chemicalml 0.2.1 → 0.4.0

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

@@ -7,12 +7,14 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PeakGroup
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :peaks, :peak, collection: true
+            attribute :peaks, :peak, collection: true
 
             attribute :ref, :string
             attribute :peak_height, :string
@@ -33,33 +35,67 @@ module Chemicalml
             attribute :atom_refs, :string
             attribute :bond_refs, :string
             attribute :molecule_refs, :string
+            attribute :peak_groups, :peakGroup, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "peak", to: :peaks
-              root "peakGroup"
-              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 "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 "xValue", to: :x_value
-              map_attribute "xWidth", to: :x_width
-              map_attribute "xUnits", to: :x_units
-              map_attribute "yMin", to: :y_min
-              map_attribute "yMax", to: :y_max
-              map_attribute "yValue", to: :y_value
-              map_attribute "yWidth", to: :y_width
-              map_attribute "yUnits", to: :y_units
-              map_attribute "atomRefs", to: :atom_refs
-              map_attribute "bondRefs", to: :bond_refs
-              map_attribute "moleculeRefs", to: :molecule_refs
+              map_element 'peak', to: :peaks
+              map_element 'peakGroup', to: :peak_groups
+              root 'peakGroup'
+              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 '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 'xValue', to: :x_value
+              map_attribute 'xWidth', to: :x_width
+              map_attribute 'xUnits', to: :x_units
+              map_attribute 'yMin', to: :y_min
+              map_attribute 'yMax', to: :y_max
+              map_attribute 'yValue', to: :y_value
+              map_attribute 'yWidth', to: :y_width
+              map_attribute 'yUnits', to: :y_units
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'bondRefs', to: :bond_refs
+              map_attribute 'moleculeRefs', to: :molecule_refs
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'peak', to: :peaks
+              map 'peakGroup', to: :peak_groups
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'peakHeight', to: :peak_height
+              map 'peakMultiplicity', to: :peak_multiplicity
+              map 'peakShape', to: :peak_shape
+              map 'integral', to: :integral
+              map 'peakUnits', to: :peak_units
+              map 'xMin', to: :x_min
+              map 'xMax', to: :x_max
+              map 'xValue', to: :x_value
+              map 'xWidth', to: :x_width
+              map 'xUnits', to: :x_units
+              map 'yMin', to: :y_min
+              map 'yMax', to: :y_max
+              map 'yValue', to: :y_value
+              map 'yWidth', to: :y_width
+              map 'yUnits', to: :y_units
+              map 'atomRefs', to: :atom_refs
+              map 'bondRefs', to: :bond_refs
+              map 'moleculeRefs', to: :molecule_refs
             end
           end
         end

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

@@ -7,25 +7,40 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PeakList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :peaks, :peak, collection: true
+            attribute :peaks, :peak, collection: true
             attribute :peak_groups, :peakGroup, collection: true
 
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "peak", to: :peaks
-              map_element "peakGroup", to: :peak_groups
-              root "peakList"
-              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_element 'peak', to: :peaks
+              map_element 'peakGroup', to: :peak_groups
+              root 'peakList'
+              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 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'peak', to: :peaks
+              map 'peakGroup', to: :peak_groups
+              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/peak_structure.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PeakStructure
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -20,21 +22,46 @@ module Chemicalml
             attribute :units, :string
             attribute :atom_refs, :string
             attribute :bond_refs, :string
+            attribute :type, :string
+            attribute :peak_structures, :peakStructure, collection: true
+
             xml do
+              map_element 'peakStructure', to: :peak_structures
               namespace Chemicalml::Cml::Namespace
-              root "peakStructure"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "peakShape", to: :peakShape
-              map_attribute "ref", to: :ref
-              map_attribute "peakMultiplicity", to: :peak_multiplicity
-              map_attribute "peakStructureType", to: :peak_structure_type
-              map_attribute "value", to: :value
-              map_attribute "units", to: :units
-              map_attribute "atomRefs", to: :atom_refs
-              map_attribute "bondRefs", to: :bond_refs
+              root 'peakStructure'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'peakShape', to: :peakShape
+              map_attribute 'ref', to: :ref
+              map_attribute 'peakMultiplicity', to: :peak_multiplicity
+              map_attribute 'peakStructureType', to: :peak_structure_type
+              map_attribute 'value', to: :value
+              map_attribute 'units', to: :units
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'bondRefs', to: :bond_refs
+              map_attribute 'type', to: :type
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'peakStructure', to: :peak_structures
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'peakShape', to: :peakShape
+              map 'ref', to: :ref
+              map 'peakMultiplicity', to: :peak_multiplicity
+              map 'peakStructureType', to: :peak_structure_type
+              map 'value', to: :value
+              map 'units', to: :units
+              map 'atomRefs', to: :atom_refs
+              map 'bondRefs', to: :bond_refs
+              map 'type', to: :type
             end
           end
         end

data/lib/chemicalml/cml/base/plane3.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Plane3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,13 +17,20 @@ module Chemicalml
             attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "plane3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'plane3'
+              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 'units', to: :units
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
             end
           end
         end

data/lib/chemicalml/cml/base/point3.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Point3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,13 +17,20 @@ module Chemicalml
             attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "point3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'point3'
+              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 'units', to: :units
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
             end
           end
         end

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

@@ -7,20 +7,31 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Potential
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :formRef, :string
+            attribute :form, :string
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "potential"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "formRef", to: :formRef
+              root 'potential'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'formRef', to: :formRef
+              map_attribute 'form', to: :form
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'formRef', to: :formRef
+              map 'form', to: :form
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PotentialForm
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,15 +16,36 @@ module Chemicalml
             attribute :type, :string
 
             attribute :name, :string
+            attribute :args, :arg, collection: true
+            attribute :expression, :expression
+            attribute :parameters, :parameter, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "potentialForm"
-              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
+              root 'potentialForm'
+              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_element 'arg', to: :args
+              map_element 'expression', to: :expression
+              map_element 'parameter', to: :parameters
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'arg', to: :args
+              map 'expression', to: :expression
+              map 'parameter', to: :parameters
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'type', to: :type
+              map 'name', to: :name
             end
           end
         end

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

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PotentialList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :potentials, :potential, collection: true
+            attribute :potentials, :potential, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "potential", to: :potentials
-              root "potentialList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'potential', to: :potentials
+              root 'potentialList'
+              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 'potential', to: :potentials
+              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/product.rb

@@ -7,7 +7,15 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Product
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :substance, :substance
+            attribute :substance_lists, :substanceList, collection: true
+            attribute :molecule, :molecule
+            attribute :electrons, :electron, collection: true
+            attribute :formula, :formula
+            attribute :amounts, :amount, collection: true
+            attribute :identifier, :identifier
 
             attribute :dict_ref, :string
             attribute :convention, :string
@@ -19,16 +27,43 @@ module Chemicalml
             attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "product"
-              map_element "substance", to: :substance
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
-              map_attribute "count", to: :count
-              map_attribute "state", to: :state
+              root 'product'
+              map_element 'substance', to: :substance
+              map_element 'substanceList', to: :substance_lists
+              map_element 'molecule', to: :molecule
+              map_element 'electron', to: :electrons
+              map_element 'formula', to: :formula
+              map_element 'amount', to: :amounts
+              map_element 'identifier', to: :identifier
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'ref', to: :ref
+              map_attribute 'role', to: :role
+              map_attribute 'count', to: :count
+              map_attribute 'state', to: :state
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'substance', to: :substance
+              map 'substanceList', to: :substance_lists
+              map 'molecule', to: :molecule
+              map 'electron', to: :electrons
+              map 'formula', to: :formula
+              map 'amount', to: :amounts
+              map 'identifier', to: :identifier
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'ref', to: :ref
+              map 'role', to: :role
+              map 'count', to: :count
+              map 'state', to: :state
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ProductList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :products, :product, collection: true
 
             attribute :dict_ref, :string
@@ -16,17 +18,35 @@ module Chemicalml
             attribute :ref, :string
             attribute :role, :string
             attribute :count, :string
+            attribute :product_lists, :productList, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "productList"
-              map_element "product", to: :products
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
-              map_attribute "count", to: :count
+              root 'productList'
+              map_element 'product', to: :products
+              map_element 'productList', to: :product_lists
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'ref', to: :ref
+              map_attribute 'role', to: :role
+              map_attribute 'count', to: :count
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'product', to: :products
+              map 'productList', to: :product_lists
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'ref', to: :ref
+              map 'role', to: :role
+              map 'count', to: :count
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Property
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -20,17 +22,33 @@ module Chemicalml
             attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "property"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_element "scalar", to: :scalar
-              map_element "array", to: :array
-              map_element "matrix", to: :matrix
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
-              map_attribute "state", to: :state
+              root 'property'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'scalar', to: :scalar
+              map_element 'array', to: :array
+              map_element 'matrix', to: :matrix
+              map_attribute 'ref', to: :ref
+              map_attribute 'role', to: :role
+              map_attribute 'state', to: :state
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'scalar', to: :scalar
+              map 'array', to: :array
+              map 'matrix', to: :matrix
+              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 'state', to: :state
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::PropertyList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,14 +19,27 @@ module Chemicalml
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "propertyList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_element "property", to: :properties
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
+              root 'propertyList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'property', to: :properties
+              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 'property', to: :properties
+              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