chemicalml 0.2.0 → 0.2.1

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: chemicalml
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Ribose Inc.
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2026-07-14 00:00:00.000000000 Z
+date: 2026-07-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lutaml-model
@@ -83,6 +83,31 @@ files:
 - TODO.align/33-polymorphic-parse.md
 - TODO.align/34-polymorphic-specs.md
 - TODO.align/35-final-spec-lint.md
+- TODO.align/36-molecular-convention-coverage.md
+- TODO.align/37-compchem-convention-coverage.md
+- TODO.align/38-dictionary-convention-coverage.md
+- TODO.align/39-unit-dictionary-convention-coverage.md
+- TODO.align/40-unit-type-dictionary-convention-coverage.md
+- TODO.align/41-expand-canonical-model-layer.md
+- TODO.align/42-translator-wire-new-models.md
+- TODO.align/43-dictionary-model-no-to-h.md
+- TODO.align/44-schema3-only-and-schema24-module.md
+- TODO.align/45-documentation-and-final-verification.md
+- TODO.align/46-lattice-vector-content.md
+- TODO.align/47-molecule-crystal-spectra-property-lists.md
+- TODO.align/48-model-list-and-module-lists.md
+- TODO.align/49-more-chemistry-models.md
+- TODO.align/50-validation-report.md
+- TODO.align/51-convention-auto-detection.md
+- TODO.align/52-schema24-legacy-elements.md
+- TODO.align/53-round-trip-integration-specs.md
+- TODO.align/54-document-versioned-parser-shim.md
+- TODO.align/55-molecule-missing-attributes.md
+- TODO.align/56-geometry-models.md
+- TODO.align/57-compchem-models.md
+- TODO.align/58-remaining-models.md
+- TODO.align/59-wire-new-models-translator.md
+- TODO.align/60-docs-and-final-verification.md
 - TODO.align/README.md
 - TODO.align/README.round10.md
 - TODO.align/README.round11.md
@@ -126,9 +151,13 @@ files:
 - lib/chemicalml/cml/base/abundance.rb
 - lib/chemicalml/cml/base/action.rb
 - lib/chemicalml/cml/base/action_list.rb
+- lib/chemicalml/cml/base/alternative.rb
 - lib/chemicalml/cml/base/amount.rb
 - lib/chemicalml/cml/base/angle.rb
+- lib/chemicalml/cml/base/annotation.rb
 - lib/chemicalml/cml/base/any_cml.rb
+- lib/chemicalml/cml/base/appinfo.rb
+- lib/chemicalml/cml/base/arg.rb
 - lib/chemicalml/cml/base/array.rb
 - lib/chemicalml/cml/base/array_list.rb
 - lib/chemicalml/cml/base/atom.rb
@@ -149,6 +178,7 @@ files:
 - lib/chemicalml/cml/base/bond_type_list.rb
 - lib/chemicalml/cml/base/cell_parameter.rb
 - lib/chemicalml/cml/base/cml_module.rb
+- lib/chemicalml/cml/base/complex_object.rb
 - lib/chemicalml/cml/base/condition_list.rb
 - lib/chemicalml/cml/base/crystal.rb
 - lib/chemicalml/cml/base/definition.rb
@@ -160,11 +190,17 @@ files:
 - lib/chemicalml/cml/base/documentation.rb
 - lib/chemicalml/cml/base/eigen.rb
 - lib/chemicalml/cml/base/electron.rb
+- lib/chemicalml/cml/base/enumeration.rb
+- lib/chemicalml/cml/base/expression.rb
+- lib/chemicalml/cml/base/float.rb
+- lib/chemicalml/cml/base/float_array.rb
 - lib/chemicalml/cml/base/formula.rb
 - lib/chemicalml/cml/base/fragment.rb
 - lib/chemicalml/cml/base/fragment_list.rb
 - lib/chemicalml/cml/base/gradient.rb
 - lib/chemicalml/cml/base/identifier.rb
+- lib/chemicalml/cml/base/integer.rb
+- lib/chemicalml/cml/base/integer_array.rb
 - lib/chemicalml/cml/base/isotope.rb
 - lib/chemicalml/cml/base/isotope_list.rb
 - lib/chemicalml/cml/base/join.rb
@@ -188,6 +224,7 @@ files:
 - lib/chemicalml/cml/base/name.rb
 - lib/chemicalml/cml/base/object.rb
 - lib/chemicalml/cml/base/observation.rb
+- lib/chemicalml/cml/base/operator.rb
 - lib/chemicalml/cml/base/parameter.rb
 - lib/chemicalml/cml/base/parameter_list.rb
 - lib/chemicalml/cml/base/particle.rb
@@ -213,6 +250,7 @@ files:
 - lib/chemicalml/cml/base/reaction_step_list.rb
 - lib/chemicalml/cml/base/reactive_centre.rb
 - lib/chemicalml/cml/base/region.rb
+- lib/chemicalml/cml/base/related_entry.rb
 - lib/chemicalml/cml/base/sample.rb
 - lib/chemicalml/cml/base/scalar.rb
 - lib/chemicalml/cml/base/spectator.rb
@@ -222,6 +260,8 @@ files:
 - lib/chemicalml/cml/base/spectrum_list.rb
 - lib/chemicalml/cml/base/sphere3.rb
 - lib/chemicalml/cml/base/stmml.rb
+- lib/chemicalml/cml/base/string.rb
+- lib/chemicalml/cml/base/string_array.rb
 - lib/chemicalml/cml/base/substance.rb
 - lib/chemicalml/cml/base/substance_list.rb
 - lib/chemicalml/cml/base/symmetry.rb
@@ -233,9 +273,11 @@ files:
 - lib/chemicalml/cml/base/table_header_cell.rb
 - lib/chemicalml/cml/base/table_row.rb
 - lib/chemicalml/cml/base/table_row_list.rb
+- lib/chemicalml/cml/base/tcell.rb
 - lib/chemicalml/cml/base/torsion.rb
 - lib/chemicalml/cml/base/transform3.rb
 - lib/chemicalml/cml/base/transition_state.rb
+- lib/chemicalml/cml/base/trow.rb
 - lib/chemicalml/cml/base/unit.rb
 - lib/chemicalml/cml/base/unit_list.rb
 - lib/chemicalml/cml/base/unit_type.rb
@@ -244,16 +286,19 @@ files:
 - lib/chemicalml/cml/base/xaxis.rb
 - lib/chemicalml/cml/base/yaxis.rb
 - lib/chemicalml/cml/base/z_matrix.rb
-- lib/chemicalml/cml/child_mappings.rb
 - lib/chemicalml/cml/elements.rb
 - lib/chemicalml/cml/namespace.rb
 - lib/chemicalml/cml/role.rb
 - lib/chemicalml/cml/role/abundance.rb
 - lib/chemicalml/cml/role/action.rb
 - lib/chemicalml/cml/role/action_list.rb
+- lib/chemicalml/cml/role/alternative.rb
 - lib/chemicalml/cml/role/amount.rb
 - lib/chemicalml/cml/role/angle.rb
+- lib/chemicalml/cml/role/annotation.rb
 - lib/chemicalml/cml/role/any_cml.rb
+- lib/chemicalml/cml/role/appinfo.rb
+- lib/chemicalml/cml/role/arg.rb
 - lib/chemicalml/cml/role/array.rb
 - lib/chemicalml/cml/role/array_list.rb
 - lib/chemicalml/cml/role/atom.rb
@@ -274,6 +319,7 @@ files:
 - lib/chemicalml/cml/role/bond_type_list.rb
 - lib/chemicalml/cml/role/cell_parameter.rb
 - lib/chemicalml/cml/role/cml_module.rb
+- lib/chemicalml/cml/role/complex_object.rb
 - lib/chemicalml/cml/role/condition_list.rb
 - lib/chemicalml/cml/role/crystal.rb
 - lib/chemicalml/cml/role/definition.rb
@@ -285,11 +331,17 @@ files:
 - lib/chemicalml/cml/role/documentation.rb
 - lib/chemicalml/cml/role/eigen.rb
 - lib/chemicalml/cml/role/electron.rb
+- lib/chemicalml/cml/role/enumeration.rb
+- lib/chemicalml/cml/role/expression.rb
+- lib/chemicalml/cml/role/float.rb
+- lib/chemicalml/cml/role/float_array.rb
 - lib/chemicalml/cml/role/formula.rb
 - lib/chemicalml/cml/role/fragment.rb
 - lib/chemicalml/cml/role/fragment_list.rb
 - lib/chemicalml/cml/role/gradient.rb
 - lib/chemicalml/cml/role/identifier.rb
+- lib/chemicalml/cml/role/integer.rb
+- lib/chemicalml/cml/role/integer_array.rb
 - lib/chemicalml/cml/role/isotope.rb
 - lib/chemicalml/cml/role/isotope_list.rb
 - lib/chemicalml/cml/role/join.rb
@@ -313,6 +365,7 @@ files:
 - lib/chemicalml/cml/role/name.rb
 - lib/chemicalml/cml/role/object.rb
 - lib/chemicalml/cml/role/observation.rb
+- lib/chemicalml/cml/role/operator.rb
 - lib/chemicalml/cml/role/parameter.rb
 - lib/chemicalml/cml/role/parameter_list.rb
 - lib/chemicalml/cml/role/particle.rb
@@ -338,6 +391,7 @@ files:
 - lib/chemicalml/cml/role/reaction_step_list.rb
 - lib/chemicalml/cml/role/reactive_centre.rb
 - lib/chemicalml/cml/role/region.rb
+- lib/chemicalml/cml/role/related_entry.rb
 - lib/chemicalml/cml/role/sample.rb
 - lib/chemicalml/cml/role/scalar.rb
 - lib/chemicalml/cml/role/spectator.rb
@@ -347,6 +401,8 @@ files:
 - lib/chemicalml/cml/role/spectrum_list.rb
 - lib/chemicalml/cml/role/sphere3.rb
 - lib/chemicalml/cml/role/stmml.rb
+- lib/chemicalml/cml/role/string.rb
+- lib/chemicalml/cml/role/string_array.rb
 - lib/chemicalml/cml/role/substance.rb
 - lib/chemicalml/cml/role/substance_list.rb
 - lib/chemicalml/cml/role/symmetry.rb
@@ -358,9 +414,11 @@ files:
 - lib/chemicalml/cml/role/table_header_cell.rb
 - lib/chemicalml/cml/role/table_row.rb
 - lib/chemicalml/cml/role/table_row_list.rb
+- lib/chemicalml/cml/role/tcell.rb
 - lib/chemicalml/cml/role/torsion.rb
 - lib/chemicalml/cml/role/transform3.rb
 - lib/chemicalml/cml/role/transition_state.rb
+- lib/chemicalml/cml/role/trow.rb
 - lib/chemicalml/cml/role/unit.rb
 - lib/chemicalml/cml/role/unit_list.rb
 - lib/chemicalml/cml/role/unit_type.rb
@@ -373,9 +431,13 @@ files:
 - lib/chemicalml/cml/schema24/abundance.rb
 - lib/chemicalml/cml/schema24/action.rb
 - lib/chemicalml/cml/schema24/action_list.rb
+- lib/chemicalml/cml/schema24/alternative.rb
 - lib/chemicalml/cml/schema24/amount.rb
 - lib/chemicalml/cml/schema24/angle.rb
+- lib/chemicalml/cml/schema24/annotation.rb
 - lib/chemicalml/cml/schema24/any_cml.rb
+- lib/chemicalml/cml/schema24/appinfo.rb
+- lib/chemicalml/cml/schema24/arg.rb
 - lib/chemicalml/cml/schema24/array.rb
 - lib/chemicalml/cml/schema24/array_list.rb
 - lib/chemicalml/cml/schema24/atom.rb
@@ -395,6 +457,8 @@ files:
 - lib/chemicalml/cml/schema24/bond_type.rb
 - lib/chemicalml/cml/schema24/bond_type_list.rb
 - lib/chemicalml/cml/schema24/cell_parameter.rb
+- lib/chemicalml/cml/schema24/cml_module.rb
+- lib/chemicalml/cml/schema24/complex_object.rb
 - lib/chemicalml/cml/schema24/condition_list.rb
 - lib/chemicalml/cml/schema24/configuration.rb
 - lib/chemicalml/cml/schema24/context.rb
@@ -408,11 +472,17 @@ files:
 - lib/chemicalml/cml/schema24/documentation.rb
 - lib/chemicalml/cml/schema24/eigen.rb
 - lib/chemicalml/cml/schema24/electron.rb
+- lib/chemicalml/cml/schema24/enumeration.rb
+- lib/chemicalml/cml/schema24/expression.rb
+- lib/chemicalml/cml/schema24/float.rb
+- lib/chemicalml/cml/schema24/float_array.rb
 - lib/chemicalml/cml/schema24/formula.rb
 - lib/chemicalml/cml/schema24/fragment.rb
 - lib/chemicalml/cml/schema24/fragment_list.rb
 - lib/chemicalml/cml/schema24/gradient.rb
 - lib/chemicalml/cml/schema24/identifier.rb
+- lib/chemicalml/cml/schema24/integer.rb
+- lib/chemicalml/cml/schema24/integer_array.rb
 - lib/chemicalml/cml/schema24/isotope.rb
 - lib/chemicalml/cml/schema24/isotope_list.rb
 - lib/chemicalml/cml/schema24/join.rb
@@ -436,6 +506,7 @@ files:
 - lib/chemicalml/cml/schema24/name.rb
 - lib/chemicalml/cml/schema24/object.rb
 - lib/chemicalml/cml/schema24/observation.rb
+- lib/chemicalml/cml/schema24/operator.rb
 - lib/chemicalml/cml/schema24/parameter.rb
 - lib/chemicalml/cml/schema24/parameter_list.rb
 - lib/chemicalml/cml/schema24/particle.rb
@@ -461,6 +532,7 @@ files:
 - lib/chemicalml/cml/schema24/reaction_step_list.rb
 - lib/chemicalml/cml/schema24/reactive_centre.rb
 - lib/chemicalml/cml/schema24/region.rb
+- lib/chemicalml/cml/schema24/related_entry.rb
 - lib/chemicalml/cml/schema24/sample.rb
 - lib/chemicalml/cml/schema24/scalar.rb
 - lib/chemicalml/cml/schema24/spectator.rb
@@ -470,6 +542,8 @@ files:
 - lib/chemicalml/cml/schema24/spectrum_list.rb
 - lib/chemicalml/cml/schema24/sphere3.rb
 - lib/chemicalml/cml/schema24/stmml.rb
+- lib/chemicalml/cml/schema24/string.rb
+- lib/chemicalml/cml/schema24/string_array.rb
 - lib/chemicalml/cml/schema24/substance.rb
 - lib/chemicalml/cml/schema24/substance_list.rb
 - lib/chemicalml/cml/schema24/symmetry.rb
@@ -481,9 +555,11 @@ files:
 - lib/chemicalml/cml/schema24/table_header_cell.rb
 - lib/chemicalml/cml/schema24/table_row.rb
 - lib/chemicalml/cml/schema24/table_row_list.rb
+- lib/chemicalml/cml/schema24/tcell.rb
 - lib/chemicalml/cml/schema24/torsion.rb
 - lib/chemicalml/cml/schema24/transform3.rb
 - lib/chemicalml/cml/schema24/transition_state.rb
+- lib/chemicalml/cml/schema24/trow.rb
 - lib/chemicalml/cml/schema24/unit.rb
 - lib/chemicalml/cml/schema24/unit_list.rb
 - lib/chemicalml/cml/schema24/unit_type.rb
@@ -616,8 +692,6 @@ files:
 - lib/chemicalml/cml/schema3/xaxis.rb
 - lib/chemicalml/cml/schema3/yaxis.rb
 - lib/chemicalml/cml/schema3/z_matrix.rb
-- lib/chemicalml/cml/translator.rb
-- lib/chemicalml/cml/translator/value_translations.rb
 - lib/chemicalml/cml/visitable.rb
 - lib/chemicalml/cml/wire_class_registry.rb
 - lib/chemicalml/context_configuration.rb
@@ -625,35 +699,79 @@ files:
 - lib/chemicalml/convention/base.rb
 - lib/chemicalml/convention/compchem.rb
 - lib/chemicalml/convention/compchem/constraints.rb
+- lib/chemicalml/convention/compchem/constraints/array_rules.rb
+- lib/chemicalml/convention/compchem/constraints/calculation_requires_finalization.rb
 - lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.rb
+- lib/chemicalml/convention/compchem/constraints/environment_at_most_one_property_list.rb
+- lib/chemicalml/convention/compchem/constraints/environment_must_not_contain_parameter.rb
+- lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_molecule.rb
+- lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_property_list.rb
+- lib/chemicalml/convention/compchem/constraints/finalization_must_not_contain_parameter.rb
+- lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_molecule.rb
+- lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_parameter_list.rb
+- lib/chemicalml/convention/compchem/constraints/initialization_must_not_contain_property.rb
+- lib/chemicalml/convention/compchem/constraints/job_list_module_must_have_id.rb
+- lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_environment.rb
+- lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_finalization.rb
+- lib/chemicalml/convention/compchem/constraints/job_module_must_have_id.rb
 - lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb
+- lib/chemicalml/convention/compchem/constraints/matrix_rules.rb
+- lib/chemicalml/convention/compchem/constraints/module_predicates.rb
+- lib/chemicalml/convention/compchem/constraints/scalar_units.rb
 - lib/chemicalml/convention/constraint.rb
+- lib/chemicalml/convention/coordinator.rb
+- lib/chemicalml/convention/detection.rb
 - lib/chemicalml/convention/dictionary.rb
 - lib/chemicalml/convention/dictionary/constraints.rb
+- lib/chemicalml/convention/dictionary/constraints/dictionary_must_have_namespace.rb
+- lib/chemicalml/convention/dictionary/constraints/dictionary_namespace_should_end_with_slash_or_hash.rb
+- lib/chemicalml/convention/dictionary/constraints/entry_id_must_match_pattern.rb
 - lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb
+- lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb
 - lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb
+- lib/chemicalml/convention/dictionary/constraints/entry_must_have_unit_type.rb
+- lib/chemicalml/convention/dictionary/constraints/entry_units_co_constraints.rb
 - lib/chemicalml/convention/molecular.rb
 - lib/chemicalml/convention/molecular/constraints.rb
+- lib/chemicalml/convention/molecular/constraints/atom_array_must_be_child_of_molecule_or_formula.rb
 - lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb
 - lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb
 - lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb
 - lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb
 - lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb
 - lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb
+- lib/chemicalml/convention/molecular/constraints/bond_array_must_be_child_of_molecule.rb
+- lib/chemicalml/convention/molecular/constraints/bond_ids_unique_within_molecule.rb
 - lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb
 - lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb
 - lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb
+- lib/chemicalml/convention/molecular/constraints/bond_order_other_must_have_dict_ref.rb
 - lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb
+- lib/chemicalml/convention/molecular/constraints/bond_stereo_cis_trans_must_have_atom_refs4.rb
+- lib/chemicalml/convention/molecular/constraints/bond_stereo_other_must_have_dict_ref.rb
+- lib/chemicalml/convention/molecular/constraints/bond_stereo_wedge_hash_must_have_atom_refs2.rb
+- lib/chemicalml/convention/molecular/constraints/molecule_atom_array_mutually_exclusive_with_children.rb
+- lib/chemicalml/convention/molecular/constraints/molecule_bond_array_mutually_exclusive_with_children.rb
+- lib/chemicalml/convention/molecular/constraints/molecule_count_must_not_appear_on_top_level.rb
 - lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb
 - lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb
 - lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb
 - lib/chemicalml/convention/registry.rb
 - lib/chemicalml/convention/unit_dictionary.rb
 - lib/chemicalml/convention/unit_dictionary/constraints.rb
+- lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_contain_at_least_one_unit.rb
+- lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_have_namespace.rb
+- lib/chemicalml/convention/unit_dictionary/constraints/unit_must_contain_definition.rb
+- lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_id.rb
 - lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb
 - lib/chemicalml/convention/unit_type_dictionary.rb
 - lib/chemicalml/convention/unit_type_dictionary/constraints.rb
+- lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_id_must_match_pattern.rb
+- lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_contain_at_least_one_unit_type.rb
+- lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_have_namespace.rb
+- lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_contain_definition.rb
 - lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb
+- lib/chemicalml/convention/validation_report.rb
 - lib/chemicalml/convention/violation.rb
 - lib/chemicalml/dictionary.rb
 - lib/chemicalml/dictionary/entry.rb
@@ -663,35 +781,6 @@ files:
 - lib/chemicalml/dictionary/model.rb
 - lib/chemicalml/dictionary/registry.rb
 - lib/chemicalml/errors.rb
-- lib/chemicalml/model.rb
-- lib/chemicalml/model/atom.rb
-- lib/chemicalml/model/atom_parity.rb
-- lib/chemicalml/model/bond.rb
-- lib/chemicalml/model/bond_stereo.rb
-- lib/chemicalml/model/cml_array.rb
-- lib/chemicalml/model/cml_module.rb
-- lib/chemicalml/model/document.rb
-- lib/chemicalml/model/formula.rb
-- lib/chemicalml/model/identifier.rb
-- lib/chemicalml/model/label.rb
-- lib/chemicalml/model/matrix.rb
-- lib/chemicalml/model/metadata.rb
-- lib/chemicalml/model/metadata_list.rb
-- lib/chemicalml/model/molecule.rb
-- lib/chemicalml/model/name.rb
-- lib/chemicalml/model/node.rb
-- lib/chemicalml/model/parameter.rb
-- lib/chemicalml/model/parameter_list.rb
-- lib/chemicalml/model/product.rb
-- lib/chemicalml/model/product_list.rb
-- lib/chemicalml/model/property.rb
-- lib/chemicalml/model/property_list.rb
-- lib/chemicalml/model/reactant.rb
-- lib/chemicalml/model/reactant_list.rb
-- lib/chemicalml/model/reaction.rb
-- lib/chemicalml/model/reaction_list.rb
-- lib/chemicalml/model/scalar.rb
-- lib/chemicalml/model/substance.rb
 - lib/chemicalml/schema.rb
 - lib/chemicalml/schema/definition.rb
 - lib/chemicalml/schema/registry.rb

data/lib/chemicalml/cml/child_mappings.rb

@@ -1,168 +0,0 @@
-# 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