chemicalml 0.1.0 → 0.2.0

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

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module TableRowList
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::TableRowList
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+                        attribute :table_rows, :tableRow, collection: true
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              map_element "tableRow", to: :table_rows
+              root "tableRowList"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Torsion
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Torsion
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :atomRefs4, :string
+            attribute :units, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "torsion"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "atomRefs4", to: :atomRefs4
+              map_attribute "units", to: :units
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base/transform3.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Transform3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Transform3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "transform3"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module TransitionState
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::TransitionState
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "transitionState"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -18,7 +18,7 @@ module Chemicalml
             attribute :description, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "unit"
               map_attribute "id", to: :id
               map_attribute "title", to: :title

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

@@ -14,7 +14,7 @@ module Chemicalml
             attribute :units, :unit, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "unitList"
               map_attribute "title", to: :title
               map_attribute "namespace", to: :namespace

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

@@ -13,7 +13,7 @@ module Chemicalml
             attribute :description, :string
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "unitType"
               map_attribute "id", to: :id
               map_attribute "name", to: :name

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

@@ -14,7 +14,7 @@ module Chemicalml
             attribute :unit_types, :unitType, collection: true
 
             xml do
-            namespace Chemicalml::Cml::Namespace
+              namespace Chemicalml::Cml::Namespace
               root "unitTypeList"
               map_attribute "title", to: :title
               map_attribute "namespace", to: :namespace

data/lib/chemicalml/cml/base/vector3.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Vector3
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Vector3
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "vector3"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Xaxis
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Xaxis
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :units, :string
+            attribute :multiplier, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "xaxis"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "units", to: :units
+              map_attribute "multiplier", to: :multiplier
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module Yaxis
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::Yaxis
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :units, :string
+            attribute :multiplier, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "yaxis"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_attribute "units", to: :units
+              map_attribute "multiplier", to: :multiplier
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module ZMatrix
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::ZMatrix
+            attribute :id, :string
+            attribute :title, :string
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root "zMatrix"
+              map_attribute "id", to: :id
+              map_attribute "title", to: :title
+              map_attribute "dictRef", to: :dict_ref
+              map_attribute "convention", to: :convention
+              map_content to: :content
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base.rb

@@ -46,6 +46,91 @@ module Chemicalml
       autoload :UnitList,         "chemicalml/cml/base/unit_list"
       autoload :UnitType,         "chemicalml/cml/base/unit_type"
       autoload :UnitTypeList,     "chemicalml/cml/base/unit_type_list"
+      autoload :Abundance, "chemicalml/cml/base/abundance"
+      autoload :Action, "chemicalml/cml/base/action"
+      autoload :ActionList, "chemicalml/cml/base/action_list"
+      autoload :Amount, "chemicalml/cml/base/amount"
+      autoload :Angle, "chemicalml/cml/base/angle"
+      autoload :AnyCml, "chemicalml/cml/base/any_cml"
+      autoload :ArrayList, "chemicalml/cml/base/array_list"
+      autoload :AtomSet, "chemicalml/cml/base/atom_set"
+      autoload :AtomType, "chemicalml/cml/base/atom_type"
+      autoload :AtomTypeList, "chemicalml/cml/base/atom_type_list"
+      autoload :AtomicBasisFunction, "chemicalml/cml/base/atomic_basis_function"
+      autoload :Band, "chemicalml/cml/base/band"
+      autoload :BandList, "chemicalml/cml/base/band_list"
+      autoload :BasisSet, "chemicalml/cml/base/basis_set"
+      autoload :BondSet, "chemicalml/cml/base/bond_set"
+      autoload :BondType, "chemicalml/cml/base/bond_type"
+      autoload :BondTypeList, "chemicalml/cml/base/bond_type_list"
+      autoload :CellParameter, "chemicalml/cml/base/cell_parameter"
+      autoload :ConditionList, "chemicalml/cml/base/condition_list"
+      autoload :Crystal, "chemicalml/cml/base/crystal"
+      autoload :Definition, "chemicalml/cml/base/definition"
+      autoload :Description, "chemicalml/cml/base/description"
+      autoload :Dimension, "chemicalml/cml/base/dimension"
+      autoload :Documentation, "chemicalml/cml/base/documentation"
+      autoload :Eigen, "chemicalml/cml/base/eigen"
+      autoload :Electron, "chemicalml/cml/base/electron"
+      autoload :Fragment, "chemicalml/cml/base/fragment"
+      autoload :FragmentList, "chemicalml/cml/base/fragment_list"
+      autoload :Gradient, "chemicalml/cml/base/gradient"
+      autoload :Isotope, "chemicalml/cml/base/isotope"
+      autoload :IsotopeList, "chemicalml/cml/base/isotope_list"
+      autoload :Join, "chemicalml/cml/base/join"
+      autoload :Kpoint, "chemicalml/cml/base/kpoint"
+      autoload :KpointList, "chemicalml/cml/base/kpoint_list"
+      autoload :Lattice, "chemicalml/cml/base/lattice"
+      autoload :LatticeVector, "chemicalml/cml/base/lattice_vector"
+      autoload :Length, "chemicalml/cml/base/length"
+      autoload :Line3, "chemicalml/cml/base/line3"
+      autoload :Link, "chemicalml/cml/base/link"
+      autoload :Map, "chemicalml/cml/base/map"
+      autoload :Mechanism, "chemicalml/cml/base/mechanism"
+      autoload :MechanismComponent, "chemicalml/cml/base/mechanism_component"
+      autoload :MoleculeList, "chemicalml/cml/base/molecule_list"
+      autoload :Object, "chemicalml/cml/base/object"
+      autoload :Observation, "chemicalml/cml/base/observation"
+      autoload :Particle, "chemicalml/cml/base/particle"
+      autoload :Peak, "chemicalml/cml/base/peak"
+      autoload :PeakGroup, "chemicalml/cml/base/peak_group"
+      autoload :PeakList, "chemicalml/cml/base/peak_list"
+      autoload :PeakStructure, "chemicalml/cml/base/peak_structure"
+      autoload :Plane3, "chemicalml/cml/base/plane3"
+      autoload :Point3, "chemicalml/cml/base/point3"
+      autoload :Potential, "chemicalml/cml/base/potential"
+      autoload :PotentialForm, "chemicalml/cml/base/potential_form"
+      autoload :PotentialList, "chemicalml/cml/base/potential_list"
+      autoload :ReactionScheme, "chemicalml/cml/base/reaction_scheme"
+      autoload :ReactionStep, "chemicalml/cml/base/reaction_step"
+      autoload :ReactionStepList, "chemicalml/cml/base/reaction_step_list"
+      autoload :ReactiveCentre, "chemicalml/cml/base/reactive_centre"
+      autoload :Region, "chemicalml/cml/base/region"
+      autoload :Sample, "chemicalml/cml/base/sample"
+      autoload :Spectator, "chemicalml/cml/base/spectator"
+      autoload :SpectatorList, "chemicalml/cml/base/spectator_list"
+      autoload :Spectrum, "chemicalml/cml/base/spectrum"
+      autoload :SpectrumData, "chemicalml/cml/base/spectrum_data"
+      autoload :SpectrumList, "chemicalml/cml/base/spectrum_list"
+      autoload :Sphere3, "chemicalml/cml/base/sphere3"
+      autoload :Stmml, "chemicalml/cml/base/stmml"
+      autoload :SubstanceList, "chemicalml/cml/base/substance_list"
+      autoload :Symmetry, "chemicalml/cml/base/symmetry"
+      autoload :System, "chemicalml/cml/base/system"
+      autoload :Table, "chemicalml/cml/base/table"
+      autoload :TableCell, "chemicalml/cml/base/table_cell"
+      autoload :TableContent, "chemicalml/cml/base/table_content"
+      autoload :TableHeader, "chemicalml/cml/base/table_header"
+      autoload :TableHeaderCell, "chemicalml/cml/base/table_header_cell"
+      autoload :TableRow, "chemicalml/cml/base/table_row"
+      autoload :TableRowList, "chemicalml/cml/base/table_row_list"
+      autoload :Torsion, "chemicalml/cml/base/torsion"
+      autoload :Transform3, "chemicalml/cml/base/transform3"
+      autoload :TransitionState, "chemicalml/cml/base/transition_state"
+      autoload :Vector3, "chemicalml/cml/base/vector3"
+      autoload :Xaxis, "chemicalml/cml/base/xaxis"
+      autoload :Yaxis, "chemicalml/cml/base/yaxis"
+      autoload :ZMatrix, "chemicalml/cml/base/z_matrix"
     end
   end
 end

data/lib/chemicalml/cml/child_mappings.rb

@@ -0,0 +1,168 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    # Defines which child elements each CML container can hold.
+    # Adding a new parent-child relationship = adding one entry
+    # here. Used by a script to update the Base mixins.
+    #
+    # Format: parent_class_name => [[child_xml_name, child_ruby_attr, child_type_symbol], ...]
+    module ChildMappings
+      MAPPINGS = {
+        # Molecule — already has names, identifiers, formulas, properties,
+        # labels, atom_array, bond_array, molecules. Add more.
+        "Molecule" => [
+          ["crystal", "crystal", :crystal],
+          ["spectrum", "spectra", :spectrum],
+          ["propertyList", "property_lists", :propertyList],
+        ],
+        # Crystal — holds scalar lattice parameters
+        "Crystal" => [
+          ["scalar", "scalars", :scalar],
+          ["lattice", "lattice", :lattice],
+          ["symmetry", "symmetry", :symmetry],
+        ],
+        # Lattice — holds latticeVector children
+        "Lattice" => [
+          ["latticeVector", "lattice_vectors", :latticeVector],
+        ],
+        # Spectrum — holds axes and peaks
+        "Spectrum" => [
+          ["xaxis", "xaxis", :xaxis],
+          ["yaxis", "yaxis", :yaxis],
+          ["peakList", "peak_list", :peakList],
+          ["conditionList", "condition_list", :conditionList],
+        ],
+        # PeakList — holds peaks
+        "PeakList" => [
+          ["peak", "peaks", :peak],
+          ["peakGroup", "peak_groups", :peakGroup],
+        ],
+        # PeakGroup — holds peaks
+        "PeakGroup" => [
+          ["peak", "peaks", :peak],
+        ],
+        # Reaction — already has reactantList, productList. Add more.
+        "Reaction" => [
+          ["spectatorList", "spectator_list", :spectatorList],
+          ["conditionList", "condition_list", :conditionList],
+          ["metadataList", "metadata_lists", :metadataList],
+        ],
+        # ReactionScheme
+        "ReactionScheme" => [
+          ["reactionStepList", "reaction_step_lists", :reactionStepList],
+          ["reaction", "reactions", :reaction],
+        ],
+        # ReactionStepList
+        "ReactionStepList" => [
+          ["reactionStep", "reaction_steps", :reactionStep],
+        ],
+        # ReactionStep
+        "ReactionStep" => [
+          ["reaction", "reaction", :reaction],
+          ["reactantList", "reactant_list", :reactantList],
+          ["productList", "product_list", :productList],
+        ],
+        # ConditionList
+        "ConditionList" => [
+          ["scalar", "scalars", :scalar],
+          ["metadata", "metadata", :metadata],
+        ],
+        # FragmentList
+        "FragmentList" => [
+          ["fragment", "fragments", :fragment],
+        ],
+        # Fragment
+        "Fragment" => [
+          ["molecule", "molecule", :molecule],
+          ["atomArray", "atom_array", :atomArray],
+          ["bondArray", "bond_array", :bondArray],
+        ],
+        # IsotopeList
+        "IsotopeList" => [
+          ["isotope", "isotopes", :isotope],
+        ],
+        # BandList
+        "BandList" => [
+          ["band", "bands", :band],
+        ],
+        # KpointList
+        "KpointList" => [
+          ["kpoint", "kpoints", :kpoint],
+        ],
+        # PotentialList
+        "PotentialList" => [
+          ["potential", "potentials", :potential],
+        ],
+        # Table
+        "Table" => [
+          ["tableContent", "table_content", :tableContent],
+          ["tableHeader", "table_header", :tableHeader],
+        ],
+        # TableContent
+        "TableContent" => [
+          ["tableRow", "table_rows", :tableRow],
+          ["tableRowList", "table_row_lists", :tableRowList],
+        ],
+        # TableHeader
+        "TableHeader" => [
+          ["tableHeaderCell", "table_header_cells", :tableHeaderCell],
+        ],
+        # TableRow
+        "TableRow" => [
+          ["tableCell", "table_cells", :tableCell],
+        ],
+        # TableRowList
+        "TableRowList" => [
+          ["tableRow", "table_rows", :tableRow],
+        ],
+        # SpectatorList
+        "SpectatorList" => [
+          ["spectator", "spectators", :spectator],
+        ],
+        # MoleculeList
+        "MoleculeList" => [
+          ["molecule", "molecules", :molecule],
+        ],
+        # SubstanceList
+        "SubstanceList" => [
+          ["substance", "substances", :substance],
+        ],
+        # ActionList
+        "ActionList" => [
+          ["action", "actions", :action],
+        ],
+        # AtomTypeList
+        "AtomTypeList" => [
+          ["atomType", "atom_types", :atomType],
+        ],
+        # BondTypeList
+        "BondTypeList" => [
+          ["bondType", "bond_types", :bondType],
+        ],
+        # Mechanism
+        "Mechanism" => [
+          ["mechanismComponent", "mechanism_components", :mechanismComponent],
+        ],
+        # SpectrumList
+        "SpectrumList" => [
+          ["spectrum", "spectra", :spectrum],
+        ],
+        # SpectrumData
+        "SpectrumData" => [
+          ["xaxis", "xaxis", :xaxis],
+          ["yaxis", "yaxis", :yaxis],
+        ],
+        # BasisSet
+        "BasisSet" => [
+          ["atomicBasisFunction", "atomic_basis_functions", :atomicBasisFunction],
+        ],
+        # System
+        "System" => [
+          ["atomArray", "atom_array", :atomArray],
+          ["molecule", "molecules", :molecule],
+        ],
+      }.freeze
+    end
+  end
+end