Module: Chemicalml

Defined in:

lib/chemicalml.rb,
lib/chemicalml/cml.rb,
lib/chemicalml/model.rb,
lib/chemicalml/errors.rb,
lib/chemicalml/schema.rb,
lib/chemicalml/version.rb,
lib/chemicalml/cml/atom.rb,
lib/chemicalml/cml/base.rb,
lib/chemicalml/cml/bond.rb,
lib/chemicalml/cml/list.rb,
lib/chemicalml/cml/name.rb,
lib/chemicalml/cml/role.rb,
lib/chemicalml/cml/unit.rb,
lib/chemicalml/cml/array.rb,
lib/chemicalml/cml/label.rb,
lib/chemicalml/cml/matrix.rb,
lib/chemicalml/cml/scalar.rb,
lib/chemicalml/convention.rb,
lib/chemicalml/dictionary.rb,
lib/chemicalml/model/atom.rb,
lib/chemicalml/model/bond.rb,
lib/chemicalml/model/name.rb,
lib/chemicalml/model/node.rb,
lib/chemicalml/cml/formula.rb,
lib/chemicalml/cml/product.rb,
lib/chemicalml/cml/schema3.rb,
lib/chemicalml/model/label.rb,
lib/chemicalml/cml/document.rb,
lib/chemicalml/cml/elements.rb,
lib/chemicalml/cml/metadata.rb,
lib/chemicalml/cml/molecule.rb,
lib/chemicalml/cml/property.rb,
lib/chemicalml/cml/reactant.rb,
lib/chemicalml/cml/reaction.rb,
lib/chemicalml/cml/schema24.rb,
lib/chemicalml/model/matrix.rb,
lib/chemicalml/model/scalar.rb,
lib/chemicalml/cml/base/atom.rb,
lib/chemicalml/cml/base/bond.rb,
lib/chemicalml/cml/base/list.rb,
lib/chemicalml/cml/base/name.rb,
lib/chemicalml/cml/base/unit.rb,
lib/chemicalml/cml/namespace.rb,
lib/chemicalml/cml/parameter.rb,
lib/chemicalml/cml/role/atom.rb,
lib/chemicalml/cml/role/bond.rb,
lib/chemicalml/cml/role/list.rb,
lib/chemicalml/cml/role/name.rb,
lib/chemicalml/cml/role/unit.rb,
lib/chemicalml/cml/substance.rb,
lib/chemicalml/cml/unit_list.rb,
lib/chemicalml/cml/unit_type.rb,
lib/chemicalml/cml/visitable.rb,
lib/chemicalml/model/formula.rb,
lib/chemicalml/model/product.rb,
lib/chemicalml/cml/atom_array.rb,
lib/chemicalml/cml/base/array.rb,
lib/chemicalml/cml/base/label.rb,
lib/chemicalml/cml/bond_array.rb,
lib/chemicalml/cml/cml_module.rb,
lib/chemicalml/cml/dictionary.rb,
lib/chemicalml/cml/identifier.rb,
lib/chemicalml/cml/role/array.rb,
lib/chemicalml/cml/role/label.rb,
lib/chemicalml/cml/translator.rb,
lib/chemicalml/model/document.rb,
lib/chemicalml/model/metadata.rb,
lib/chemicalml/model/molecule.rb,
lib/chemicalml/model/property.rb,
lib/chemicalml/model/reactant.rb,
lib/chemicalml/model/reaction.rb,
lib/chemicalml/cml/atom_parity.rb,
lib/chemicalml/cml/base/matrix.rb,
lib/chemicalml/cml/base/scalar.rb,
lib/chemicalml/cml/bond_stereo.rb,
lib/chemicalml/cml/role/matrix.rb,
lib/chemicalml/cml/role/scalar.rb,
lib/chemicalml/convention/base.rb,
lib/chemicalml/dictionary/enum.rb,
lib/chemicalml/dictionary/link.rb,
lib/chemicalml/model/cml_array.rb,
lib/chemicalml/model/parameter.rb,
lib/chemicalml/model/substance.rb,
lib/chemicalml/schema/registry.rb,
lib/chemicalml/cml/base/formula.rb,
lib/chemicalml/cml/base/product.rb,
lib/chemicalml/cml/product_list.rb,
lib/chemicalml/cml/role/formula.rb,
lib/chemicalml/cml/role/product.rb,
lib/chemicalml/dictionary/entry.rb,
lib/chemicalml/dictionary/model.rb,
lib/chemicalml/model/cml_module.rb,
lib/chemicalml/model/identifier.rb,
lib/chemicalml/versioned_parser.rb,
lib/chemicalml/cml/base/document.rb,
lib/chemicalml/cml/base/metadata.rb,
lib/chemicalml/cml/base/molecule.rb,
lib/chemicalml/cml/base/property.rb,
lib/chemicalml/cml/base/reactant.rb,
lib/chemicalml/cml/base/reaction.rb,
lib/chemicalml/cml/metadata_list.rb,
lib/chemicalml/cml/property_list.rb,
lib/chemicalml/cml/reactant_list.rb,
lib/chemicalml/cml/reaction_list.rb,
lib/chemicalml/cml/role/document.rb,
lib/chemicalml/cml/role/metadata.rb,
lib/chemicalml/cml/role/molecule.rb,
lib/chemicalml/cml/role/property.rb,
lib/chemicalml/cml/role/reactant.rb,
lib/chemicalml/cml/role/reaction.rb,
lib/chemicalml/dictionary/loader.rb,
lib/chemicalml/schema/definition.rb,
lib/chemicalml/cml/base/parameter.rb,
lib/chemicalml/cml/base/substance.rb,
lib/chemicalml/cml/base/unit_list.rb,
lib/chemicalml/cml/base/unit_type.rb,
lib/chemicalml/cml/parameter_list.rb,
lib/chemicalml/cml/role/parameter.rb,
lib/chemicalml/cml/role/substance.rb,
lib/chemicalml/cml/role/unit_list.rb,
lib/chemicalml/cml/role/unit_type.rb,
lib/chemicalml/cml/unit_type_list.rb,
lib/chemicalml/model/product_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/dictionary.rb,
lib/chemicalml/cml/base/identifier.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/dictionary.rb,
lib/chemicalml/cml/role/identifier.rb,
lib/chemicalml/convention/compchem.rb,
lib/chemicalml/convention/registry.rb,
lib/chemicalml/dictionary/registry.rb,
lib/chemicalml/model/metadata_list.rb,
lib/chemicalml/model/property_list.rb,
lib/chemicalml/model/reactant_list.rb,
lib/chemicalml/model/reaction_list.rb,
lib/chemicalml/cml/base/atom_parity.rb,
lib/chemicalml/cml/base/bond_stereo.rb,
lib/chemicalml/cml/dictionary_entry.rb,
lib/chemicalml/cml/role/atom_parity.rb,
lib/chemicalml/cml/role/bond_stereo.rb,
lib/chemicalml/cml/wire_class_macro.rb,
lib/chemicalml/convention/molecular.rb,
lib/chemicalml/convention/violation.rb,
lib/chemicalml/model/parameter_list.rb,
lib/chemicalml/cml/base/product_list.rb,
lib/chemicalml/cml/role/product_list.rb,
lib/chemicalml/context_configuration.rb,
lib/chemicalml/convention/constraint.rb,
lib/chemicalml/convention/dictionary.rb,
lib/chemicalml/cml/base/metadata_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/role/metadata_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/base/parameter_list.rb,
lib/chemicalml/cml/base/unit_type_list.rb,
lib/chemicalml/cml/role/parameter_list.rb,
lib/chemicalml/cml/role/unit_type_list.rb,
lib/chemicalml/cml/base/dictionary_entry.rb,
lib/chemicalml/cml/role/dictionary_entry.rb,
lib/chemicalml/cml/schema3/configuration.rb,
lib/chemicalml/cml/schema24/configuration.rb,
lib/chemicalml/convention/unit_dictionary.rb,
lib/chemicalml/convention/compchem/constraints.rb,
lib/chemicalml/convention/unit_type_dictionary.rb,
lib/chemicalml/convention/molecular/constraints.rb,
lib/chemicalml/cml/translator/value_translations.rb,
lib/chemicalml/convention/dictionary/constraints.rb,
lib/chemicalml/convention/unit_dictionary/constraints.rb,
lib/chemicalml/convention/unit_type_dictionary/constraints.rb,
lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb,
lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb,
lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb,
lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb,
lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb,
lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.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/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb

Overview

Backward-compatible alias. New code should reference the versioned class directly: Chemicalml::Cml::Schema3::DictionaryEntry.

Defined Under Namespace

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

Constant Summary

VERSION =

"0.1.0"

Class Method Summary

• .parse(xml, schema: :schema3, namespace_exist: true) ⇒ Object
• .parser_for(schema) ⇒ Object
• .serialize(document, **opts) ⇒ Object

Class Method Details

.parse(xml, schema: :schema3, namespace_exist: true) ⇒ Object

# File 'lib/chemicalml.rb', line 30

def parse(xml, schema: :schema3, namespace_exist: true)
  parser_for(schema).parse(xml, namespace_exist: namespace_exist)
end

.parser_for(schema) ⇒ Object

# File 'lib/chemicalml.rb', line 38

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, **opts) ⇒ Object

# File 'lib/chemicalml.rb', line 34

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