chemicalml 0.1.0 → 0.2.0

data/lib/chemicalml/cml/elements.rb

@@ -7,52 +7,140 @@ module Chemicalml
     # adding one entry to `ALL`. Both `Schema3::Configuration` and
     # `Schema24::Configuration` walk this list.
     module Elements
-      # Maps the Ruby class name (Symbol, e.g. `:Atom`) to the XML
-      # element id used in the lutaml-model type registry
-      # (e.g. `:atom`, `:atomArray`).
       ALL = {
-        Array:           :array,
-        Atom:            :atom,
-        AtomArray:       :atomArray,
-        AtomParity:      :atomParity,
-        Bond:            :bond,
-        BondArray:       :bondArray,
-        BondStereo:      :bondStereo,
-        Dictionary:      :dictionary,
-        DictionaryEntry: :entry,
-        Document:        :document,
-        Formula:         :formula,
-        Identifier:      :identifier,
-        Label:           :label,
-        List:            :list,
-        Matrix:          :matrix,
-        Metadata:        :metadata,
-        MetadataList:    :metadataList,
-        Module:          :module,
-        Molecule:        :molecule,
-        Name:            :name,
-        Parameter:       :parameter,
-        ParameterList:   :parameterList,
-        Product:         :product,
-        ProductList:     :productList,
-        Property:        :property,
-        PropertyList:    :propertyList,
-        Reaction:        :reaction,
-        ReactionList:    :reactionList,
-        Reactant:        :reactant,
-        ReactantList:    :reactantList,
-        Scalar:          :scalar,
-        Substance:       :substance,
-        Unit:            :unit,
-        UnitList:        :unitList,
-        UnitType:        :unitType,
-        UnitTypeList:    :unitTypeList,
+        # Originally modeled elements
+        Array:             :array,
+        Atom:              :atom,
+        AtomArray:         :atomArray,
+        AtomParity:        :atomParity,
+        Bond:              :bond,
+        BondArray:         :bondArray,
+        BondStereo:        :bondStereo,
+        Dictionary:        :dictionary,
+        DictionaryEntry:   :entry,
+        Document:          :document,
+        Formula:           :formula,
+        Identifier:        :identifier,
+        Label:             :label,
+        List:              :list,
+        Matrix:            :matrix,
+        Metadata:          :metadata,
+        MetadataList:      :metadataList,
+        Module:            :module,
+        Molecule:          :molecule,
+        Name:              :name,
+        Parameter:         :parameter,
+        ParameterList:     :parameterList,
+        Product:           :product,
+        ProductList:       :productList,
+        Property:          :property,
+        PropertyList:      :propertyList,
+        Reaction:          :reaction,
+        ReactionList:      :reactionList,
+        Reactant:          :reactant,
+        ReactantList:      :reactantList,
+        Scalar:            :scalar,
+        Substance:         :substance,
+        Unit:              :unit,
+        UnitList:          :unitList,
+        UnitType:          :unitType,
+        UnitTypeList:      :unitTypeList,
+        # Full schema coverage — every CML element from the XSD
+        Abundance:           :abundance,
+        Action:              :action,
+        ActionList:          :actionList,
+        Amount:              :amount,
+        Angle:               :angle,
+        AnyCml:              :anyCml,
+        ArrayList:           :arrayList,
+        AtomSet:             :atomSet,
+        AtomType:            :atomType,
+        AtomTypeList:        :atomTypeList,
+        AtomicBasisFunction: :atomicBasisFunction,
+        Band:                :band,
+        BandList:            :bandList,
+        BasisSet:            :basisSet,
+        BondSet:             :bondSet,
+        BondType:            :bondType,
+        BondTypeList:        :bondTypeList,
+        CellParameter:       :cellParameter,
+        ConditionList:       :conditionList,
+        Crystal:             :crystal,
+        Definition:          :definition,
+        Description:         :description,
+        Dimension:           :dimension,
+        Documentation:       :documentation,
+        Eigen:               :eigen,
+        Electron:            :electron,
+        Fragment:            :fragment,
+        FragmentList:        :fragmentList,
+        Gradient:            :gradient,
+        Isotope:             :isotope,
+        IsotopeList:         :isotopeList,
+        Join:                :join,
+        Kpoint:              :kpoint,
+        KpointList:          :kpointList,
+        Lattice:             :lattice,
+        LatticeVector:       :latticeVector,
+        Length:              :length,
+        Line3:               :line3,
+        Link:                :link,
+        Map:                 :map,
+        Mechanism:           :mechanism,
+        MechanismComponent:  :mechanismComponent,
+        MoleculeList:        :moleculeList,
+        Object:              :object,
+        Observation:         :observation,
+        Particle:            :particle,
+        Peak:                :peak,
+        PeakGroup:           :peakGroup,
+        PeakList:            :peakList,
+        PeakStructure:       :peakStructure,
+        Plane3:              :plane3,
+        Point3:              :point3,
+        Potential:           :potential,
+        PotentialForm:       :potentialForm,
+        PotentialList:       :potentialList,
+        ReactionScheme:      :reactionScheme,
+        ReactionStep:        :reactionStep,
+        ReactionStepList:    :reactionStepList,
+        ReactiveCentre:      :reactiveCentre,
+        Region:              :region,
+        Sample:              :sample,
+        Spectator:           :spectator,
+        SpectatorList:       :spectatorList,
+        Spectrum:            :spectrum,
+        SpectrumData:        :spectrumData,
+        SpectrumList:        :spectrumList,
+        Sphere3:             :sphere3,
+        Stmml:               :stmml,
+        SubstanceList:       :substanceList,
+        Symmetry:            :symmetry,
+        System:              :system,
+        Table:               :table,
+        TableCell:           :tableCell,
+        TableContent:        :tableContent,
+        TableHeader:         :tableHeader,
+        TableHeaderCell:     :tableHeaderCell,
+        TableRow:            :tableRow,
+        TableRowList:        :tableRowList,
+        Torsion:             :torsion,
+        Transform3:          :transform3,
+        TransitionState:     :transitionState,
+        Vector3:             :vector3,
+        Xaxis:               :xaxis,
+        Yaxis:               :yaxis,
+        ZMatrix:             :zMatrix,
       }.freeze
 
-      # Elements that exist in Schema 3 but NOT in Schema 2.4. Used by
-      # `Schema24::Configuration` to skip registration of classes that
-      # don't exist for that version.
+      # Elements that exist in Schema 3 but NOT in Schema 2.4.
       SCHEMA3_ONLY = %i[Module].freeze
+
+      # Reverse index: XML element name (String) → Ruby class name
+      # (Symbol). O(1) lookup for VersionedParser root detection.
+      XML_TO_CLASS = ALL.each_with_object({}) do |(cls, xml_id), h|
+        h[xml_id.to_s] = cls
+      end.freeze
     end
   end
 end

data/lib/chemicalml/cml/role/abundance.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <abundance> element, regardless of schema version.
+      module Abundance
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/action.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <action> element, regardless of schema version.
+      module Action
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/action_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <actionList> element, regardless of schema version.
+      module ActionList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/amount.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <amount> element, regardless of schema version.
+      module Amount
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/angle.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <angle> element, regardless of schema version.
+      module Angle
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/any_cml.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <anyCml> element, regardless of schema version.
+      module AnyCml
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/array_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <arrayList> element, regardless of schema version.
+      module ArrayList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom_set.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <atomSet> element, regardless of schema version.
+      module AtomSet
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom_type.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <atomType> element, regardless of schema version.
+      module AtomType
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom_type_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <atomTypeList> element, regardless of schema version.
+      module AtomTypeList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atomic_basis_function.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <atomicBasisFunction> element, regardless of schema version.
+      module AtomicBasisFunction
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/band.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <band> element, regardless of schema version.
+      module Band
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/band_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <bandList> element, regardless of schema version.
+      module BandList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/basis_set.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <basisSet> element, regardless of schema version.
+      module BasisSet
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond_set.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <bondSet> element, regardless of schema version.
+      module BondSet
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond_type.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <bondType> element, regardless of schema version.
+      module BondType
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond_type_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <bondTypeList> element, regardless of schema version.
+      module BondTypeList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/cell_parameter.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <cellParameter> element, regardless of schema version.
+      module CellParameter
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/condition_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <conditionList> element, regardless of schema version.
+      module ConditionList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/crystal.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <crystal> element, regardless of schema version.
+      module Crystal
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/definition.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <definition> element, regardless of schema version.
+      module Definition
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/description.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <description> element, regardless of schema version.
+      module Description
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/dimension.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <dimension> element, regardless of schema version.
+      module Dimension
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/documentation.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <documentation> element, regardless of schema version.
+      module Documentation
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/eigen.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <eigen> element, regardless of schema version.
+      module Eigen
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/electron.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <electron> element, regardless of schema version.
+      module Electron
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/fragment.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <fragment> element, regardless of schema version.
+      module Fragment
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/fragment_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <fragmentList> element, regardless of schema version.
+      module FragmentList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/gradient.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <gradient> element, regardless of schema version.
+      module Gradient
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/isotope.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <isotope> element, regardless of schema version.
+      module Isotope
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/isotope_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <isotopeList> element, regardless of schema version.
+      module IsotopeList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/join.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <join> element, regardless of schema version.
+      module Join
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/kpoint.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <kpoint> element, regardless of schema version.
+      module Kpoint
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/kpoint_list.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <kpointList> element, regardless of schema version.
+      module KpointList
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/lattice.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for wire classes implementing the CML
+      # <lattice> element, regardless of schema version.
+      module Lattice
+      end
+    end
+  end
+end