collection: true
 
+            attribute :ref, :string
+            attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "fragment", to: :fragments
-              root "fragmentList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'fragment', to: :fragments
+              root 'fragmentList'
+              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 'role', to: :role
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'fragment', to: :fragments
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'role', to: :role
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Gradient
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,14 +18,25 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "gradient"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "units", to: :units
+              root 'gradient'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'units', to: :units
               map_content to: :content
             end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
+            end
           end
         end
       end

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

@@ -7,16 +7,34 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Identifier
+
             attribute :value, :string
             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
+              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
+            key_value do
+              map 'value', to: :value
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'version', to: :version
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'tautomeric', to: :tautomeric
             end
           end
         end

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

@@ -0,0 +1,52 @@
+# 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
+            key_value do
+              map 'builtin', to: :builtin
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'units', to: :units
+              map 'unitsRef', to: :units_ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,55 @@
+# 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
+            key_value do
+              map 'builtin', to: :builtin
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'size', to: :size
+              map 'units', to: :units
+              map 'unitsRef', to: :units_ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Isotope
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,17 +16,36 @@ module Chemicalml
             attribute :number, :string
             attribute :elementType, :string
             attribute :spinMultiplicity, :string
+            attribute :spin, :string
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "isotope"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "number", to: :number
-              map_attribute "elementType", to: :elementType
-              map_attribute "spinMultiplicity", to: :spinMultiplicity
+              root 'isotope'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'number', to: :number
+              map_attribute 'elementType', to: :elementType
+              map_attribute 'spinMultiplicity', to: :spinMultiplicity
+              map_attribute 'spin', to: :spin
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'number', to: :number
+              map 'elementType', to: :elementType
+              map 'spinMultiplicity', to: :spinMultiplicity
+              map 'spin', to: :spin
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,21 +7,32 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::IsotopeList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :isotopes, :isotope, collection: true
+            attribute :isotopes, :isotope, collection: true
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "isotope", to: :isotopes
-              root "isotopeList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'isotope', to: :isotopes
+              root 'isotopeList'
+              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
+            key_value do
+              map 'isotope', to: :isotopes
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,20 +7,42 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Join
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :atomRefs2, :string
 
+            attribute :ref, :string
+            attribute :molecule_refs2, :string
+            attribute :order, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "join"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRefs2", to: :atomRefs2
+              root 'join'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              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
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRefs2', to: :atomRefs2
+              map 'ref', to: :ref
+              map 'moleculeRefs2', to: :molecule_refs2
+              map 'order', to: :order
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Kpoint
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,15 +15,25 @@ module Chemicalml
             attribute :weight, :string
             attribute :content, :string
 
+            attribute :label, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "kpoint"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "weight", to: :weight
+              root 'kpoint'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'weight', to: :weight
               map_content to: :content
+              map_attribute 'label', to: :label
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'weight', to: :weight
+              map 'label', to: :label
             end
           end
         end

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

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::KpointList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :kpoints, :kpoint, collection: true
+            attribute :kpoints, :kpoint, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "kpoint", to: :kpoints
-              root "kpointList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'kpoint', to: :kpoints
+              root 'kpointList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+            end
+            key_value do
+              map 'kpoint', to: :kpoints
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

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

@@ -7,18 +7,28 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Label
+
             attribute :id, :string
             attribute :value, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :object_class, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "label"
-              map_attribute "id", to: :id
-              map_attribute "value", to: :value
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'label'
+              map_attribute 'id', to: :id
+              map_attribute 'value', to: :value
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'objectClass', to: :object_class
+            end
+            key_value do
+              map 'id', to: :id
+              map 'value', to: :value
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'objectClass', to: :object_class
             end
           end
         end