Module: Chemicalml

Defined in:: lib/chemicalml.rb,
lib/chemicalml/cli.rb,
lib/chemicalml/cml.rb,
lib/chemicalml/errors.rb,
lib/chemicalml/logger.rb,
lib/chemicalml/schema.rb,
lib/chemicalml/version.rb,
lib/chemicalml/cli/base.rb,
lib/chemicalml/cml/base.rb,
lib/chemicalml/cml/role.rb,
lib/chemicalml/cml/enums.rb,
lib/chemicalml/convention.rb,
lib/chemicalml/dictionary.rb,
lib/chemicalml/cli/command.rb,
lib/chemicalml/cml/aliases.rb,
lib/chemicalml/cml/schema3.rb,
lib/chemicalml/cml/base/arg.rb,
lib/chemicalml/cml/base/map.rb,
lib/chemicalml/cml/elements.rb,
lib/chemicalml/cml/patterns.rb,
lib/chemicalml/cml/role/arg.rb,
lib/chemicalml/cml/role/map.rb,
lib/chemicalml/cml/schema24.rb,
lib/chemicalml/cml/base/atom.rb,
lib/chemicalml/cml/base/band.rb,
lib/chemicalml/cml/base/bond.rb,
lib/chemicalml/cml/base/join.rb,
lib/chemicalml/cml/base/link.rb,
lib/chemicalml/cml/base/list.rb,
lib/chemicalml/cml/base/name.rb,
lib/chemicalml/cml/base/peak.rb,
lib/chemicalml/cml/base/trow.rb,
lib/chemicalml/cml/base/unit.rb,
lib/chemicalml/cml/namespace.rb,
lib/chemicalml/cml/role/atom.rb,
lib/chemicalml/cml/role/band.rb,
lib/chemicalml/cml/role/bond.rb,
lib/chemicalml/cml/role/join.rb,
lib/chemicalml/cml/role/link.rb,
lib/chemicalml/cml/role/list.rb,
lib/chemicalml/cml/role/name.rb,
lib/chemicalml/cml/role/peak.rb,
lib/chemicalml/cml/role/trow.rb,
lib/chemicalml/cml/role/unit.rb,
lib/chemicalml/cml/visitable.rb,
lib/chemicalml/cml/base/angle.rb,
lib/chemicalml/cml/base/array.rb,
lib/chemicalml/cml/base/eigen.rb,
lib/chemicalml/cml/base/float.rb,
lib/chemicalml/cml/base/label.rb,
lib/chemicalml/cml/base/line3.rb,
lib/chemicalml/cml/base/stmml.rb,
lib/chemicalml/cml/base/table.rb,
lib/chemicalml/cml/base/tcell.rb,
lib/chemicalml/cml/base/xaxis.rb,
lib/chemicalml/cml/base/yaxis.rb,
lib/chemicalml/cml/role/angle.rb,
lib/chemicalml/cml/role/array.rb,
lib/chemicalml/cml/role/eigen.rb,
lib/chemicalml/cml/role/float.rb,
lib/chemicalml/cml/role/label.rb,
lib/chemicalml/cml/role/line3.rb,
lib/chemicalml/cml/role/stmml.rb,
lib/chemicalml/cml/role/table.rb,
lib/chemicalml/cml/role/tcell.rb,
lib/chemicalml/cml/role/xaxis.rb,
lib/chemicalml/cml/role/yaxis.rb,
lib/chemicalml/cml/base/action.rb,
lib/chemicalml/cml/base/amount.rb,
lib/chemicalml/cml/base/kpoint.rb,
lib/chemicalml/cml/base/length.rb,
lib/chemicalml/cml/base/matrix.rb,
lib/chemicalml/cml/base/object.rb,
lib/chemicalml/cml/base/plane3.rb,
lib/chemicalml/cml/base/point3.rb,
lib/chemicalml/cml/base/region.rb,
lib/chemicalml/cml/base/sample.rb,
lib/chemicalml/cml/base/scalar.rb,
lib/chemicalml/cml/base/string.rb,
lib/chemicalml/cml/base/system.rb,
lib/chemicalml/cml/role/action.rb,
lib/chemicalml/cml/role/amount.rb,
lib/chemicalml/cml/role/kpoint.rb,
lib/chemicalml/cml/role/length.rb,
lib/chemicalml/cml/role/matrix.rb,
lib/chemicalml/cml/role/object.rb,
lib/chemicalml/cml/role/plane3.rb,
lib/chemicalml/cml/role/point3.rb,
lib/chemicalml/cml/role/region.rb,
lib/chemicalml/cml/role/sample.rb,
lib/chemicalml/cml/role/scalar.rb,
lib/chemicalml/cml/role/string.rb,
lib/chemicalml/cml/role/system.rb,
lib/chemicalml/cml/schema3/map.rb,
lib/chemicalml/convention/base.rb,
lib/chemicalml/dictionary/enum.rb,
lib/chemicalml/dictionary/link.rb,
lib/chemicalml/schema/registry.rb,
lib/chemicalml/cli/info_command.rb,
lib/chemicalml/cml/base/any_cml.rb,
lib/chemicalml/cml/base/appinfo.rb,
lib/chemicalml/cml/base/crystal.rb,
lib/chemicalml/cml/base/formula.rb,
lib/chemicalml/cml/base/integer.rb,
lib/chemicalml/cml/base/isotope.rb,
lib/chemicalml/cml/base/lattice.rb,
lib/chemicalml/cml/base/product.rb,
lib/chemicalml/cml/base/sphere3.rb,
lib/chemicalml/cml/base/torsion.rb,
lib/chemicalml/cml/base/vector3.rb,
lib/chemicalml/cml/role/any_cml.rb,
lib/chemicalml/cml/role/appinfo.rb,
lib/chemicalml/cml/role/crystal.rb,
lib/chemicalml/cml/role/formula.rb,
lib/chemicalml/cml/role/integer.rb,
lib/chemicalml/cml/role/isotope.rb,
lib/chemicalml/cml/role/lattice.rb,
lib/chemicalml/cml/role/product.rb,
lib/chemicalml/cml/role/sphere3.rb,
lib/chemicalml/cml/role/torsion.rb,
lib/chemicalml/cml/role/vector3.rb,
lib/chemicalml/cml/schema24/arg.rb,
lib/chemicalml/cml/schema24/map.rb,
lib/chemicalml/cml/schema3/atom.rb,
lib/chemicalml/cml/schema3/band.rb,
lib/chemicalml/cml/schema3/bond.rb,
lib/chemicalml/cml/schema3/join.rb,
lib/chemicalml/cml/schema3/link.rb,
lib/chemicalml/cml/schema3/list.rb,
lib/chemicalml/cml/schema3/name.rb,
lib/chemicalml/cml/schema3/peak.rb,
lib/chemicalml/cml/schema3/unit.rb,
lib/chemicalml/dictionary/entry.rb,
lib/chemicalml/dictionary/model.rb,
lib/chemicalml/versioned_parser.rb,
lib/chemicalml/cli/enums_command.rb,
lib/chemicalml/cml/base/atom_set.rb,
lib/chemicalml/cml/base/bond_set.rb,
lib/chemicalml/cml/base/document.rb,
lib/chemicalml/cml/base/electron.rb,
lib/chemicalml/cml/base/fragment.rb,
lib/chemicalml/cml/base/gradient.rb,
lib/chemicalml/cml/base/metadata.rb,
lib/chemicalml/cml/base/molecule.rb,
lib/chemicalml/cml/base/operator.rb,
lib/chemicalml/cml/base/particle.rb,
lib/chemicalml/cml/base/property.rb,
lib/chemicalml/cml/base/reactant.rb,
lib/chemicalml/cml/base/reaction.rb,
lib/chemicalml/cml/base/spectrum.rb,
lib/chemicalml/cml/base/symmetry.rb,
lib/chemicalml/cml/base/z_matrix.rb,
lib/chemicalml/cml/role/atom_set.rb,
lib/chemicalml/cml/role/bond_set.rb,
lib/chemicalml/cml/role/document.rb,
lib/chemicalml/cml/role/electron.rb,
lib/chemicalml/cml/role/fragment.rb,
lib/chemicalml/cml/role/gradient.rb,
lib/chemicalml/cml/role/metadata.rb,
lib/chemicalml/cml/role/molecule.rb,
lib/chemicalml/cml/role/operator.rb,
lib/chemicalml/cml/role/particle.rb,
lib/chemicalml/cml/role/property.rb,
lib/chemicalml/cml/role/reactant.rb,
lib/chemicalml/cml/role/reaction.rb,
lib/chemicalml/cml/role/spectrum.rb,
lib/chemicalml/cml/role/symmetry.rb,
lib/chemicalml/cml/role/z_matrix.rb,
lib/chemicalml/cml/schema24/atom.rb,
lib/chemicalml/cml/schema24/band.rb,
lib/chemicalml/cml/schema24/bond.rb,
lib/chemicalml/cml/schema24/join.rb,
lib/chemicalml/cml/schema24/link.rb,
lib/chemicalml/cml/schema24/list.rb,
lib/chemicalml/cml/schema24/name.rb,
lib/chemicalml/cml/schema24/peak.rb,
lib/chemicalml/cml/schema24/trow.rb,
lib/chemicalml/cml/schema24/unit.rb,
lib/chemicalml/cml/schema3/angle.rb,
lib/chemicalml/cml/schema3/array.rb,
lib/chemicalml/cml/schema3/eigen.rb,
lib/chemicalml/cml/schema3/label.rb,
lib/chemicalml/cml/schema3/line3.rb,
lib/chemicalml/cml/schema3/stmml.rb,
lib/chemicalml/cml/schema3/table.rb,
lib/chemicalml/cml/schema3/xaxis.rb,
lib/chemicalml/cml/schema3/yaxis.rb,
lib/chemicalml/dictionary/loader.rb,
lib/chemicalml/schema/definition.rb,
lib/chemicalml/cml/base/abundance.rb,
lib/chemicalml/cml/base/atom_type.rb,
lib/chemicalml/cml/base/band_list.rb,
lib/chemicalml/cml/base/basis_set.rb,
lib/chemicalml/cml/base/bond_type.rb,
lib/chemicalml/cml/base/dimension.rb,
lib/chemicalml/cml/base/mechanism.rb,
lib/chemicalml/cml/base/parameter.rb,
lib/chemicalml/cml/base/peak_list.rb,
lib/chemicalml/cml/base/potential.rb,
lib/chemicalml/cml/base/spectator.rb,
lib/chemicalml/cml/base/substance.rb,
lib/chemicalml/cml/base/table_row.rb,
lib/chemicalml/cml/base/unit_list.rb,
lib/chemicalml/cml/base/unit_type.rb,
lib/chemicalml/cml/role/abundance.rb,
lib/chemicalml/cml/role/atom_type.rb,
lib/chemicalml/cml/role/band_list.rb,
lib/chemicalml/cml/role/basis_set.rb,
lib/chemicalml/cml/role/bond_type.rb,
lib/chemicalml/cml/role/dimension.rb,
lib/chemicalml/cml/role/mechanism.rb,
lib/chemicalml/cml/role/parameter.rb,
lib/chemicalml/cml/role/peak_list.rb,
lib/chemicalml/cml/role/potential.rb,
lib/chemicalml/cml/role/spectator.rb,
lib/chemicalml/cml/role/substance.rb,
lib/chemicalml/cml/role/table_row.rb,
lib/chemicalml/cml/role/unit_list.rb,
lib/chemicalml/cml/role/unit_type.rb,
lib/chemicalml/cml/schema24/angle.rb,
lib/chemicalml/cml/schema24/array.rb,
lib/chemicalml/cml/schema24/eigen.rb,
lib/chemicalml/cml/schema24/float.rb,
lib/chemicalml/cml/schema24/label.rb,
lib/chemicalml/cml/schema24/line3.rb,
lib/chemicalml/cml/schema24/stmml.rb,
lib/chemicalml/cml/schema24/table.rb,
lib/chemicalml/cml/schema24/tcell.rb,
lib/chemicalml/cml/schema24/xaxis.rb,
lib/chemicalml/cml/schema24/yaxis.rb,
lib/chemicalml/cml/schema3/action.rb,
lib/chemicalml/cml/schema3/amount.rb,
lib/chemicalml/cml/schema3/kpoint.rb,
lib/chemicalml/cml/schema3/length.rb,
lib/chemicalml/cml/schema3/matrix.rb,
lib/chemicalml/cml/schema3/object.rb,
lib/chemicalml/cml/schema3/plane3.rb,
lib/chemicalml/cml/schema3/point3.rb,
lib/chemicalml/cml/schema3/region.rb,
lib/chemicalml/cml/schema3/sample.rb,
lib/chemicalml/cml/schema3/scalar.rb,
lib/chemicalml/cml/schema3/system.rb,
lib/chemicalml/convention/cascade.rb,
lib/chemicalml/cli/inspect_command.rb,
lib/chemicalml/cml/base/annotation.rb,
lib/chemicalml/cml/base/array_list.rb,
lib/chemicalml/cml/base/atom_array.rb,
lib/chemicalml/cml/base/bond_array.rb,
lib/chemicalml/cml/base/cml_module.rb,
lib/chemicalml/cml/base/definition.rb,
lib/chemicalml/cml/base/dictionary.rb,
lib/chemicalml/cml/base/expression.rb,
lib/chemicalml/cml/base/identifier.rb,
lib/chemicalml/cml/base/peak_group.rb,
lib/chemicalml/cml/base/table_cell.rb,
lib/chemicalml/cml/base/transform3.rb,
lib/chemicalml/cml/role/annotation.rb,
lib/chemicalml/cml/role/array_list.rb,
lib/chemicalml/cml/role/atom_array.rb,
lib/chemicalml/cml/role/bond_array.rb,
lib/chemicalml/cml/role/cml_module.rb,
lib/chemicalml/cml/role/definition.rb,
lib/chemicalml/cml/role/dictionary.rb,
lib/chemicalml/cml/role/expression.rb,
lib/chemicalml/cml/role/identifier.rb,
lib/chemicalml/cml/role/peak_group.rb,
lib/chemicalml/cml/role/table_cell.rb,
lib/chemicalml/cml/role/transform3.rb,
lib/chemicalml/cml/schema24/action.rb,
lib/chemicalml/cml/schema24/amount.rb,
lib/chemicalml/cml/schema24/kpoint.rb,
lib/chemicalml/cml/schema24/length.rb,
lib/chemicalml/cml/schema24/matrix.rb,
lib/chemicalml/cml/schema24/object.rb,
lib/chemicalml/cml/schema24/plane3.rb,
lib/chemicalml/cml/schema24/point3.rb,
lib/chemicalml/cml/schema24/region.rb,
lib/chemicalml/cml/schema24/sample.rb,
lib/chemicalml/cml/schema24/scalar.rb,
lib/chemicalml/cml/schema24/string.rb,
lib/chemicalml/cml/schema24/system.rb,
lib/chemicalml/cml/schema3/any_cml.rb,
lib/chemicalml/cml/schema3/context.rb,
lib/chemicalml/cml/schema3/crystal.rb,
lib/chemicalml/cml/schema3/formula.rb,
lib/chemicalml/cml/schema3/isotope.rb,
lib/chemicalml/cml/schema3/lattice.rb,
lib/chemicalml/cml/schema3/product.rb,
lib/chemicalml/cml/schema3/sphere3.rb,
lib/chemicalml/cml/schema3/torsion.rb,
lib/chemicalml/cml/schema3/vector3.rb,
lib/chemicalml/convention/compchem.rb,
lib/chemicalml/convention/registry.rb,
lib/chemicalml/dictionary/registry.rb,
lib/chemicalml/cli/elements_command.rb,
lib/chemicalml/cli/validate_command.rb,
lib/chemicalml/cml/base/action_list.rb,
lib/chemicalml/cml/base/alternative.rb,
lib/chemicalml/cml/base/atom_parity.rb,
lib/chemicalml/cml/base/bond_stereo.rb,
lib/chemicalml/cml/base/description.rb,
lib/chemicalml/cml/base/enumeration.rb,
lib/chemicalml/cml/base/float_array.rb,
lib/chemicalml/cml/base/kpoint_list.rb,
lib/chemicalml/cml/base/observation.rb,
lib/chemicalml/cml/role/action_list.rb,
lib/chemicalml/cml/role/alternative.rb,
lib/chemicalml/cml/role/atom_parity.rb,
lib/chemicalml/cml/role/bond_stereo.rb,
lib/chemicalml/cml/role/description.rb,
lib/chemicalml/cml/role/enumeration.rb,
lib/chemicalml/cml/role/float_array.rb,
lib/chemicalml/cml/role/kpoint_list.rb,
lib/chemicalml/cml/role/observation.rb,
lib/chemicalml/cml/schema24/any_cml.rb,
lib/chemicalml/cml/schema24/appinfo.rb,
lib/chemicalml/cml/schema24/context.rb,
lib/chemicalml/cml/schema24/crystal.rb,
lib/chemicalml/cml/schema24/formula.rb,
lib/chemicalml/cml/schema24/integer.rb,
lib/chemicalml/cml/schema24/isotope.rb,
lib/chemicalml/cml/schema24/lattice.rb,
lib/chemicalml/cml/schema24/product.rb,
lib/chemicalml/cml/schema24/sphere3.rb,
lib/chemicalml/cml/schema24/torsion.rb,
lib/chemicalml/cml/schema24/vector3.rb,
lib/chemicalml/cml/schema3/atom_set.rb,
lib/chemicalml/cml/schema3/bond_set.rb,
lib/chemicalml/cml/schema3/document.rb,
lib/chemicalml/cml/schema3/electron.rb,
lib/chemicalml/cml/schema3/fragment.rb,
lib/chemicalml/cml/schema3/gradient.rb,
lib/chemicalml/cml/schema3/metadata.rb,
lib/chemicalml/cml/schema3/molecule.rb,
lib/chemicalml/cml/schema3/particle.rb,
lib/chemicalml/cml/schema3/property.rb,
lib/chemicalml/cml/schema3/reactant.rb,
lib/chemicalml/cml/schema3/reaction.rb,
lib/chemicalml/cml/schema3/spectrum.rb,
lib/chemicalml/cml/schema3/symmetry.rb,
lib/chemicalml/cml/schema3/z_matrix.rb,
lib/chemicalml/convention/detection.rb,
lib/chemicalml/convention/molecular.rb,
lib/chemicalml/convention/violation.rb,
lib/chemicalml/cml/base/isotope_list.rb,
lib/chemicalml/cml/base/product_list.rb,
lib/chemicalml/cml/base/string_array.rb,
lib/chemicalml/cml/base/table_header.rb,
lib/chemicalml/cml/role/isotope_list.rb,
lib/chemicalml/cml/role/product_list.rb,
lib/chemicalml/cml/role/string_array.rb,
lib/chemicalml/cml/role/table_header.rb,
lib/chemicalml/cml/schema24/atom_set.rb,
lib/chemicalml/cml/schema24/bond_set.rb,
lib/chemicalml/cml/schema24/document.rb,
lib/chemicalml/cml/schema24/electron.rb,
lib/chemicalml/cml/schema24/fragment.rb,
lib/chemicalml/cml/schema24/gradient.rb,
lib/chemicalml/cml/schema24/metadata.rb,
lib/chemicalml/cml/schema24/molecule.rb,
lib/chemicalml/cml/schema24/operator.rb,
lib/chemicalml/cml/schema24/particle.rb,
lib/chemicalml/cml/schema24/property.rb,
lib/chemicalml/cml/schema24/reactant.rb,
lib/chemicalml/cml/schema24/reaction.rb,
lib/chemicalml/cml/schema24/spectrum.rb,
lib/chemicalml/cml/schema24/symmetry.rb,
lib/chemicalml/cml/schema24/z_matrix.rb,
lib/chemicalml/cml/schema3/abundance.rb,
lib/chemicalml/cml/schema3/atom_type.rb,
lib/chemicalml/cml/schema3/band_list.rb,
lib/chemicalml/cml/schema3/basis_set.rb,
lib/chemicalml/cml/schema3/bond_type.rb,
lib/chemicalml/cml/schema3/dimension.rb,
lib/chemicalml/cml/schema3/mechanism.rb,
lib/chemicalml/cml/schema3/parameter.rb,
lib/chemicalml/cml/schema3/peak_list.rb,
lib/chemicalml/cml/schema3/potential.rb,
lib/chemicalml/cml/schema3/spectator.rb,
lib/chemicalml/cml/schema3/substance.rb,
lib/chemicalml/cml/schema3/table_row.rb,
lib/chemicalml/cml/schema3/unit_list.rb,
lib/chemicalml/cml/schema3/unit_type.rb,
lib/chemicalml/context_configuration.rb,
lib/chemicalml/convention/constraint.rb,
lib/chemicalml/convention/dictionary.rb,
lib/chemicalml/cml/base/documentation.rb,
lib/chemicalml/cml/base/fragment_list.rb,
lib/chemicalml/cml/base/integer_array.rb,
lib/chemicalml/cml/base/metadata_list.rb,
lib/chemicalml/cml/base/molecule_list.rb,
lib/chemicalml/cml/base/property_list.rb,
lib/chemicalml/cml/base/reactant_list.rb,
lib/chemicalml/cml/base/reaction_list.rb,
lib/chemicalml/cml/base/reaction_step.rb,
lib/chemicalml/cml/base/related_entry.rb,
lib/chemicalml/cml/base/spectrum_data.rb,
lib/chemicalml/cml/base/spectrum_list.rb,
lib/chemicalml/cml/base/table_content.rb,
lib/chemicalml/cml/reference_resolver.rb,
lib/chemicalml/cml/role/documentation.rb,
lib/chemicalml/cml/role/fragment_list.rb,
lib/chemicalml/cml/role/integer_array.rb,
lib/chemicalml/cml/role/metadata_list.rb,
lib/chemicalml/cml/role/molecule_list.rb,
lib/chemicalml/cml/role/property_list.rb,
lib/chemicalml/cml/role/reactant_list.rb,
lib/chemicalml/cml/role/reaction_list.rb,
lib/chemicalml/cml/role/reaction_step.rb,
lib/chemicalml/cml/role/related_entry.rb,
lib/chemicalml/cml/role/spectrum_data.rb,
lib/chemicalml/cml/role/spectrum_list.rb,
lib/chemicalml/cml/role/table_content.rb,
lib/chemicalml/cml/schema24/abundance.rb,
lib/chemicalml/cml/schema24/atom_type.rb,
lib/chemicalml/cml/schema24/band_list.rb,
lib/chemicalml/cml/schema24/basis_set.rb,
lib/chemicalml/cml/schema24/bond_type.rb,
lib/chemicalml/cml/schema24/dimension.rb,
lib/chemicalml/cml/schema24/mechanism.rb,
lib/chemicalml/cml/schema24/parameter.rb,
lib/chemicalml/cml/schema24/peak_list.rb,
lib/chemicalml/cml/schema24/potential.rb,
lib/chemicalml/cml/schema24/spectator.rb,
lib/chemicalml/cml/schema24/substance.rb,
lib/chemicalml/cml/schema24/table_row.rb,
lib/chemicalml/cml/schema24/unit_list.rb,
lib/chemicalml/cml/schema24/unit_type.rb,
lib/chemicalml/cml/schema3/array_list.rb,
lib/chemicalml/cml/schema3/atom_array.rb,
lib/chemicalml/cml/schema3/bond_array.rb,
lib/chemicalml/cml/schema3/cml_module.rb,
lib/chemicalml/cml/schema3/definition.rb,
lib/chemicalml/cml/schema3/dictionary.rb,
lib/chemicalml/cml/schema3/identifier.rb,
lib/chemicalml/cml/schema3/peak_group.rb,
lib/chemicalml/cml/schema3/table_cell.rb,
lib/chemicalml/cml/schema3/transform3.rb,
lib/chemicalml/convention/coordinator.rb,
lib/chemicalml/convention/simple_unit.rb,
lib/chemicalml/cli/constraints_command.rb,
lib/chemicalml/cli/conventions_command.rb,
lib/chemicalml/cml/base/atom_type_list.rb,
lib/chemicalml/cml/base/bond_type_list.rb,
lib/chemicalml/cml/base/cell_parameter.rb,
lib/chemicalml/cml/base/complex_object.rb,
lib/chemicalml/cml/base/condition_list.rb,
lib/chemicalml/cml/base/lattice_vector.rb,
lib/chemicalml/cml/base/parameter_list.rb,
lib/chemicalml/cml/base/peak_structure.rb,
lib/chemicalml/cml/base/potential_form.rb,
lib/chemicalml/cml/base/potential_list.rb,
lib/chemicalml/cml/base/spectator_list.rb,
lib/chemicalml/cml/base/substance_list.rb,
lib/chemicalml/cml/base/table_row_list.rb,
lib/chemicalml/cml/base/unit_type_list.rb,
lib/chemicalml/cml/role/atom_type_list.rb,
lib/chemicalml/cml/role/bond_type_list.rb,
lib/chemicalml/cml/role/cell_parameter.rb,
lib/chemicalml/cml/role/complex_object.rb,
lib/chemicalml/cml/role/condition_list.rb,
lib/chemicalml/cml/role/lattice_vector.rb,
lib/chemicalml/cml/role/parameter_list.rb,
lib/chemicalml/cml/role/peak_structure.rb,
lib/chemicalml/cml/role/potential_form.rb,
lib/chemicalml/cml/role/potential_list.rb,
lib/chemicalml/cml/role/spectator_list.rb,
lib/chemicalml/cml/role/substance_list.rb,
lib/chemicalml/cml/role/table_row_list.rb,
lib/chemicalml/cml/role/unit_type_list.rb,
lib/chemicalml/cml/schema24/annotation.rb,
lib/chemicalml/cml/schema24/array_list.rb,
lib/chemicalml/cml/schema24/atom_array.rb,
lib/chemicalml/cml/schema24/bond_array.rb,
lib/chemicalml/cml/schema24/cml_module.rb,
lib/chemicalml/cml/schema24/definition.rb,
lib/chemicalml/cml/schema24/dictionary.rb,
lib/chemicalml/cml/schema24/expression.rb,
lib/chemicalml/cml/schema24/identifier.rb,
lib/chemicalml/cml/schema24/peak_group.rb,
lib/chemicalml/cml/schema24/table_cell.rb,
lib/chemicalml/cml/schema24/transform3.rb,
lib/chemicalml/cml/schema3/action_list.rb,
lib/chemicalml/cml/schema3/atom_parity.rb,
lib/chemicalml/cml/schema3/bond_stereo.rb,
lib/chemicalml/cml/schema3/description.rb,
lib/chemicalml/cml/schema3/kpoint_list.rb,
lib/chemicalml/cml/schema3/observation.rb,
lib/chemicalml/cml/wire_class_registry.rb,
lib/chemicalml/convention/spectroscopy.rb,
lib/chemicalml/cli/dictionaries_command.rb,
lib/chemicalml/cml/base/common_children.rb,
lib/chemicalml/cml/base/reaction_scheme.rb,
lib/chemicalml/cml/base/reactive_centre.rb,
lib/chemicalml/cml/canonical_comparison.rb,
lib/chemicalml/cml/role/reaction_scheme.rb,
lib/chemicalml/cml/role/reactive_centre.rb,
lib/chemicalml/cml/schema24/action_list.rb,
lib/chemicalml/cml/schema24/alternative.rb,
lib/chemicalml/cml/schema24/atom_parity.rb,
lib/chemicalml/cml/schema24/bond_stereo.rb,
lib/chemicalml/cml/schema24/description.rb,
lib/chemicalml/cml/schema24/enumeration.rb,
lib/chemicalml/cml/schema24/float_array.rb,
lib/chemicalml/cml/schema24/kpoint_list.rb,
lib/chemicalml/cml/schema24/observation.rb,
lib/chemicalml/cml/schema3/isotope_list.rb,
lib/chemicalml/cml/schema3/product_list.rb,
lib/chemicalml/cml/schema3/table_header.rb,
lib/chemicalml/cml/base/dictionary_entry.rb,
lib/chemicalml/cml/base/transition_state.rb,
lib/chemicalml/cml/role/dictionary_entry.rb,
lib/chemicalml/cml/role/transition_state.rb,
lib/chemicalml/cml/schema24/isotope_list.rb,
lib/chemicalml/cml/schema24/product_list.rb,
lib/chemicalml/cml/schema24/string_array.rb,
lib/chemicalml/cml/schema24/table_header.rb,
lib/chemicalml/cml/schema3/configuration.rb,
lib/chemicalml/cml/schema3/documentation.rb,
lib/chemicalml/cml/schema3/fragment_list.rb,
lib/chemicalml/cml/schema3/metadata_list.rb,
lib/chemicalml/cml/schema3/molecule_list.rb,
lib/chemicalml/cml/schema3/property_list.rb,
lib/chemicalml/cml/schema3/reactant_list.rb,
lib/chemicalml/cml/schema3/reaction_list.rb,
lib/chemicalml/cml/schema3/reaction_step.rb,
lib/chemicalml/cml/schema3/spectrum_data.rb,
lib/chemicalml/cml/schema3/spectrum_list.rb,
lib/chemicalml/cml/schema3/table_content.rb,
lib/chemicalml/cml/base/table_header_cell.rb,
lib/chemicalml/cml/role/table_header_cell.rb,
lib/chemicalml/cml/schema24/configuration.rb,
lib/chemicalml/cml/schema24/documentation.rb,
lib/chemicalml/cml/schema24/fragment_list.rb,
lib/chemicalml/cml/schema24/integer_array.rb,
lib/chemicalml/cml/schema24/metadata_list.rb,
lib/chemicalml/cml/schema24/molecule_list.rb,
lib/chemicalml/cml/schema24/property_list.rb,
lib/chemicalml/cml/schema24/reactant_list.rb,
lib/chemicalml/cml/schema24/reaction_list.rb,
lib/chemicalml/cml/schema24/reaction_step.rb,
lib/chemicalml/cml/schema24/related_entry.rb,
lib/chemicalml/cml/schema24/spectrum_data.rb,
lib/chemicalml/cml/schema24/spectrum_list.rb,
lib/chemicalml/cml/schema24/table_content.rb,
lib/chemicalml/cml/schema3/atom_type_list.rb,
lib/chemicalml/cml/schema3/bond_type_list.rb,
lib/chemicalml/cml/schema3/cell_parameter.rb,
lib/chemicalml/cml/schema3/condition_list.rb,
lib/chemicalml/cml/schema3/lattice_vector.rb,
lib/chemicalml/cml/schema3/parameter_list.rb,
lib/chemicalml/cml/schema3/peak_structure.rb,
lib/chemicalml/cml/schema3/potential_form.rb,
lib/chemicalml/cml/schema3/potential_list.rb,
lib/chemicalml/cml/schema3/spectator_list.rb,
lib/chemicalml/cml/schema3/substance_list.rb,
lib/chemicalml/cml/schema3/table_row_list.rb,
lib/chemicalml/cml/schema3/unit_type_list.rb,
lib/chemicalml/convention/unit_dictionary.rb,
lib/chemicalml/cml/base/reaction_step_list.rb,
lib/chemicalml/cml/role/reaction_step_list.rb,
lib/chemicalml/cml/schema24/atom_type_list.rb,
lib/chemicalml/cml/schema24/bond_type_list.rb,
lib/chemicalml/cml/schema24/cell_parameter.rb,
lib/chemicalml/cml/schema24/complex_object.rb,
lib/chemicalml/cml/schema24/condition_list.rb,
lib/chemicalml/cml/schema24/lattice_vector.rb,
lib/chemicalml/cml/schema24/parameter_list.rb,
lib/chemicalml/cml/schema24/peak_structure.rb,
lib/chemicalml/cml/schema24/potential_form.rb,
lib/chemicalml/cml/schema24/potential_list.rb,
lib/chemicalml/cml/schema24/spectator_list.rb,
lib/chemicalml/cml/schema24/substance_list.rb,
lib/chemicalml/cml/schema24/table_row_list.rb,
lib/chemicalml/cml/schema24/unit_type_list.rb,
lib/chemicalml/cml/schema3/reaction_scheme.rb,
lib/chemicalml/cml/schema3/reactive_centre.rb,
lib/chemicalml/cml/base/mechanism_component.rb,
lib/chemicalml/cml/role/mechanism_component.rb,
lib/chemicalml/cml/schema24/reaction_scheme.rb,
lib/chemicalml/cml/schema24/reactive_centre.rb,
lib/chemicalml/cml/schema3/dictionary_entry.rb,
lib/chemicalml/cml/schema3/transition_state.rb,
lib/chemicalml/convention/validation_report.rb,
lib/chemicalml/cml/schema24/dictionary_entry.rb,
lib/chemicalml/cml/schema24/transition_state.rb,
lib/chemicalml/cml/schema3/table_header_cell.rb,
lib/chemicalml/cml/base/atomic_basis_function.rb,
lib/chemicalml/cml/role/atomic_basis_function.rb,
lib/chemicalml/cml/schema24/table_header_cell.rb,
lib/chemicalml/cml/schema3/reaction_step_list.rb,
lib/chemicalml/convention/cascade/constraints.rb,
lib/chemicalml/cml/schema24/reaction_step_list.rb,
lib/chemicalml/cml/schema3/mechanism_component.rb,
lib/chemicalml/convention/compchem/constraints.rb,
lib/chemicalml/convention/unit_type_dictionary.rb,
lib/chemicalml/cml/schema24/mechanism_component.rb,
lib/chemicalml/convention/molecular/constraints.rb,
lib/chemicalml/cml/schema3/atomic_basis_function.rb,
lib/chemicalml/convention/dictionary/constraints.rb,
lib/chemicalml/cml/schema24/atomic_basis_function.rb,
lib/chemicalml/convention/simple_unit/constraints.rb,
lib/chemicalml/convention/spectroscopy/constraints.rb,
lib/chemicalml/convention/unit_dictionary/constraints.rb,
lib/chemicalml/convention/compchem/constraints/array_rules.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints.rb,
lib/chemicalml/convention/compchem/constraints/matrix_rules.rb,
lib/chemicalml/convention/compchem/constraints/scalar_units.rb,
lib/chemicalml/convention/compchem/constraints/module_predicates.rb,
lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb,
lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb,
lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb,
lib/chemicalml/convention/compchem/constraints/job_module_must_have_id.rb,
lib/chemicalml/convention/simple_unit/constraints/unit_must_have_power.rb,
lib/chemicalml/convention/molecular/constraints/dict_ref_should_resolve.rb,
lib/chemicalml/convention/simple_unit/constraints/unit_must_have_symbol.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_id.rb,
lib/chemicalml/convention/simple_unit/constraints/root_must_be_unit_list.rb,
lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb,
lib/chemicalml/convention/molecular/constraints/references_should_resolve.rb,
lib/chemicalml/convention/dictionary/constraints/entry_must_have_unit_type.rb,
lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb,
lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb,
lib/chemicalml/convention/spectroscopy/constraints/peak_should_have_values.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_title.rb,
lib/chemicalml/convention/compchem/constraints/job_list_module_must_have_id.rb,
lib/chemicalml/convention/dictionary/constraints/entry_units_co_constraints.rb,
lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb,
lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb,
lib/chemicalml/convention/dictionary/constraints/entry_id_must_match_pattern.rb,
lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb,
lib/chemicalml/convention/molecular/constraints/bond_id_should_match_pattern.rb,
lib/chemicalml/convention/molecular/constraints/bond_order_should_be_in_enum.rb,
lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_format.rb,
lib/chemicalml/convention/compchem/constraints/finalization_must_have_content.rb,
lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb,
lib/chemicalml/convention/molecular/constraints/bond_stereo_should_be_in_enum.rb,
lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_content.rb,
lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb,
lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_parent_si.rb,
lib/chemicalml/convention/cascade/constraints/reaction_scheme_must_have_content.rb,
lib/chemicalml/convention/compchem/constraints/initialization_must_have_content.rb,
lib/chemicalml/convention/dictionary/constraints/dictionary_must_have_namespace.rb,
lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb,
lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb,
lib/chemicalml/convention/molecular/constraints/bond_ids_unique_within_molecule.rb,
lib/chemicalml/convention/spectroscopy/constraints/peak_list_must_contain_peaks.rb,
lib/chemicalml/convention/compchem/constraints/calculation_requires_finalization.rb,
lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_molecule.rb,
lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb,
lib/chemicalml/convention/molecular/constraints/molecule_id_should_match_pattern.rb,
lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_convention.rb,
lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_environment.rb,
lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_molecule.rb,
lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_finalization.rb,
lib/chemicalml/convention/molecular/constraints/bond_atom_refs2_should_be_distinct.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_contain_definition.rb,
lib/chemicalml/convention/cascade/constraints/reaction_step_list_must_contain_steps.rb,
lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb,
lib/chemicalml/convention/molecular/constraints/bond_order_other_must_have_dict_ref.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_have_namespace.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_parent_si_should_resolve.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_unit_type_should_resolve.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/molecular/constraints/bond_array_must_be_child_of_molecule.rb,
lib/chemicalml/convention/molecular/constraints/bond_stereo_other_must_have_dict_ref.rb,
lib/chemicalml/convention/molecular/constraints/molecule_chirality_should_be_in_enum.rb,
lib/chemicalml/convention/compchem/constraints/environment_must_not_contain_parameter.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/molecular/constraints/atom_parity_should_include_parent_atom.rb,
lib/chemicalml/convention/cascade/constraints/reaction_step_must_have_reaction_or_lists.rb,
lib/chemicalml/convention/compchem/constraints/initialization_must_not_contain_property.rb,
lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_parameter_list.rb,
lib/chemicalml/convention/cascade/constraints/reactive_centre_atom_refs_should_be_present.rb,
lib/chemicalml/convention/molecular/constraints/atom_parity_atom_refs4_should_be_distinct.rb,
lib/chemicalml/convention/molecular/constraints/bond_stereo_atom_refs4_should_be_distinct.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb,
lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb,
lib/chemicalml/convention/molecular/constraints/bond_stereo_cis_trans_must_have_atom_refs4.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_id_must_match_pattern.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb,
lib/chemicalml/convention/molecular/constraints/bond_stereo_wedge_hash_must_have_atom_refs2.rb,
lib/chemicalml/convention/molecular/constraints/molecule_count_must_not_appear_on_top_level.rb,
lib/chemicalml/convention/molecular/constraints/property_scalar_data_type_matches_dictionary.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_contain_definition.rb,
lib/chemicalml/convention/molecular/constraints/atom_element_type_should_be_in_periodic_table.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_have_namespace.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_contain_at_least_one_unit.rb,
lib/chemicalml/convention/molecular/constraints/atom_array_must_be_child_of_molecule_or_formula.rb,
lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_multiplier_or_constant_to_si.rb,
lib/chemicalml/convention/dictionary/constraints/dictionary_namespace_should_end_with_slash_or_hash.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/unit_type_dictionary/constraints/unit_type_list_must_contain_at_least_one_unit_type.rb

Overview

Generates all backward-compatible Chemicalml::Cml::* aliases pointing at the corresponding Schema3::* classes.

All 36 aliases are generated in a single file (loaded lazily when the first alias is referenced) rather than 36 individual files. This is DRY without violating the autoload rule: the file loads lazily via autoload, and const_set here ALIASES existing classes (Schema3::Foo already exists) rather than creating new ones.

Defined Under Namespace

Modules: Cli, Cml, ContextConfiguration, Convention, Dictionary, Schema, VersionedParser Classes: Error, Logger, ParseError

Constant Summary collapse

VERSION =

'0.3.0'

Class Method Summary collapse

.parse(xml, schema: :schema3, namespace_exist: true) ⇒ Chemicalml::Cml::Schema3::Document, ...
Parse a CML XML string into a wire document.
.parse_file(path, schema: :schema3, namespace_exist: true) ⇒ Chemicalml::Cml::Schema3::Document, ...
Parse a CML file from disk.
.parser_for(schema) ⇒ Module
Resolve the versioned-parser module for a schema id.
.serialize(document) ⇒ String
Serialize a wire document back to XML.
.validate(document, logger: nil) ⇒ Chemicalml::Convention::ValidationReport
Auto-detect the convention from the document's root and validate.

Class Method Details

.parse(xml, schema: :schema3, namespace_exist: true) ⇒ `Chemicalml::Cml::Schema3::Document`, ...

Parse a CML XML string into a wire document.

Examples:

Parse a Schema3 document

doc = Chemicalml.parse("<cml xmlns='...'>...</cml>")

Parse a Schema2.4 document

doc = Chemicalml.parse(xml, schema: :schema24)

Parameters:

xml (String) —
the XML content.
schema (Symbol) (defaults to: :schema3) —
one of :schema3 (default) or :schema24.
namespace_exist (Boolean) (defaults to: true) —
whether the XML already declares the CML namespace. When false, the parser injects it.

Returns:

(Chemicalml::Cml::Schema3::Document, Chemicalml::Cml::Schema24::Document, Chemicalml::Cml::Schema3::Molecule, ...) —
the parsed root, dispatch by detected root element.

Raises:

(ArgumentError) —
if xml is nil/empty or schema is unknown.
(Chemicalml::ParseError) —
on malformed XML.

# File 'lib/chemicalml.rb', line 53

def parse(xml, schema: :schema3, namespace_exist: true)
  raise ArgumentError, 'xml must not be nil' if xml.nil?
  raise ArgumentError, 'xml must not be empty' if xml.to_s.strip.empty?

  parser_for(schema).parse(xml, namespace_exist: namespace_exist)
end

.parse_file(path, schema: :schema3, namespace_exist: true) ⇒ `Chemicalml::Cml::Schema3::Document`, ...

Parse a CML file from disk. Convenience wrapper around parse that handles the File.read boilerplate.

Parameters:

path (String) —
path to the CML file.
schema (Symbol) (defaults to: :schema3) —
:schema3 (default) or :schema24.
namespace_exist (Boolean) (defaults to: true) —
forwarded to parse.

Returns:

(Chemicalml::Cml::Schema3::Document, Chemicalml::Cml::Schema24::Document, Chemicalml::Cml::Schema3::Molecule, ...) —
the parsed root, dispatch by detected root element.

Raises:

(ArgumentError) —
if the file doesn't exist or is empty.

# File 'lib/chemicalml.rb', line 68

def parse_file(path, schema: :schema3, namespace_exist: true)
  raise ArgumentError, "file not found: #{path}" unless File.exist?(path)

  parse(File.read(path), schema: schema, namespace_exist: namespace_exist)
end

.parser_for(schema) ⇒ `Module`

Resolve the versioned-parser module for a schema id.

Parameters:

schema (Symbol) —
:schema3 or :schema24.

Returns:

(Module) —
the matching Schema3 or Schema24 module.

Raises:

(ArgumentError) —
if schema is unknown.

# File 'lib/chemicalml.rb', line 88

def parser_for(schema)
  case schema.to_sym
  when :schema3  then Chemicalml::Cml::Schema3
  when :schema24 then Chemicalml::Cml::Schema24
  else
    raise ArgumentError, "unsupported schema: #{schema.inspect} " \
                         '(supported: :schema3, :schema24)'
  end
end

.serialize(document) ⇒ `String`

Serialize a wire document back to XML.

Parameters:

document (Lutaml::Model::Serializable) —
a CML wire instance.
opts (Hash) —
forwarded to Lutaml::Model::Serializable#to_xml.

Returns:

(String) —
the serialized XML.



79
80
81

# File 'lib/chemicalml.rb', line 79

def serialize(document, **)
  document.to_xml(**)
end

.validate(document, logger: nil) ⇒ `Chemicalml::Convention::ValidationReport`

Auto-detect the convention from the document's root and validate. Top-level convenience for Convention.detect_and_validate.

Parameters:

document (Lutaml::Model::Serializable) —
the CML document.
logger (Chemicalml::Logger, nil) (defaults to: nil) —
optional logger for progress.

Returns:

(Chemicalml::Convention::ValidationReport) —
the report.

Raises:

(ArgumentError) —
if no convention is declared.

# File 'lib/chemicalml.rb', line 105

def validate(document, logger: nil)
  logger&.info 'Auto-detecting convention…'
  report = Convention.detect_and_validate(document)
  logger&.info "Validation complete: #{report.size} violation(s)"
  report
end

Module: Chemicalml

Overview

Defined Under Namespace

Constant Summary collapse

Class Method Summary collapse

Class Method Details

.parse(xml, schema: :schema3, namespace_exist: true) ⇒ Chemicalml::Cml::Schema3::Document, ...

Examples:

Parse a Schema3 document

Parse a Schema2.4 document

.parse_file(path, schema: :schema3, namespace_exist: true) ⇒ Chemicalml::Cml::Schema3::Document, ...

.parser_for(schema) ⇒ Module

.serialize(document) ⇒ String

.validate(document, logger: nil) ⇒ Chemicalml::Convention::ValidationReport

.parse(xml, schema: :schema3, namespace_exist: true) ⇒ `Chemicalml::Cml::Schema3::Document`, ...

.parse_file(path, schema: :schema3, namespace_exist: true) ⇒ `Chemicalml::Cml::Schema3::Document`, ...

.parser_for(schema) ⇒ `Module`

.serialize(document) ⇒ `String`

.validate(document, logger: nil) ⇒ `Chemicalml::Convention::ValidationReport`