chemicalml 0.2.1 → 0.4.0

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

@@ -7,7 +7,15 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Reactant
+            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 "reactant"
-              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 'reactant'
+              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/reactant_list.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactantList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :reactants, :reactant, collection: true
 
             attribute :dict_ref, :string
@@ -16,17 +18,35 @@ module Chemicalml
             attribute :ref, :string
             attribute :role, :string
             attribute :count, :string
+            attribute :reactant_lists, :reactantList, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "reactantList"
-              map_element "reactant", to: :reactants
-              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 'reactantList'
+              map_element 'reactant', to: :reactants
+              map_element 'reactantList', to: :reactant_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 'reactant', to: :reactants
+              map 'reactantList', to: :reactant_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/reaction.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Reaction
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :type, :string
@@ -15,10 +17,16 @@ module Chemicalml
             attribute :convention, :string
             attribute :reactant_list, :reactantList
             attribute :product_list, :productList
-
-                        attribute :spectator_list, :spectatorList
+            attribute :spectator_list, :spectatorList
+            attribute :substance_lists, :substanceList, collection: true
             attribute :condition_list, :conditionList
-            attribute :metadata_lists, :metadataList, collection: true
+            attribute :identifiers, :identifier, collection: true
+            attribute :objects, :object, collection: true
+            attribute :property_lists, :propertyList, collection: true
+            attribute :maps, :map, collection: true
+            attribute :mechanisms, :mechanism, collection: true
+            attribute :reactive_centres, :reactiveCentre, collection: true
+            attribute :transition_states, :transitionState, collection: true
 
             attribute :reaction_format, :string
             attribute :ref, :string
@@ -30,23 +38,69 @@ module Chemicalml
             attribute :yield, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "reaction"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "type", to: :type
-              map_attribute "state", to: :state
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_element "reactantList", to: :reactant_list
-              map_element "productList", to: :product_list
-              map_attribute "reactionFormat", to: :reaction_format
-              map_attribute "ref", to: :ref
-              map_attribute "reactionRole", to: :reaction_role
-              map_attribute "reactionType", to: :reaction_type
-              map_attribute "atomMap", to: :atom_map
-              map_attribute "electronMap", to: :electron_map
-              map_attribute "bondMap", to: :bond_map
-              map_attribute "yield", to: :yield
+              root 'reaction'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'type', to: :type
+              map_attribute 'state', to: :state
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'reactantList', to: :reactant_list
+              map_element 'productList', to: :product_list
+              map_element 'spectatorList', to: :spectator_list
+              map_element 'substanceList', to: :substance_lists
+              map_element 'conditionList', to: :condition_list
+              map_element 'identifier', to: :identifiers
+              map_element 'object', to: :objects
+              map_element 'propertyList', to: :property_lists
+              map_element 'map', to: :maps
+              map_element 'mechanism', to: :mechanisms
+              map_element 'reactiveCentre', to: :reactive_centres
+              map_element 'transitionState', to: :transition_states
+              map_attribute 'reactionFormat', to: :reaction_format
+              map_attribute 'format', to: :reaction_format
+              map_attribute 'ref', to: :ref
+              map_attribute 'reactionRole', to: :reaction_role
+              map_attribute 'role', to: :reaction_role
+              map_attribute 'reactionType', to: :reaction_type
+              map_attribute 'atomMap', to: :atom_map
+              map_attribute 'electronMap', to: :electron_map
+              map_attribute 'bondMap', to: :bond_map
+              map_attribute 'yield', to: :yield
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'reactantList', to: :reactant_list
+              map 'productList', to: :product_list
+              map 'spectatorList', to: :spectator_list
+              map 'substanceList', to: :substance_lists
+              map 'conditionList', to: :condition_list
+              map 'identifier', to: :identifiers
+              map 'object', to: :objects
+              map 'propertyList', to: :property_lists
+              map 'map', to: :maps
+              map 'mechanism', to: :mechanisms
+              map 'reactiveCentre', to: :reactive_centres
+              map 'transitionState', to: :transition_states
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'type', to: :type
+              map 'state', to: :state
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'reactionFormat', to: :reaction_format
+              map 'format', to: :reaction_format
+              map 'ref', to: :ref
+              map 'reactionRole', to: :reaction_role
+              map 'role', to: :reaction_role
+              map 'reactionType', to: :reaction_type
+              map 'atomMap', to: :atom_map
+              map 'electronMap', to: :electron_map
+              map 'bondMap', to: :bond_map
+              map 'yield', to: :yield
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactionList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :reactions, :reaction, collection: true
 
             attribute :dict_ref, :string
@@ -17,14 +19,27 @@ module Chemicalml
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "reactionList"
-              map_element "reaction", to: :reactions
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "name", to: :name
-              map_attribute "ref", to: :ref
+              root 'reactionList'
+              map_element 'reaction', to: :reactions
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'name', to: :name
+              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 'reaction', to: :reactions
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'name', to: :name
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,12 +7,14 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactionScheme
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :reaction_step_lists, :reactionStepList, collection: true
+            attribute :reaction_step_lists, :reactionStepList, collection: true
             attribute :reactions, :reaction, collection: true
 
             attribute :ref, :string
@@ -20,20 +22,48 @@ module Chemicalml
             attribute :reaction_type, :string
             attribute :state, :string
             attribute :reaction_format, :string
+            attribute :type, :string
+            attribute :reaction_schemes, :reactionScheme, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "reactionStepList", to: :reaction_step_lists
-              map_element "reaction", to: :reactions
-              root "reactionScheme"
-              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 "reactionRole", to: :reaction_role
-              map_attribute "reactionType", to: :reaction_type
-              map_attribute "state", to: :state
-              map_attribute "reactionFormat", to: :reaction_format
+              map_element 'reactionStepList', to: :reaction_step_lists
+              map_element 'reactionScheme', to: :reaction_schemes
+              map_element 'reaction', to: :reactions
+              root 'reactionScheme'
+              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 'reactionRole', to: :reaction_role
+              map_attribute 'role', to: :reaction_role
+              map_attribute 'reactionType', to: :reaction_type
+              map_attribute 'type', to: :reaction_type
+              map_attribute 'state', to: :state
+              map_attribute 'reactionFormat', to: :reaction_format
+              map_attribute 'format', to: :reaction_format
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'reactionStepList', to: :reaction_step_lists
+              map 'reactionScheme', to: :reaction_schemes
+              map 'reaction', to: :reactions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'reactionRole', to: :reaction_role
+              map 'role', to: :reaction_role
+              map 'reactionType', to: :reaction_type
+              map 'type', to: :reaction_type
+              map 'state', to: :state
+              map 'reactionFormat', to: :reaction_format
+              map 'format', to: :reaction_format
             end
           end
         end

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

@@ -7,12 +7,14 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactionStep
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :reaction, :reaction
+            attribute :reaction, :reaction
             attribute :reactant_list, :reactantList
             attribute :product_list, :productList
 
@@ -21,17 +23,33 @@ module Chemicalml
             attribute :ratio, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "reaction", to: :reaction
-              map_element "reactantList", to: :reactant_list
-              map_element "productList", to: :product_list
-              root "reactionStep"
-              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 "yield", to: :yield
-              map_attribute "ratio", to: :ratio
+              map_element 'reaction', to: :reaction
+              map_element 'reactantList', to: :reactant_list
+              map_element 'productList', to: :product_list
+              root 'reactionStep'
+              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 'yield', to: :yield
+              map_attribute 'ratio', to: :ratio
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'reaction', to: :reaction
+              map 'reactantList', to: :reactant_list
+              map 'productList', to: :product_list
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'yield', to: :yield
+              map 'ratio', to: :ratio
             end
           end
         end

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

@@ -7,12 +7,14 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactionStepList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :reaction_steps, :reactionStep, collection: true
+            attribute :reaction_steps, :reactionStep, collection: true
 
             attribute :ref, :string
             attribute :reaction_step_list_type, :string
@@ -20,16 +22,33 @@ module Chemicalml
             attribute :type, :string
             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
-              map_attribute "ref", to: :ref
-              map_attribute "reactionStepListType", to: :reaction_step_list_type
-              map_attribute "reactionFormat", to: :reaction_format
-              map_attribute "type", to: :type
+              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
+              map_attribute 'ref', to: :ref
+              map_attribute 'reactionStepListType', to: :reaction_step_list_type
+              map_attribute 'reactionFormat', to: :reaction_format
+              map_attribute 'format', to: :reaction_format
+              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 'reactionStep', to: :reaction_steps
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'reactionStepListType', to: :reaction_step_list_type
+              map 'reactionFormat', to: :reaction_format
+              map 'format', to: :reaction_format
+              map 'type', to: :type
             end
           end
         end

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

@@ -7,20 +7,45 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ReactiveCentre
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :atomRefs, :string
+            attribute :atom_sets, :atomSet, collection: true
+            attribute :atom_type_lists, :atomTypeList, collection: true
+            attribute :bond_sets, :bondSet, collection: true
+            attribute :bond_type_lists, :bondTypeList, collection: true
 
             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
+              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
+              map_element 'atomSet', to: :atom_sets
+              map_element 'atomTypeList', to: :atom_type_lists
+              map_element 'bondSet', to: :bond_sets
+              map_element 'bondTypeList', to: :bond_type_lists
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'atomSet', to: :atom_sets
+              map 'atomTypeList', to: :atom_type_lists
+              map 'bondSet', to: :bond_sets
+              map 'bondTypeList', to: :bond_type_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRefs', to: :atomRefs
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Region
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -18,15 +19,25 @@ module Chemicalml
             attribute :region_refs, :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
-              map_attribute "sphere3", to: :sphere3
-              map_attribute "box3", to: :box3
-              map_attribute "atomSetRef", to: :atom_set_ref
-              map_attribute "regionRefs", to: :region_refs
+              root 'region'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'sphere3', to: :sphere3
+              map_attribute 'box3', to: :box3
+              map_attribute 'atomSetRef', to: :atom_set_ref
+              map_attribute 'regionRefs', to: :region_refs
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'sphere3', to: :sphere3
+              map 'box3', to: :box3
+              map 'atomSetRef', to: :atom_set_ref
+              map 'regionRefs', to: :region_refs
             end
           end
         end

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

@@ -7,17 +7,25 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::RelatedEntry
+
             attribute :related_entry_type, :string
+            attribute :type, :string
             attribute :href, :string
             attribute :content, :string
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "relatedEntry"
-              map_attribute "relatedEntryType", to: :related_entry_type
-              map_attribute "href", to: :href
+              root 'relatedEntry'
+              map_attribute 'relatedEntryType', to: :related_entry_type
+              map_attribute 'type', to: :type
+              map_attribute 'href', to: :href
               map_content to: :content
             end
+            key_value do
+              map 'relatedEntryType', to: :related_entry_type
+              map 'type', to: :type
+              map 'href', to: :href
+            end
           end
         end
       end