Index _ | A | B | C | D | E | F | G | H | I | J | M | N | O | P | Q | R | S | T | U | V _ __init__() (openff.toolkit.topology.Molecule method) A add_atom() (openff.toolkit.topology.Molecule method) add_bond() (openff.toolkit.topology.Molecule method) add_conformer() (openff.toolkit.topology.Molecule method) add_default_hierarchy_schemes() (openff.toolkit.topology.Molecule method) add_hierarchy_scheme() (openff.toolkit.topology.Molecule method) add_molecule() (openff.qcsubmit.datasets.BasicDataset method) add_qc_spec() (openff.qcsubmit.datasets.BasicDataset method) amber_impropers (openff.toolkit.topology.Molecule property) angles (openff.toolkit.topology.Molecule property) apply_elf_conformer_selection() (openff.toolkit.topology.Molecule method) are_isomorphic() (openff.toolkit.topology.Molecule static method) assign_fractional_bond_orders() (openff.toolkit.topology.Molecule method) assign_partial_charges() (openff.toolkit.topology.Molecule method) atom() (openff.toolkit.topology.Molecule method) atom_index() (openff.toolkit.topology.Molecule method) atoms (openff.toolkit.topology.Molecule property) B bar() bond() (openff.toolkit.topology.Molecule method) bonds (openff.toolkit.topology.Molecule property) built-in function format_exception() send_message() C canonical_order_atoms() (openff.toolkit.topology.Molecule method) check_max_length_ten() (pydantic_example.ExampleSettings class method) chemical_environment_matches() (openff.toolkit.topology.Molecule method) clear_qcspecs() (openff.qcsubmit.datasets.BasicDataset method) components (openff.qcsubmit.datasets.BasicDataset property) compute_tag (openff.qcsubmit.datasets.BasicDataset attribute) conformers (openff.toolkit.topology.Molecule property) construct() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) copy() (openff.qcsubmit.datasets.BasicDataset method) (pydantic_example.ExampleSettings method) coverage_report() (openff.qcsubmit.datasets.BasicDataset method) D dataset (openff.qcsubmit.datasets.BasicDataset attribute) dataset_name (openff.qcsubmit.datasets.BasicDataset attribute) dataset_tagline (openff.qcsubmit.datasets.BasicDataset attribute) dataset_tags (openff.qcsubmit.datasets.BasicDataset attribute) delete_hierarchy_scheme() (openff.toolkit.topology.Molecule method) description (openff.qcsubmit.datasets.BasicDataset attribute) dict() (openff.qcsubmit.datasets.BasicDataset method) (pydantic_example.ExampleSettings method) driver (openff.qcsubmit.datasets.BasicDataset attribute) E enumerate_protomers() (openff.toolkit.topology.Molecule method) enumerate_stereoisomers() (openff.toolkit.topology.Molecule method) enumerate_tautomers() (openff.toolkit.topology.Molecule method) environment export_dataset() (openff.qcsubmit.datasets.BasicDataset method) F field_plain (pydantic_example.ExampleSettings attribute) field_plain_with_validator (pydantic_example.ExampleSettings attribute) field_with_constraints_and_description (pydantic_example.ExampleSettings attribute) field_with_validator_and_alias (pydantic_example.ExampleSettings attribute) field_with_validator_and_alias_typeless (pydantic_example.ExampleSettings attribute) filter_molecules() (openff.qcsubmit.datasets.BasicDataset method) filtered (openff.qcsubmit.datasets.BasicDataset property) filtered_molecules (openff.qcsubmit.datasets.BasicDataset attribute) find_rotatable_bonds() (openff.toolkit.topology.Molecule method) foo() (in module numpydoc_example) Foo.Client (built-in class) format_exception() built-in function from_bson() (openff.toolkit.topology.Molecule class method) from_dict() (openff.toolkit.topology.Molecule class method) from_file() (openff.toolkit.topology.Molecule class method) from_inchi() (openff.toolkit.topology.Molecule class method) from_iupac() (openff.toolkit.topology.Molecule class method) from_json() (openff.toolkit.topology.Molecule class method) from_mapped_smiles() (openff.toolkit.topology.Molecule class method) from_messagepack() (openff.toolkit.topology.Molecule class method) from_openeye() (openff.toolkit.topology.Molecule class method) from_orm() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) from_pdb_and_smiles() (openff.toolkit.topology.Molecule class method) from_pickle() (openff.toolkit.topology.Molecule class method) from_polymer_pdb() (openff.toolkit.topology.Molecule class method) from_qcschema() (openff.toolkit.topology.Molecule class method) from_rdkit() (openff.toolkit.topology.Molecule class method) from_smiles() (openff.toolkit.topology.Molecule class method) from_toml() (openff.toolkit.topology.Molecule class method) from_topology() (openff.toolkit.topology.Molecule class method) from_xml() (openff.toolkit.topology.Molecule class method) from_yaml() (openff.toolkit.topology.Molecule class method) G generate_conformers() (openff.toolkit.topology.Molecule method) generate_unique_atom_names() (openff.toolkit.topology.Molecule method) get_bond_between() (openff.toolkit.topology.Molecule method) get_molecule_entry() (openff.qcsubmit.datasets.BasicDataset method) global substitutions H has_unique_atom_names (openff.toolkit.topology.Molecule property) hierarchy_schemes (openff.toolkit.topology.Molecule property) hill_formula (openff.toolkit.topology.Molecule property) I impropers (openff.toolkit.topology.Molecule property) is_isomorphic_with() (openff.toolkit.topology.Molecule method) J json() (openff.qcsubmit.datasets.BasicDataset method) (pydantic_example.ExampleSettings method) M metadata (openff.qcsubmit.datasets.BasicDataset attribute) method_without_sig() (pydantic_example.ExampleSettings method) module numpydoc_example pydantic_example Molecule (class in openff.toolkit.topology) molecules (openff.qcsubmit.datasets.BasicDataset property) molecules_to_file() (openff.qcsubmit.datasets.BasicDataset method) MyAnimal() (class) N n_angles (openff.toolkit.topology.Molecule property) n_atoms (openff.toolkit.topology.Molecule property) n_bonds (openff.toolkit.topology.Molecule property) n_components (openff.qcsubmit.datasets.BasicDataset property) n_conformers (openff.toolkit.topology.Molecule property) n_filtered (openff.qcsubmit.datasets.BasicDataset property) n_impropers (openff.toolkit.topology.Molecule property) n_molecules (openff.qcsubmit.datasets.BasicDataset property) n_propers (openff.toolkit.topology.Molecule property) n_qc_specs (openff.qcsubmit.datasets.BasicDataset property) n_records (openff.qcsubmit.datasets.BasicDataset property) name (openff.toolkit.topology.Molecule property) nth_degree_neighbors() (openff.toolkit.topology.Molecule method) numpydoc_example module O ordered_connection_table_hash() (openff.toolkit.topology.Molecule method) P parse_file() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) parse_obj() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) parse_raw() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) partial_charges (openff.toolkit.topology.Molecule property) perceive_residues() (openff.toolkit.topology.Molecule method) priority (openff.qcsubmit.datasets.BasicDataset attribute) propers (openff.toolkit.topology.Molecule property) properties (openff.toolkit.topology.Molecule property) provenance (openff.qcsubmit.datasets.BasicDataset attribute) pydantic_example module Q qc_specifications (openff.qcsubmit.datasets.BasicDataset attribute) R remap() (openff.toolkit.topology.Molecule method) remove_qcspec() (openff.qcsubmit.datasets.BasicDataset method) S schema() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) schema_json() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) send_message() built-in function smirnoff_impropers (openff.toolkit.topology.Molecule property) source directory strip_atom_stereochemistry() (openff.toolkit.topology.Molecule method) submit() (openff.qcsubmit.datasets.BasicDataset method) substitutions global T to_bson() (openff.toolkit.topology.Molecule method) to_dict() (openff.toolkit.topology.Molecule method) to_file() (openff.toolkit.topology.Molecule method) to_hill_formula() (openff.toolkit.topology.Molecule method) to_inchi() (openff.toolkit.topology.Molecule method) to_inchikey() (openff.toolkit.topology.Molecule method) to_iupac() (openff.toolkit.topology.Molecule method) to_json() (openff.toolkit.topology.Molecule method) to_messagepack() (openff.toolkit.topology.Molecule method) to_networkx() (openff.toolkit.topology.Molecule method) to_openeye() (openff.toolkit.topology.Molecule method) to_pickle() (openff.toolkit.topology.Molecule method) to_qcschema() (openff.toolkit.topology.Molecule method) to_rdkit() (openff.toolkit.topology.Molecule method) to_smiles() (openff.toolkit.topology.Molecule method) to_tasks() (openff.qcsubmit.datasets.BasicDataset method) to_toml() (openff.toolkit.topology.Molecule method) to_topology() (openff.toolkit.topology.Molecule method) to_xml() (openff.toolkit.topology.Molecule method) to_yaml() (openff.toolkit.topology.Molecule method) torsions (openff.toolkit.topology.Molecule property) total_charge (openff.toolkit.topology.Molecule property) type (openff.qcsubmit.datasets.BasicDataset attribute) U update_forward_refs() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) update_hierarchy_schemes() (openff.toolkit.topology.Molecule method) V validate() (openff.qcsubmit.datasets.BasicDataset class method) (pydantic_example.ExampleSettings class method) visualize() (openff.qcsubmit.datasets.BasicDataset method) (openff.toolkit.topology.Molecule method)