Index _ | A | B | C | D | E | F | G | H | I | J | K | M | N | O | P | R | S | T | U | V | W | X | Z _ __all__ (in module automol) (in module automol.geom) (in module automol.rd) (in module automol.utils) (in module automol.utils.element) __new__() (automol.ident.Algorithm method) __repr__() (automol.geom.core.Geometry method) __str__ (automol.geom.core.Geometry attribute) __version__ (in module automol) _algorithms (automol.ident.AlgorithmRegistry attribute) _assign_orbit() (in module automol.geom.analysis) _coordinates_validator() (in module automol.utils.types) _float_array_serializer() (in module automol.utils.types) _float_array_validator() (in module automol.utils.types) _hungarian_correspondence() (in module automol.geom.analysis) _load_elements() (in module automol.utils.element.core) _MAX_BRUTE_FORCE_ELEMENTS (in module automol.geom.analysis) _repr_html_() (automol.geom.core.Geometry method) _rmsd_from_correspondence() (in module automol.geom.analysis) _validate_algorithm_kind() (automol.ident.Identity method) A A (automol.utils.element.core.Element attribute) add_atom_numbers() (in module automol.rd.mol) add_coordinates() (in module automol.rd.mol) add_geometry() (automol.geom.io.View method) add_vector() (automol.geom.io.View method) add_vectors() (automol.geom.io.View method) add_xyz_axes() (automol.geom.io.View method) adjacency_matrix() (in module automol.geom.analysis) algorithm (automol.ident.AlgorithmDef attribute) (automol.ident.Identity attribute) Algorithm (class in automol.ident) AlgorithmAlreadyRegisteredError AlgorithmDef (class in automol.ident) AlgorithmFns (class in automol.ident) AlgorithmRegistry (class in automol.ident) algorithms_for_kind() (automol.ident.AlgorithmRegistry class method) all_algorithms() (automol.ident.AlgorithmRegistry class method) angles() (in module automol.geom.analysis) ANGSTROM (in module automol.utils.constants) ANGSTROM_TO_BOHR (in module automol.utils.constants) assign_stereochemistry() (in module automol.rd.mol) assignment_rmsd() (in module automol.geom.analysis) atom_count (automol.geom.core.Geometry property) atomic_numbers (automol.geom.core.Geometry property) automol module automol.geom module automol.geom.analysis module automol.geom.core module automol.geom.io module automol.ident module automol.rd module automol.rd.mol module automol.utils module automol.utils.constants module automol.utils.element module automol.utils.element.core module automol.utils.exc module automol.utils.types module B BOHR (in module automol.utils.constants) BOHR_TO_ANGSTROM (in module automol.utils.constants) BOHR_TO_METERS (in module automol.utils.constants) bond_graph() (in module automol.geom.analysis) bonding_capacity() (in module automol.utils.element.core) bonds() (in module automol.geom.analysis) C C (in module automol.utils.constants) C_CENTIMETERS_PER_SECOND (in module automol.utils.constants) C_METERS_PER_SECOND (in module automol.utils.constants) canonical_ranks() (in module automol.rd.mol) center_of_mass() (in module automol.geom.analysis) CENTIMETER (in module automol.utils.constants) CENTIMETERS_PER_SECOND (in module automol.utils.constants) CHAR (in module automol.geom.io) charge (automol.geom.core.Geometry attribute) charge() (in module automol.rd.mol) chiral_centers() (in module automol.rd.mol) coordinates (automol.geom.core.Geometry attribute) coordinates() (in module automol.rd.mol) CoordinatesField (in module automol.utils.types) covalent_radii (automol.geom.core.Geometry property) covalent_radius (automol.utils.element.core.Element attribute) covalent_radius() (in module automol.utils.element.core) D DALTON (in module automol.utils.constants) DALTON_TO_KILOGRAMS (in module automol.utils.constants) DEGREE (in module automol.utils.constants) DEGREES_TO_RADIANS (in module automol.utils.constants) dihedrals() (in module automol.geom.analysis) distance_keys() (in module automol.geom.analysis) distance_matrix() (in module automol.geom.analysis) E eckart_frame() (in module automol.geom.core) Element (class in automol.utils.element.core) ELEMENT_BY_NUMBER (in module automol.utils.element.core) ELEMENT_BY_SYMBOL (in module automol.utils.element.core) ElementNotFoundError F FloatArray (in module automol.utils.types) FloatArrayField (in module automol.utils.types) from_geometry() (automol.ident.Identity class method) from_inchi() (in module automol.rd.mol) from_key() (in module automol.utils.element.core) from_rdkit_mol() (in module automol.geom.core) from_smiles() (in module automol.rd.mol) from_stereo_mol_graph() (in module automol.geom.core) from_value() (automol.ident.Identity class method) from_xyz_block() (automol.geom.core.Geometry class method) (in module automol.geom.io) (in module automol.rd.mol) from_xyz_file() (automol.geom.core.Geometry class method) (in module automol.geom.io) G Geometry (class in automol.geom.core) geometry() (automol.ident.Identity method) geometry_fn (automol.ident.AlgorithmDef attribute) geometry_fn() (automol.ident.AlgorithmFns static method) (automol.ident.RDKitInChI static method) (automol.ident.RDKitSMILES static method) GeometryConversionError get() (automol.ident.AlgorithmRegistry class method) group (automol.utils.element.core.Element attribute) group() (in module automol.utils.element.core) H harmonic_zpv() (in module automol.geom.analysis) HARTREE (in module automol.utils.constants) HARTREE_TO_JOULES (in module automol.utils.constants) has_coordinates() (in module automol.rd.mol) HashGenerationError HILL_FORMULA (automol.ident.Algorithm attribute) HillFormula (class in automol.ident) hungarian_correspondence() (in module automol.geom.analysis) I Identity (class in automol.ident) identity_fn (automol.ident.AlgorithmDef attribute) identity_fn() (automol.ident.AlgorithmFns static method) (automol.ident.HillFormula static method) (automol.ident.RDKitInChI static method) (automol.ident.RDKitSMILES static method) inchi() (in module automol.rd.mol) inertia_axes() (in module automol.geom.analysis) inertia_moments() (in module automol.geom.analysis) inertia_tensor() (in module automol.geom.analysis) J JOULE (in module automol.utils.constants) JOULES_TO_HARTREE (in module automol.utils.constants) K kabsch_align() (in module automol.geom.analysis) KILOGRAM (in module automol.utils.constants) KILOGRAMS_TO_DALTON (in module automol.utils.constants) kind (automol.ident.Algorithm attribute) (automol.ident.Identity attribute) M mass (automol.utils.element.core.Element attribute) mass() (in module automol.utils.element.core) mass_number() (in module automol.utils.element.core) mass_weight_vector() (in module automol.geom.analysis) masses (automol.geom.core.Geometry property) METER (in module automol.utils.constants) METERS_PER_SECOND (in module automol.utils.constants) METERS_TO_BOHR (in module automol.utils.constants) model_config (automol.geom.core.Geometry attribute) module automol automol.geom automol.geom.analysis automol.geom.core automol.geom.io automol.ident automol.rd automol.rd.mol automol.utils automol.utils.constants automol.utils.element automol.utils.element.core automol.utils.exc automol.utils.types N normal_mode_projection() (in module automol.geom.analysis) number() (in module automol.utils.element.core) O orbit_classes() (in module automol.geom.analysis) P period (automol.utils.element.core.Element attribute) period() (in module automol.utils.element.core) PERIOD_SHELL_CAPACITY (in module automol.utils.element.core) R RADIAN (in module automol.utils.constants) RADIANS_TO_DEGREES (in module automol.utils.constants) RDKIT_INCHI (automol.ident.Algorithm attribute) rdkit_mol() (in module automol.geom.core) RDKIT_SMILES (automol.ident.Algorithm attribute) RDKitInChI (class in automol.ident) RDKitSMILES (class in automol.ident) reflect() (in module automol.geom.core) register() (automol.ident.AlgorithmRegistry class method) register_def() (automol.ident.AlgorithmRegistry class method) relabel_atoms() (automol.geom.core.Geometry method) render_gif() (in module automol.geom.io) render_svg() (in module automol.geom.io) RMSD_THRESHOLD (in module automol.geom.analysis) rotate() (in module automol.geom.core) rotation_to_inertia_axes() (in module automol.geom.analysis) rotational_analysis() (in module automol.geom.analysis) rotational_normal_modes() (in module automol.geom.analysis) S SECOND (in module automol.utils.constants) set_bond() (in module automol.geom.core) set_coordinates() (in module automol.rd.mol) shell_capacity() (in module automol.utils.element.core) smiles() (in module automol.rd.mol) spin (automol.geom.core.Geometry attribute) spin() (in module automol.rd.mol) stereo_mol_graph() (in module automol.geom.core) symbol (automol.utils.element.core.Element attribute) SYMBOL (in module automol.geom.io) symbol() (in module automol.utils.element.core) symbols (automol.geom.core.Geometry attribute) symbols() (in module automol.rd.mol) T transition() (in module automol.geom.core) translate() (in module automol.geom.core) translational_normal_modes() (in module automol.geom.analysis) U UnknownAlgorithmError ureg (in module automol.utils.constants) V valence (automol.utils.element.core.Element attribute) valence() (in module automol.utils.element.core) valences (automol.geom.core.Geometry property) validate_coordinates_shape() (automol.geom.core.Geometry class method) value (automol.ident.Identity attribute) vibrational_analysis() (in module automol.geom.analysis) VIBRATIONAL_FORCE_TO_INV_CM_FREQUENCY (in module automol.utils.constants) View (class in automol.geom.io) view() (in module automol.geom.io) W WAVENUMBER (in module automol.utils.constants) X XTBError xyz_block() (automol.geom.core.Geometry method) (in module automol.geom.io) (in module automol.rd.mol) xyz_file() (automol.geom.core.Geometry method) (in module automol.geom.io) XYZ_LINE (in module automol.geom.io) XYZFormatError Z Z (automol.utils.element.core.Element attribute)