chemicalml 0.1.0 → 0.2.0

data/lib/chemicalml/cml.rb

@@ -7,49 +7,143 @@ module Chemicalml
   # Shared attribute + xml-mapping declarations live under `Base::*`
   # and are included by both schema-versioned class hierarchies.
   module Cml
-    autoload :Array, "chemicalml/cml/array"
-    autoload :Atom, "chemicalml/cml/atom"
-    autoload :AtomArray, "chemicalml/cml/atom_array"
-    autoload :AtomParity, "chemicalml/cml/atom_parity"
-    autoload :Base, "chemicalml/cml/base"
-    autoload :Bond, "chemicalml/cml/bond"
-    autoload :BondArray, "chemicalml/cml/bond_array"
-    autoload :BondStereo, "chemicalml/cml/bond_stereo"
-    autoload :Dictionary, "chemicalml/cml/dictionary"
-    autoload :DictionaryEntry, "chemicalml/cml/dictionary_entry"
-    autoload :Document, "chemicalml/cml/document"
-    autoload :Elements, "chemicalml/cml/elements"
-    autoload :Formula, "chemicalml/cml/formula"
-    autoload :Identifier, "chemicalml/cml/identifier"
-    autoload :Label, "chemicalml/cml/label"
-    autoload :List, "chemicalml/cml/list"
-    autoload :Matrix, "chemicalml/cml/matrix"
-    autoload :Metadata, "chemicalml/cml/metadata"
-    autoload :MetadataList, "chemicalml/cml/metadata_list"
-    autoload :Module, "chemicalml/cml/cml_module"
-    autoload :Molecule, "chemicalml/cml/molecule"
-    autoload :Name, "chemicalml/cml/name"
-    autoload :Namespace, "chemicalml/cml/namespace"
-    autoload :Parameter, "chemicalml/cml/parameter"
-    autoload :ParameterList, "chemicalml/cml/parameter_list"
-    autoload :Product, "chemicalml/cml/product"
-    autoload :ProductList, "chemicalml/cml/product_list"
-    autoload :Property, "chemicalml/cml/property"
-    autoload :PropertyList, "chemicalml/cml/property_list"
-    autoload :Reaction, "chemicalml/cml/reaction"
-    autoload :ReactionList, "chemicalml/cml/reaction_list"
-    autoload :Reactant, "chemicalml/cml/reactant"
-    autoload :ReactantList, "chemicalml/cml/reactant_list"
-    autoload :Role, "chemicalml/cml/role"
-    autoload :Scalar, "chemicalml/cml/scalar"
-    autoload :Schema3, "chemicalml/cml/schema3"
-    autoload :Schema24, "chemicalml/cml/schema24"
-    autoload :Substance, "chemicalml/cml/substance"
-    autoload :Translator, "chemicalml/cml/translator"
-    autoload :Unit, "chemicalml/cml/unit"
-    autoload :UnitList, "chemicalml/cml/unit_list"
-    autoload :UnitType, "chemicalml/cml/unit_type"
-    autoload :UnitTypeList, "chemicalml/cml/unit_type_list"
-    autoload :Visitable, "chemicalml/cml/visitable"
+    # Structural modules (each in its own file, loaded independently).
+    autoload :Base,              "chemicalml/cml/base"
+    autoload :ChildMappings,    "chemicalml/cml/child_mappings"
+    autoload :Elements,          "chemicalml/cml/elements"
+    autoload :Namespace,         "chemicalml/cml/namespace"
+    autoload :Role,              "chemicalml/cml/role"
+    autoload :Schema3,           "chemicalml/cml/schema3"
+    autoload :Schema24,          "chemicalml/cml/schema24"
+    autoload :Translator,        "chemicalml/cml/translator"
+    autoload :Visitable,         "chemicalml/cml/visitable"
+    autoload :WireClassRegistry, "chemicalml/cml/wire_class_registry"
+
+    # Backward-compatible aliases (Cml::Foo = Schema3::Foo). All 36
+    # aliases load from a single file via autoload — the file loads
+    # lazily when the first alias is referenced, then defines all of
+    # them via const_set (aliasing existing Schema3 classes, not
+    # creating new ones).
+    autoload :Array,           "chemicalml/cml/aliases"
+    autoload :Atom,            "chemicalml/cml/aliases"
+    autoload :AtomArray,       "chemicalml/cml/aliases"
+    autoload :AtomParity,      "chemicalml/cml/aliases"
+    autoload :Bond,            "chemicalml/cml/aliases"
+    autoload :BondArray,       "chemicalml/cml/aliases"
+    autoload :BondStereo,      "chemicalml/cml/aliases"
+    autoload :Dictionary,      "chemicalml/cml/aliases"
+    autoload :DictionaryEntry, "chemicalml/cml/aliases"
+    autoload :Document,        "chemicalml/cml/aliases"
+    autoload :Formula,         "chemicalml/cml/aliases"
+    autoload :Identifier,      "chemicalml/cml/aliases"
+    autoload :Label,           "chemicalml/cml/aliases"
+    autoload :List,            "chemicalml/cml/aliases"
+    autoload :Matrix,          "chemicalml/cml/aliases"
+    autoload :Metadata,        "chemicalml/cml/aliases"
+    autoload :MetadataList,    "chemicalml/cml/aliases"
+    autoload :Module,          "chemicalml/cml/aliases"
+    autoload :Molecule,        "chemicalml/cml/aliases"
+    autoload :Name,            "chemicalml/cml/aliases"
+    autoload :Parameter,       "chemicalml/cml/aliases"
+    autoload :ParameterList,   "chemicalml/cml/aliases"
+    autoload :Product,         "chemicalml/cml/aliases"
+    autoload :ProductList,     "chemicalml/cml/aliases"
+    autoload :Property,        "chemicalml/cml/aliases"
+    autoload :PropertyList,    "chemicalml/cml/aliases"
+    autoload :Reaction,        "chemicalml/cml/aliases"
+    autoload :ReactionList,    "chemicalml/cml/aliases"
+    autoload :Reactant,        "chemicalml/cml/aliases"
+    autoload :ReactantList,    "chemicalml/cml/aliases"
+    autoload :Scalar,          "chemicalml/cml/aliases"
+    autoload :Substance,       "chemicalml/cml/aliases"
+    autoload :Unit,            "chemicalml/cml/aliases"
+    autoload :UnitList,        "chemicalml/cml/aliases"
+    autoload :UnitType,        "chemicalml/cml/aliases"
+    autoload :UnitTypeList,    "chemicalml/cml/aliases"
+    autoload :Abundance, "chemicalml/cml/aliases"
+    autoload :Action, "chemicalml/cml/aliases"
+    autoload :ActionList, "chemicalml/cml/aliases"
+    autoload :Amount, "chemicalml/cml/aliases"
+    autoload :Angle, "chemicalml/cml/aliases"
+    autoload :AnyCml, "chemicalml/cml/aliases"
+    autoload :ArrayList, "chemicalml/cml/aliases"
+    autoload :AtomSet, "chemicalml/cml/aliases"
+    autoload :AtomType, "chemicalml/cml/aliases"
+    autoload :AtomTypeList, "chemicalml/cml/aliases"
+    autoload :AtomicBasisFunction, "chemicalml/cml/aliases"
+    autoload :Band, "chemicalml/cml/aliases"
+    autoload :BandList, "chemicalml/cml/aliases"
+    autoload :BasisSet, "chemicalml/cml/aliases"
+    autoload :BondSet, "chemicalml/cml/aliases"
+    autoload :BondType, "chemicalml/cml/aliases"
+    autoload :BondTypeList, "chemicalml/cml/aliases"
+    autoload :CellParameter, "chemicalml/cml/aliases"
+    autoload :ConditionList, "chemicalml/cml/aliases"
+    autoload :Crystal, "chemicalml/cml/aliases"
+    autoload :Definition, "chemicalml/cml/aliases"
+    autoload :Description, "chemicalml/cml/aliases"
+    autoload :Dimension, "chemicalml/cml/aliases"
+    autoload :Documentation, "chemicalml/cml/aliases"
+    autoload :Eigen, "chemicalml/cml/aliases"
+    autoload :Electron, "chemicalml/cml/aliases"
+    autoload :Fragment, "chemicalml/cml/aliases"
+    autoload :FragmentList, "chemicalml/cml/aliases"
+    autoload :Gradient, "chemicalml/cml/aliases"
+    autoload :Isotope, "chemicalml/cml/aliases"
+    autoload :IsotopeList, "chemicalml/cml/aliases"
+    autoload :Join, "chemicalml/cml/aliases"
+    autoload :Kpoint, "chemicalml/cml/aliases"
+    autoload :KpointList, "chemicalml/cml/aliases"
+    autoload :Lattice, "chemicalml/cml/aliases"
+    autoload :LatticeVector, "chemicalml/cml/aliases"
+    autoload :Length, "chemicalml/cml/aliases"
+    autoload :Line3, "chemicalml/cml/aliases"
+    autoload :Link, "chemicalml/cml/aliases"
+    autoload :Map, "chemicalml/cml/aliases"
+    autoload :Mechanism, "chemicalml/cml/aliases"
+    autoload :MechanismComponent, "chemicalml/cml/aliases"
+    autoload :MoleculeList, "chemicalml/cml/aliases"
+    autoload :Object, "chemicalml/cml/aliases"
+    autoload :Observation, "chemicalml/cml/aliases"
+    autoload :Particle, "chemicalml/cml/aliases"
+    autoload :Peak, "chemicalml/cml/aliases"
+    autoload :PeakGroup, "chemicalml/cml/aliases"
+    autoload :PeakList, "chemicalml/cml/aliases"
+    autoload :PeakStructure, "chemicalml/cml/aliases"
+    autoload :Plane3, "chemicalml/cml/aliases"
+    autoload :Point3, "chemicalml/cml/aliases"
+    autoload :Potential, "chemicalml/cml/aliases"
+    autoload :PotentialForm, "chemicalml/cml/aliases"
+    autoload :PotentialList, "chemicalml/cml/aliases"
+    autoload :ReactionScheme, "chemicalml/cml/aliases"
+    autoload :ReactionStep, "chemicalml/cml/aliases"
+    autoload :ReactionStepList, "chemicalml/cml/aliases"
+    autoload :ReactiveCentre, "chemicalml/cml/aliases"
+    autoload :Region, "chemicalml/cml/aliases"
+    autoload :Sample, "chemicalml/cml/aliases"
+    autoload :Spectator, "chemicalml/cml/aliases"
+    autoload :SpectatorList, "chemicalml/cml/aliases"
+    autoload :Spectrum, "chemicalml/cml/aliases"
+    autoload :SpectrumData, "chemicalml/cml/aliases"
+    autoload :SpectrumList, "chemicalml/cml/aliases"
+    autoload :Sphere3, "chemicalml/cml/aliases"
+    autoload :Stmml, "chemicalml/cml/aliases"
+    autoload :SubstanceList, "chemicalml/cml/aliases"
+    autoload :Symmetry, "chemicalml/cml/aliases"
+    autoload :System, "chemicalml/cml/aliases"
+    autoload :Table, "chemicalml/cml/aliases"
+    autoload :TableCell, "chemicalml/cml/aliases"
+    autoload :TableContent, "chemicalml/cml/aliases"
+    autoload :TableHeader, "chemicalml/cml/aliases"
+    autoload :TableHeaderCell, "chemicalml/cml/aliases"
+    autoload :TableRow, "chemicalml/cml/aliases"
+    autoload :TableRowList, "chemicalml/cml/aliases"
+    autoload :Torsion, "chemicalml/cml/aliases"
+    autoload :Transform3, "chemicalml/cml/aliases"
+    autoload :TransitionState, "chemicalml/cml/aliases"
+    autoload :Vector3, "chemicalml/cml/aliases"
+    autoload :Xaxis, "chemicalml/cml/aliases"
+    autoload :Yaxis, "chemicalml/cml/aliases"
+    autoload :ZMatrix, "chemicalml/cml/aliases"
   end
 end

data/lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class AtomCoordinatesMustBePaired < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Atom)
+
+            violations = []
+            has_x2 = !node.x2.to_s.empty?
+            has_y2 = !node.y2.to_s.empty?
+            if has_x2 != has_y2
+              violations << violation(path: path.empty? ? "atom" : path.join("/"),
+                                      message: "x2 and y2 must both be present or both absent")
+            end
+
+            has_x3 = !node.x3.to_s.empty?
+            has_y3 = !node.y3.to_s.empty?
+            has_z3 = !node.z3.to_s.empty?
+            if [has_x3, has_y3, has_z3].any? && ![has_x3, has_y3, has_z3].all?
+              violations << violation(path: path.empty? ? "atom" : path.join("/"),
+                                      message: "x3, y3, and z3 must all be present together")
+            end
+            violations
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class AtomIdMustMatchPattern < Chemicalml::Convention::Constraint::NodeConstraint
+          ID_PATTERN = /\A[A-Za-z][A-Za-z0-9._\-]*\z/.freeze
+
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Atom)
+
+            id = node.id.to_s
+            return [] if id.empty?
+            return [] if id.match?(ID_PATTERN)
+
+            [violation(path: path.empty? ? "atom" : path.join("/"),
+                       message: "atom id #{id.inspect} must start with a letter and " \
+                                "contain only letters, digits, dot, hyphen, or underscore",
+                       severity: :warning)]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class AtomMustHaveElementType < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Atom)
+
+            return [] unless node.element_type.to_s.empty?
+
+            [violation(path: path.empty? ? "atom" : path.join("/"),
+                       message: "atom must have an elementType attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class AtomMustHaveId < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Atom)
+
+            return [] unless node.id.to_s.empty?
+
+            [violation(path: path.empty? ? "atom" : path.join("/"),
+                       message: "atom must have an id attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class BondMustHaveAtomRefs2 < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Bond)
+
+            return [] unless node.atom_refs2.to_s.strip.empty?
+
+            [violation(path: path.empty? ? "bond" : path.join("/"),
+                       message: "bond must have an atomRefs2 attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class BondMustHaveOrder < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Bond)
+
+            return [] unless node.order.to_s.strip.empty?
+
+            [violation(path: path.empty? ? "bond" : path.join("/"),
+                       message: "bond must have an order attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb

@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class BondOrderShouldNotBeNumeric < Chemicalml::Convention::Constraint::NodeConstraint
+          VALID_ORDERS = %w[S D T Q A other].freeze
+
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Bond)
+
+            order = node.order.to_s
+            return [] if order.empty?
+
+            return [] if VALID_ORDERS.include?(order) || node.dict_ref.to_s.size.positive?
+
+            [violation(path: path.empty? ? "bond" : path.join("/"),
+                       message: "bond order #{order.inspect} is not recommended " \
+                                "(use S/D/T/Q/A or 'other' with dictRef)",
+                       severity: :warning)]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class MoleculeMustHaveId < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Molecule)
+
+            return [] unless node.id.to_s.empty?
+
+            [violation(path: path.empty? ? "molecule" : path.join("/"),
+                       message: "molecule must have an id attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class PropertyMustHaveDictRef < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Property)
+
+            return [] unless node.dict_ref.to_s.empty?
+
+            [violation(path: path.empty? ? "property" : path.join("/"),
+                       message: "property must have a dictRef attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Convention
+    module Molecular
+      module Constraints
+        class ScalarMustHaveDataType < Chemicalml::Convention::Constraint::NodeConstraint
+          def check_node(node, path)
+            return [] unless node.is_a?(Chemicalml::Cml::Role::Scalar)
+
+            return [] unless node.data_type.to_s.empty?
+
+            [violation(path: path.empty? ? "scalar" : path.join("/"),
+                       message: "scalar must have a dataType attribute")]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/convention/molecular/constraints.rb

@@ -3,9 +3,6 @@
 module Chemicalml
   module Convention
     module Molecular
-      # Namespace container for all molecular-convention constraint
-      # classes. One class per file, registered from the parent
-      # `molecular.rb`.
       module Constraints
         autoload :AtomArrayMustContainAtoms,
                  "chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms"
@@ -13,6 +10,26 @@ module Chemicalml
                  "chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule"
         autoload :BondMustReferenceAtomsInSameMolecule,
                  "chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule"
+        autoload :AtomMustHaveId,
+                 "chemicalml/convention/molecular/constraints/atom_must_have_id"
+        autoload :AtomMustHaveElementType,
+                 "chemicalml/convention/molecular/constraints/atom_must_have_element_type"
+        autoload :BondMustHaveAtomRefs2,
+                 "chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2"
+        autoload :BondMustHaveOrder,
+                 "chemicalml/convention/molecular/constraints/bond_must_have_order"
+        autoload :MoleculeMustHaveId,
+                 "chemicalml/convention/molecular/constraints/molecule_must_have_id"
+        autoload :AtomCoordinatesMustBePaired,
+                 "chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired"
+        autoload :PropertyMustHaveDictRef,
+                 "chemicalml/convention/molecular/constraints/property_must_have_dict_ref"
+        autoload :ScalarMustHaveDataType,
+                 "chemicalml/convention/molecular/constraints/scalar_must_have_data_type"
+        autoload :BondOrderShouldNotBeNumeric,
+                 "chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric"
+        autoload :AtomIdMustMatchPattern,
+                 "chemicalml/convention/molecular/constraints/atom_id_must_match_pattern"
       end
     end
   end

data/lib/chemicalml/convention/molecular.rb

@@ -24,6 +24,16 @@ module Chemicalml
       register Constraints::AtomArrayMustContainAtoms
       register Constraints::AtomIdsUniqueWithinMolecule
       register Constraints::BondMustReferenceAtomsInSameMolecule
+      register Constraints::AtomMustHaveId
+      register Constraints::AtomMustHaveElementType
+      register Constraints::BondMustHaveAtomRefs2
+      register Constraints::BondMustHaveOrder
+      register Constraints::MoleculeMustHaveId
+      register Constraints::AtomCoordinatesMustBePaired
+      register Constraints::PropertyMustHaveDictRef
+      register Constraints::ScalarMustHaveDataType
+      register Constraints::BondOrderShouldNotBeNumeric
+      register Constraints::AtomIdMustMatchPattern
     end
   end
 end

data/lib/chemicalml/model/atom.rb

@@ -5,16 +5,24 @@ module Chemicalml
     # A chemical atom. Carries every attribute CML's `<atom>` carries
     # that's chemistry-relevant: element symbol, formal charge,
     # isotope, count (multiplicity), hydrogen count, lone pairs,
-    # radical electrons, spin multiplicity.
+    # radical electrons, spin multiplicity, 2D/3D coordinates,
+    # fractional coordinates. Optional `atom_parity` for atom-centre
+    # chirality.
     class Atom < Node
       attr_accessor :id, :element, :formal_charge, :isotope,
                     :count, :hydrogen_count, :lone_pairs,
-                    :radical_electrons, :spin_multiplicity, :title
+                    :radical_electrons, :spin_multiplicity, :title,
+                    :x2, :y2, :x3, :y3, :z3,
+                    :x_fract, :y_fract, :z_fract,
+                    :atom_parity
 
       def initialize(element:, id: nil, formal_charge: nil,
                      isotope: nil, count: nil, hydrogen_count: nil,
                      lone_pairs: nil, radical_electrons: nil,
-                     spin_multiplicity: nil, title: nil)
+                     spin_multiplicity: nil, title: nil,
+                     x2: nil, y2: nil, x3: nil, y3: nil, z3: nil,
+                     x_fract: nil, y_fract: nil, z_fract: nil,
+                     atom_parity: nil)
         @element = element
         @id = id
         @formal_charge = formal_charge
@@ -25,6 +33,19 @@ module Chemicalml
         @radical_electrons = radical_electrons
         @spin_multiplicity = spin_multiplicity
         @title = title
+        @x2 = x2
+        @y2 = y2
+        @x3 = x3
+        @y3 = y3
+        @z3 = z3
+        @x_fract = x_fract
+        @y_fract = y_fract
+        @z_fract = z_fract
+        @atom_parity = atom_parity
+      end
+
+      def children
+        [atom_parity].compact
       end
 
       def value_attributes
@@ -32,7 +53,10 @@ module Chemicalml
           element: element, id: id, formal_charge: formal_charge,
           isotope: isotope, count: count, hydrogen_count: hydrogen_count,
           lone_pairs: lone_pairs, radical_electrons: radical_electrons,
-          spin_multiplicity: spin_multiplicity, title: title
+          spin_multiplicity: spin_multiplicity, title: title,
+          x2: x2, y2: y2, x3: x3, y3: y3, z3: z3,
+          x_fract: x_fract, y_fract: y_fract, z_fract: z_fract,
+          atom_parity: atom_parity
         }
       end
     end

data/lib/chemicalml/model/atom_parity.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Model
+    # Atom-centre chirality. CML `<atomParity>` element with
+    # `atomRefs4` (four atom IDs in order) and a `value` (typically
+    # `"1"`, `"-1"`, or `"0"`).
+    class AtomParity < Node
+      attr_accessor :atom_refs4, :value
+
+      def initialize(atom_refs4:, value:)
+        @atom_refs4 = atom_refs4
+        @value = value
+      end
+
+      def value_attributes
+        { atom_refs4: atom_refs4, value: value }
+      end
+    end
+  end
+end

data/lib/chemicalml/model/bond.rb

@@ -4,6 +4,7 @@ module Chemicalml
   module Model
     # A bond between two atoms. Endpoint references are string IDs
     # matching `Atom#id`; the kind enum follows CML conventions.
+    # Optional `bond_stereo` carries cis/trans/wedge/hatch info.
     class Bond < Node
       KINDS = %i[single double triple quadruple aromatic wedge hash
                  dative wavy].freeze
@@ -13,16 +14,21 @@ module Chemicalml
         aromatic: "A", wedge: "W", hash: "H", dative: "DG", wavy: "V"
       }.freeze
 
-      attr_accessor :id, :atom_refs, :kind
+      attr_accessor :id, :atom_refs, :kind, :bond_stereo
 
-      def initialize(id: nil, atom_refs:, kind: :single)
+      def initialize(id: nil, atom_refs:, kind: :single, bond_stereo: nil)
         @id = id
         @atom_refs = atom_refs
         @kind = kind
+        @bond_stereo = bond_stereo
+      end
+
+      def children
+        [bond_stereo].compact
       end
 
       def value_attributes
-        { id: id, atom_refs: atom_refs, kind: kind }
+        { id: id, atom_refs: atom_refs, kind: kind, bond_stereo: bond_stereo }
       end
 
       def cml_order

data/lib/chemicalml/model/bond_stereo.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Model
+    # Bond stereochemistry. CML `<bondStereo>` element. Carries
+    # either `atom_refs2` (for `W`/`H` wedge/hatch) or `atom_refs4`
+    # (for `C`/`T` cis/trans). The `value` is the convention letter:
+    # `W`, `H`, `C`, `T`, or `other` (with a `dict_ref`).
+    class BondStereo < Node
+      attr_accessor :atom_refs2, :atom_refs4, :dict_ref, :value
+
+      def initialize(value:, atom_refs2: nil, atom_refs4: nil, dict_ref: nil)
+        @value = value
+        @atom_refs2 = atom_refs2
+        @atom_refs4 = atom_refs4
+        @dict_ref = dict_ref
+      end
+
+      def value_attributes
+        {
+          value: value,
+          atom_refs2: atom_refs2,
+          atom_refs4: atom_refs4,
+          dict_ref: dict_ref
+        }
+      end
+    end
+  end
+end