chemicalml 0.2.1 → 0.3.0

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Dimension
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -21,18 +22,31 @@ module Chemicalml
             attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "dimension"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "dataType", to: :dataType
-              map_attribute "units", to: :units
-              map_attribute "dimensionBasis", to: :dimension_basis
-              map_attribute "name", to: :name
-              map_attribute "power", to: :power
-              map_attribute "preserve", to: :preserve
-              map_attribute "unitType", to: :unit_type
+              root 'dimension'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'dataType', to: :dataType
+              map_attribute 'units', to: :units
+              map_attribute 'dimensionBasis', to: :dimension_basis
+              map_attribute 'name', to: :name
+              map_attribute 'power', to: :power
+              map_attribute 'preserve', to: :preserve
+              map_attribute 'unitType', to: :unit_type
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'dataType', to: :dataType
+              map 'units', to: :units
+              map 'dimensionBasis', to: :dimension_basis
+              map 'name', to: :name
+              map 'power', to: :power
+              map 'preserve', to: :preserve
+              map 'unitType', to: :unit_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Document
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,14 +18,23 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "cml"
-              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: :molecules
-              map_element "reactionList", to: :reaction_lists
-              map_element "reaction", to: :reactions
+              root 'cml'
+              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: :molecules
+              map_element 'reactionList', to: :reaction_lists
+              map_element 'reaction', to: :reactions
+            end
+            key_value do
+              map 'molecule', to: :molecules
+              map 'reactionList', to: :reaction_lists
+              map 'reaction', to: :reactions
+              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/documentation.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Documentation
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,13 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "documentation"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'documentation'
+              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
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+            end
           end
         end
       end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Eigen
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,17 +18,39 @@ module Chemicalml
             attribute :content, :string
 
             attribute :eigen_orientation, :string
+            attribute :orientation, :string
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "eigen"
-              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_attribute "type", to: :type
+              root 'eigen'
+              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_attribute 'type', to: :type
               map_content to: :content
-              map_attribute "eigenOrientation", to: :eigen_orientation
+              map_attribute 'eigenOrientation', to: :eigen_orientation
+              map_attribute 'orientation', to: :orientation
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
+              map 'type', to: :type
+              map 'eigenOrientation', to: :eigen_orientation
+              map 'orientation', to: :orientation
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Electron
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -21,18 +22,31 @@ module Chemicalml
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "electron"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRef", to: :atomRef
-              map_attribute "bondRef", to: :bondRef
-              map_attribute "count", to: :count
-              map_attribute "spinMultiplicity", to: :spinMultiplicity
-              map_attribute "atomRefs", to: :atom_refs
-              map_attribute "bondRefs", to: :bond_refs
-              map_attribute "ref", to: :ref
+              root 'electron'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRef', to: :atomRef
+              map_attribute 'bondRef', to: :bondRef
+              map_attribute 'count', to: :count
+              map_attribute 'spinMultiplicity', to: :spinMultiplicity
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'bondRefs', to: :bond_refs
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRef', to: :atomRef
+              map 'bondRef', to: :bondRef
+              map 'count', to: :count
+              map 'spinMultiplicity', to: :spinMultiplicity
+              map 'atomRefs', to: :atom_refs
+              map 'bondRefs', to: :bond_refs
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Enumeration
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,13 +17,21 @@ module Chemicalml
             attribute :default, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "enumeration"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "value", to: :value
-              map_attribute "default", to: :default
+              root 'enumeration'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'value', to: :value
+              map_attribute 'default', to: :default
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'value', to: :value
+              map 'default', to: :default
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Expression
+
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
@@ -14,15 +15,29 @@ module Chemicalml
             attribute :data_type, :string
             attribute :content, :string
 
+            attribute :operators, :operator, collection: true
+            attribute :parameters, :parameter, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "expression"
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "dataType", to: :data_type
+              root 'expression'
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'dataType', to: :data_type
               map_content to: :content
+              map_element 'operator', to: :operators
+              map_element 'parameter', to: :parameters
+            end
+            key_value do
+              map 'operator', to: :operators
+              map 'parameter', to: :parameters
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'dataType', to: :data_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Float
+
             attribute :builtin, :string
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -20,18 +21,29 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "float"
-              map_attribute "builtin", to: :builtin
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "min", to: :min
-              map_attribute "max", to: :max
-              map_attribute "units", to: :units
-              map_attribute "unitsRef", to: :units_ref
+              root 'float'
+              map_attribute 'builtin', to: :builtin
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'min', to: :min
+              map_attribute 'max', to: :max
+              map_attribute 'units', to: :units
+              map_attribute 'unitsRef', to: :units_ref
               map_content to: :content
             end
+            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

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::FloatArray
+
             attribute :builtin, :string
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -21,19 +22,31 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "floatArray"
-              map_attribute "builtin", to: :builtin
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "min", to: :min
-              map_attribute "max", to: :max
-              map_attribute "size", to: :size
-              map_attribute "units", to: :units
-              map_attribute "unitsRef", to: :units_ref
+              root 'floatArray'
+              map_attribute 'builtin', to: :builtin
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'min', to: :min
+              map_attribute 'max', to: :max
+              map_attribute 'size', to: :size
+              map_attribute 'units', to: :units
+              map_attribute 'unitsRef', to: :units_ref
               map_content to: :content
             end
+            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

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

@@ -7,12 +7,14 @@ 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
 
@@ -21,17 +23,33 @@ module Chemicalml
             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_attribute "ref", to: :ref
-              map_attribute "role", to: :role
-              map_attribute "countExpression", to: :count_expression
+              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

@@ -7,25 +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_attribute "ref", to: :ref
-              map_attribute "role", to: :role
+              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