chemicalml 0.1.0

data/data/dictionaries/unit_type.yaml

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+# Unit Types Dictionary
+#
+# Source: http://www.xml-cml.org/unit/unitType/
+# License: CC-BY-3.0 (http://creativecommons.org/licenses/by/3.0/)
+
+---
+namespace: http://www.xml-cml.org/unit/unitType/
+prefix: unitType
+title: CML Unit Types
+description: |
+  Unit types abstract over units: e.g. the units metre, angstrom and
+  picometre are all of type *length*; Kelvin is of type *temperature*.
+
+entries:
+  - id: length
+    term: Length
+    definition: A measure of one-dimensional distance.
+  - id: mass
+    term: Mass
+    definition: A measure of the amount of matter in an object.
+  - id: time
+    term: Time
+    definition: A measure of duration.
+  - id: temperature
+    term: Temperature
+    definition: A measure of thermal energy.
+  - id: electricCurrent
+    term: Electric Current
+    definition: A measure of the flow of electric charge.
+  - id: amountOfSubstance
+    term: Amount of Substance
+    definition: A measure of the number of particles in a sample.
+  - id: luminousIntensity
+    term: Luminous Intensity
+    definition: A measure of the wavelength-weighted power emitted by a light source.
+  - id: angle
+    term: Angle
+    definition: A measure of a plane angle.
+  - id: solidAngle
+    term: Solid Angle
+    definition: A measure of a two-dimensional angle in three-dimensional space.
+  - id: area
+    term: Area
+    definition: A measure of two-dimensional extent.
+  - id: volume
+    term: Volume
+    definition: A measure of three-dimensional extent.
+  - id: velocity
+    term: Velocity
+    definition: A measure of the rate of change of position.
+  - id: acceleration
+    term: Acceleration
+    definition: A measure of the rate of change of velocity.
+  - id: force
+    term: Force
+    definition: A measure of an influence that changes the motion of an object.
+  - id: pressure
+    term: Pressure
+    definition: A measure of force per unit area.
+  - id: energy
+    term: Energy
+    definition: A measure of the capacity to do work.
+  - id: power
+    term: Power
+    definition: A measure of the rate of doing work.
+  - id: electricCharge
+    term: Electric Charge
+    definition: A measure of the quantity of electricity.
+  - id: electricPotential
+    term: Electric Potential
+    definition: A measure of the electric potential energy per unit charge.
+  - id: electricCapacitance
+    term: Electric Capacitance
+    definition: A measure of the ability to store electric charge.
+  - id: electricResistance
+    term: Electric Resistance
+    definition: A measure of opposition to the flow of electric current.
+  - id: electricConductance
+    term: Electric Conductance
+    definition: A measure of how easily electric current flows.
+  - id: magneticFlux
+    term: Magnetic Flux
+    definition: A measure of the quantity of magnetism.
+  - id: magneticFluxDensity
+    term: Magnetic Flux Density
+    definition: A measure of the magnetic field strength.
+  - id: inductance
+    term: Inductance
+    definition: A measure of the property of an electric conductor to oppose changes in current.
+  - id: frequency
+    term: Frequency
+    definition: A measure of the number of occurrences of a repeating event per unit time.
+  - id: wavenumber
+    term: Wavenumber
+    definition: A measure of the spatial frequency of a wave.
+  - id: molarMass
+    term: Molar Mass
+    definition: A measure of the mass per amount of substance.
+  - id: molarEnergy
+    term: Molar Energy
+    definition: A measure of energy per amount of substance.
+  - id: dipoleMoment
+    term: Dipole Moment
+    definition: A measure of the separation of positive and negative charges.
+  - id: polarizability
+    term: Polarizability
+    definition: A measure of the tendency of a charge distribution to be distorted by an external electric field.
+  - id: dimensionless
+    term: Dimensionless
+    definition: A quantity with no physical dimensions.
+  - id: none
+    term: None
+    definition: Used for entries that conceptually have no units.

data/lib/chemicalml/cml/array.rb

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+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Array.
+module Chemicalml
+  module Cml
+    remove_const(:Array) if const_defined?(:Array, false)
+    const_set(:Array, Chemicalml::Cml::Schema3::Array)
+  end
+end

data/lib/chemicalml/cml/atom.rb

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+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Atom.
+module Chemicalml
+  module Cml
+    remove_const(:Atom) if const_defined?(:Atom, false)
+    const_set(:Atom, Chemicalml::Cml::Schema3::Atom)
+  end
+end

data/lib/chemicalml/cml/atom_array.rb

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+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::AtomArray.
+module Chemicalml
+  module Cml
+    remove_const(:AtomArray) if const_defined?(:AtomArray, false)
+    const_set(:AtomArray, Chemicalml::Cml::Schema3::AtomArray)
+  end
+end

data/lib/chemicalml/cml/atom_parity.rb

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+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::AtomParity.
+module Chemicalml
+  module Cml
+    remove_const(:AtomParity) if const_defined?(:AtomParity, false)
+    const_set(:AtomParity, Chemicalml::Cml::Schema3::AtomParity)
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Array
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Array
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :data_type, :string
+            attribute :units, :string
+            attribute :size, :string
+            attribute :delimiter, :string
+            attribute :content, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "array"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "dataType", to: :data_type
+              map_attribute "units", to: :units
+              map_attribute "size", to: :size
+              map_attribute "delimiter", to: :delimiter
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Atom
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Atom
+            attribute :id, :string
+            attribute :element_type, :string
+            attribute :count, :string
+            attribute :formal_charge, :string
+            attribute :hydrogen_count, :string
+            attribute :isotope, :string
+            attribute :isotope_number, :string
+            attribute :spin_multiplicity, :string
+            attribute :title, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "atom"
+              map_attribute "id", to: :id
+              map_attribute "elementType", to: :element_type
+              map_attribute "count", to: :count
+              map_attribute "formalCharge", to: :formal_charge
+              map_attribute "hydrogenCount", to: :hydrogen_count
+              map_attribute "isotope", to: :isotope
+              map_attribute "isotopeNumber", to: :isotope_number
+              map_attribute "spinMultiplicity", to: :spin_multiplicity
+              map_attribute "title", to: :title
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module AtomArray
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::AtomArray
+            attribute :atoms, :atom, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "atomArray"
+              map_element "atom", to: :atoms
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module AtomParity
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::AtomParity
+            attribute :atom_refs4, :string
+            attribute :content, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "atomParity"
+              map_attribute "atomRefs4", to: :atom_refs4
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Bond
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Bond
+            attribute :id, :string
+            attribute :atom_refs2, :string
+            attribute :order, :string
+            attribute :title, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "bond"
+              map_attribute "id", to: :id
+              map_attribute "atomRefs2", to: :atom_refs2
+              map_attribute "order", to: :order
+              map_attribute "title", to: :title
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BondArray
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BondArray
+            attribute :bonds, :bond, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "bondArray"
+              map_element "bond", to: :bonds
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module BondStereo
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::BondStereo
+            attribute :atom_refs2, :string
+            attribute :atom_refs4, :string
+            attribute :dict_ref, :string
+            attribute :content, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "bondStereo"
+              map_attribute "atomRefs2", to: :atom_refs2
+              map_attribute "atomRefs4", to: :atom_refs4
+              map_attribute "dictRef", to: :dict_ref
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Module
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Module
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :molecules, :molecule, collection: true
+            attribute :modules, :module, collection: true
+            attribute :parameter_lists, :parameterList, collection: true
+            attribute :property_lists, :propertyList, collection: true
+            attribute :metadata_lists, :metadataList, collection: true
+            attribute :lists, :list, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "module"
+              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 "module", to: :modules
+              map_element "parameterList", to: :parameter_lists
+              map_element "propertyList", to: :property_lists
+              map_element "metadataList", to: :metadata_lists
+              map_element "list", to: :lists
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Dictionary
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Dictionary
+            attribute :title, :string
+            attribute :namespace, :string
+            attribute :dictionary_prefix, :string
+            attribute :convention, :string
+            attribute :description, :string
+            attribute :entries, :entry, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "dictionary"
+              map_attribute "title", to: :title
+              map_attribute "namespace", to: :namespace
+              map_attribute "dictionaryPrefix", to: :dictionary_prefix
+              map_attribute "convention", to: :convention
+              map_element "description", to: :description
+              map_element "entry", to: :entries
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module DictionaryEntry
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::DictionaryEntry
+            attribute :id, :string
+            attribute :term, :string
+            attribute :data_type, :string
+            attribute :unit_type, :string
+            attribute :units, :string
+            attribute :definition, :string
+            attribute :description, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "entry"
+              map_attribute "id", to: :id
+              map_attribute "term", to: :term
+              map_attribute "dataType", to: :data_type
+              map_attribute "unitType", to: :unit_type
+              map_attribute "units", to: :units
+              map_element "definition", to: :definition
+              map_element "description", to: :description
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Document
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Document
+            attribute :molecules, :molecule, collection: true
+            attribute :reaction_lists, :reactionList, collection: true
+            attribute :reactions, :reaction, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "cml"
+              map_element "molecule", to: :molecules
+              map_element "reactionList", to: :reaction_lists
+              map_element "reaction", to: :reactions
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Formula
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Formula
+            attribute :id, :string
+            attribute :title, :string
+            attribute :concise, :string
+            attribute :inline, :string
+            attribute :formal_charge, :string
+            attribute :count, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :atom_array, :atomArray
+
+            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
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Identifier
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Identifier
+            attribute :value, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "identifier"
+              map_attribute "value", to: :value
+              map_attribute "convention", to: :convention
+              map_attribute "dictRef", to: :dict_ref
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Label
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Label
+            attribute :id, :string
+            attribute :value, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "label"
+              map_attribute "id", to: :id
+              map_attribute "value", to: :value
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module List
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::List
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :scalars, :scalar, collection: true
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
+            attribute :lists, :list, collection: true
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "list"
+              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: :scalars
+              map_element "array", to: :arrays
+              map_element "matrix", to: :matrices
+              map_element "list", to: :lists
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Matrix
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Matrix
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :data_type, :string
+            attribute :units, :string
+            attribute :rows, :string
+            attribute :columns, :string
+            attribute :delimiter, :string
+            attribute :content, :string
+
+            xml do
+            namespace Chemicalml::Cml::Namespace
+              root "matrix"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "dataType", to: :data_type
+              map_attribute "units", to: :units
+              map_attribute "rows", to: :rows
+              map_attribute "columns", to: :columns
+              map_attribute "delimiter", to: :delimiter
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end