chemicalml 0.2.1 → 0.4.0

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

@@ -7,7 +7,10 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Molecule
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
+            attribute :concise, :string
             attribute :title, :string
             attribute :count, :string
             attribute :formal_charge, :string
@@ -15,18 +18,27 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :chirality, :string
-            attribute :names, :name, collection: true
+            attribute :formula, :string
             attribute :identifiers, :identifier, collection: true
             attribute :formulas, :formula, collection: true
             attribute :properties, :property, collection: true
-            attribute :labels, :label, collection: true
             attribute :atom_array, :atomArray
             attribute :bond_array, :bondArray
             attribute :molecules, :molecule, collection: true
-
-                        attribute :crystal, :crystal
+            attribute :crystal, :crystal
             attribute :spectra, :spectrum
             attribute :property_lists, :propertyList, collection: true
+            attribute :electrons, :electron, collection: true
+            attribute :angles, :angle, collection: true
+            attribute :lengths, :length, collection: true
+            attribute :torsions, :torsion, collection: true
+            attribute :joins, :join, collection: true
+            attribute :scalars, :scalar, collection: true
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
+            attribute :lists, :list, collection: true
+            attribute :symmetries, :symmetry, collection: true
+            attribute :z_matrix, :zMatrix
 
             attribute :ref, :string
             attribute :idgen, :string
@@ -35,28 +47,82 @@ module Chemicalml
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "molecule"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "count", to: :count
-              map_attribute "formalCharge", to: :formal_charge
-              map_attribute "spinMultiplicity", to: :spin_multiplicity
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "chirality", to: :chirality
-              map_element "name", to: :names
-              map_element "identifier", to: :identifiers
-              map_element "formula", to: :formulas
-              map_element "property", to: :properties
-              map_element "label", to: :labels
-              map_element "atomArray", to: :atom_array
-              map_element "bondArray", to: :bond_array
-              map_element "molecule", to: :molecules
-              map_attribute "ref", to: :ref
-              map_attribute "idgen", to: :idgen
-              map_attribute "process", to: :process
-              map_attribute "symmetryOriented", to: :symmetry_oriented
-              map_attribute "role", to: :role
+              root 'molecule'
+              map_attribute 'id', to: :id
+              map_attribute 'concise', to: :concise
+              map_attribute 'title', to: :title
+              map_attribute 'count', to: :count
+              map_attribute 'formalCharge', to: :formal_charge
+              map_attribute 'spinMultiplicity', to: :spin_multiplicity
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'chirality', to: :chirality
+              map_attribute 'formula', to: :formula
+              map_element 'identifier', to: :identifiers
+              map_element 'formula', to: :formulas
+              map_element 'property', to: :properties
+              map_element 'atomArray', to: :atom_array
+              map_element 'bondArray', to: :bond_array
+              map_element 'molecule', to: :molecules
+              map_element 'crystal', to: :crystal
+              map_element 'spectrum', to: :spectra
+              map_element 'propertyList', to: :property_lists
+              map_element 'electron', to: :electrons
+              map_element 'angle', to: :angles
+              map_element 'length', to: :lengths
+              map_element 'torsion', to: :torsions
+              map_element 'join', to: :joins
+              map_element 'scalar', to: :scalars
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+              map_element 'list', to: :lists
+              map_element 'symmetry', to: :symmetries
+              map_element 'zMatrix', to: :z_matrix
+              map_attribute 'ref', to: :ref
+              map_attribute 'idgen', to: :idgen
+              map_attribute 'process', to: :process
+              map_attribute 'symmetryOriented', to: :symmetry_oriented
+              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 'identifier', to: :identifiers
+              map 'formula', to: :formulas
+              map 'property', to: :properties
+              map 'atomArray', to: :atom_array
+              map 'bondArray', to: :bond_array
+              map 'molecule', to: :molecules
+              map 'crystal', to: :crystal
+              map 'spectrum', to: :spectra
+              map 'propertyList', to: :property_lists
+              map 'electron', to: :electrons
+              map 'angle', to: :angles
+              map 'length', to: :lengths
+              map 'torsion', to: :torsions
+              map 'join', to: :joins
+              map 'scalar', to: :scalars
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'list', to: :lists
+              map 'symmetry', to: :symmetries
+              map 'zMatrix', to: :z_matrix
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'count', to: :count
+              map 'formalCharge', to: :formal_charge
+              map 'spinMultiplicity', to: :spin_multiplicity
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'chirality', to: :chirality
+              map 'formula', to: :formula
+              map 'ref', to: :ref
+              map 'idgen', to: :idgen
+              map 'process', to: :process
+              map 'symmetryOriented', to: :symmetry_oriented
+              map 'role', to: :role
             end
           end
         end

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

@@ -7,23 +7,41 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::MoleculeList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :molecules, :molecule, collection: true
+            attribute :molecules, :molecule, collection: true
 
             attribute :ref, :string
+            attribute :molecule_lists, :moleculeList, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "molecule", to: :molecules
-              root "moleculeList"
-              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 'molecule', to: :molecules
+              map_element 'moleculeList', to: :molecule_lists
+              root 'moleculeList'
+              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 'molecule', to: :molecules
+              map 'moleculeList', to: :molecule_lists
+              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/name.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Name
+
             attribute :content, :string
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -14,11 +15,16 @@ module Chemicalml
             attribute :id, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "name"
+              root 'name'
               map_content to: :content
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "id", to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'id', to: :id
+            end
+            key_value do
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'id', to: :id
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Object
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,14 +18,23 @@ module Chemicalml
             attribute :count, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "object"
-              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_attribute "count", to: :count
+              root 'object'
+              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_attribute 'count', to: :count
+            end
+            key_value do
+              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
+              map 'count', to: :count
             end
           end
         end

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

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

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Operator
+
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
@@ -16,14 +17,21 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "operator"
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "type", to: :type
+              root 'operator'
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'type', to: :type
               map_content to: :content
             end
+            key_value do
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'type', to: :type
+            end
           end
         end
       end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Parameter
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -22,19 +24,37 @@ module Chemicalml
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "parameter"
-              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 "value", to: :value
-              map_attribute "constraint", to: :constraint
-              map_attribute "name", to: :name
-              map_attribute "role", to: :role
+              root 'parameter'
+              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 'value', to: :value
+              map_attribute 'constraint', to: :constraint
+              map_attribute 'name', to: :name
+              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 '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 'value', to: :value
+              map 'constraint', to: :constraint
+              map 'name', to: :name
+              map 'role', to: :role
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ParameterList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,16 +17,33 @@ module Chemicalml
             attribute :convention, :string
             attribute :ref, :string
             attribute :role, :string
+            attribute :parameter_lists, :parameterList, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "parameterList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_element "parameter", to: :parameters
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
-              map_attribute "role", to: :role
+              root 'parameterList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'parameter', to: :parameters
+              map_element 'parameterList', to: :parameter_lists
+              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 'parameter', to: :parameters
+              map 'parameterList', to: :parameter_lists
+              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/particle.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Particle
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -18,15 +19,25 @@ module Chemicalml
             attribute :z3, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "particle"
-              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 "x3", to: :x3
-              map_attribute "y3", to: :y3
-              map_attribute "z3", to: :z3
+              root 'particle'
+              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 'x3', to: :x3
+              map_attribute 'y3', to: :y3
+              map_attribute 'z3', to: :z3
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'type', to: :type
+              map 'x3', to: :x3
+              map 'y3', to: :y3
+              map 'z3', to: :z3
             end
           end
         end

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

@@ -7,6 +7,12 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Peak
+            include Chemicalml::Cml::Base::CommonChildren
+
+            attribute :atoms, :atom, collection: true
+            attribute :bonds, :bond, collection: true
+            attribute :molecules, :molecule, collection: true
+            attribute :peak_structures, :peakStructure, collection: true
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -31,36 +37,77 @@ module Chemicalml
             attribute :y_max, :string
             attribute :y_width, :string
             attribute :atom_refs, :string
+            attribute :atom_refs_values, :string, collection: true
             attribute :bond_refs, :string
             attribute :molecule_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "peak"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "xValue", to: :xValue
-              map_attribute "xUnits", to: :xUnits
-              map_attribute "xMultiplier", to: :xMultiplier
-              map_attribute "yValue", to: :yValue
-              map_attribute "yUnits", to: :yUnits
-              map_attribute "yMultiplicity", to: :yMultiplicity
-              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 "xWidth", to: :x_width
-              map_attribute "yMin", to: :y_min
-              map_attribute "yMax", to: :y_max
-              map_attribute "yWidth", to: :y_width
-              map_attribute "atomRefs", to: :atom_refs
-              map_attribute "bondRefs", to: :bond_refs
-              map_attribute "moleculeRefs", to: :molecule_refs
+              root 'peak'
+              map_element 'atom', to: :atoms
+              map_element 'bond', to: :bonds
+              map_element 'molecule', to: :molecules
+              map_element 'peakStructure', to: :peak_structures
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'xValue', to: :xValue
+              map_attribute 'xUnits', to: :xUnits
+              map_attribute 'xMultiplier', to: :xMultiplier
+              map_attribute 'yValue', to: :yValue
+              map_attribute 'yUnits', to: :yUnits
+              map_attribute 'yMultiplicity', to: :yMultiplicity
+              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 'xWidth', to: :x_width
+              map_attribute 'yMin', to: :y_min
+              map_attribute 'yMax', to: :y_max
+              map_attribute 'yWidth', to: :y_width
+              map_attribute 'atomRefs', to: :atom_refs
+              map_element 'atomRefs', to: :atom_refs_values
+              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 'atom', to: :atoms
+              map 'bond', to: :bonds
+              map 'molecule', to: :molecules
+              map 'peakStructure', to: :peak_structures
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'xValue', to: :xValue
+              map 'xUnits', to: :xUnits
+              map 'xMultiplier', to: :xMultiplier
+              map 'yValue', to: :yValue
+              map 'yUnits', to: :yUnits
+              map 'yMultiplicity', to: :yMultiplicity
+              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 'xWidth', to: :x_width
+              map 'yMin', to: :y_min
+              map 'yMax', to: :y_max
+              map 'yWidth', to: :y_width
+              map 'atomRefs', to: :atom_refs_values
+              map 'bondRefs', to: :bond_refs
+              map 'moleculeRefs', to: :molecule_refs
             end
           end
         end