Index A | B | C | D | E | F | G | H | I | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A add() (molorient.classes.square_matrix.SquareMatrix method) (molorient.classes.vector.Vector method) align_highest_order_to_z() (in module molorient.orientation.standardize_axes.nwchem_orientation) apply_posthoc_fixup() (in module molorient.orientation.standardize_axes.nwchem_orientation) arccos_series() (in module molorient.helpers.trig_helpers) arcsin_series() (in module molorient.helpers.trig_helpers) arctan2() (in module molorient.helpers.trig_helpers) arctan_series() (in module molorient.helpers.trig_helpers) assign() (molorient.classes.square_matrix.SquareMatrix method) (molorient.classes.vector.Vector method) Atom (class in molorient.classes.atom) B best_candidate() (in module molorient.helpers.diagonalization) build_inertia_tensor() (in module molorient.helpers.diagonalization) build_parser() (in module molorient.cli) build_tensor() (in module molorient.orientation.standardize_axes.nwchem_orientation) C canon_axes() (in module molorient.orientation.standardize_axes.nwchem_orientation) charge (molorient.classes.atom.Atom attribute) classify_moments() (in module molorient.orientation.standardize_axes.axis_standardization) classify_top() (in module molorient.orientation.standardize_axes.nwchem_orientation) cn_axes_finder() (in module molorient.orientation.standardize_axes.axis_standardization) CONV (in module molorient.orientation.standardize_axes.nwchem_orientation) cos_series() (in module molorient.helpers.trig_helpers) cross() (molorient.classes.vector.Vector method) cs_correction() (in module molorient.orientation.standardize_axes.nwchem_orientation) D detect_axis_order() (in module molorient.orientation.standardize_axes.nwchem_orientation) diagonalize() (in module molorient.orientation.standardize_axes.nwchem_orientation) dot() (molorient.classes.vector.Vector method) E eigval_solver() (in module molorient.helpers.diagonalization) eigvec_solver() (in module molorient.helpers.diagonalization) element (molorient.classes.atom.Atom attribute) element_mass() (in module molorient.orientation.standardize_axes.nwchem_orientation) elements (molorient.classes.square_matrix.SquareMatrix attribute) (molorient.classes.vector.Vector attribute) F find_cn_axes() (in module molorient.orientation.standardize_axes.axis_standardization) find_perpendicular_c2() (in module molorient.orientation.standardize_axes.nwchem_orientation) from_atom() (molorient.classes.vector.Vector class method) from_columns() (molorient.classes.square_matrix.SquareMatrix class method) G geom_tol() (in module molorient.helpers.precision) group_operations() (in module molorient.orientation.standardize_axes.nwchem_orientation) H heaviest_first_key() (in module molorient.orientation.sort_atoms) I identity() (molorient.classes.square_matrix.SquareMatrix class method) inertia_tensor() (in module molorient.orientation.standardize_axes.axis_standardization) inverse() (molorient.classes.square_matrix.SquareMatrix method) M main() (in module molorient.cli) maps_onto() (in module molorient.orientation.standardize_axes.nwchem_orientation) mass_centered() (in module molorient.orientation.standardize_axes.nwchem_orientation) mass_inertia_tensor() (in module molorient.orientation.standardize_axes.nwchem_orientation) MAX_OPS (in module molorient.orientation.standardize_axes.nwchem_orientation) module molorient molorient.classes molorient.classes.atom molorient.classes.square_matrix molorient.classes.vector molorient.cli molorient.helpers molorient.helpers.diagonalization molorient.helpers.precision molorient.helpers.trig_helpers molorient.orient_system molorient.orientation molorient.orientation.sort_atoms molorient.orientation.standardize_axes molorient.orientation.standardize_axes.axis_standardization molorient.orientation.standardize_axes.nwchem_orientation molorient.orientation.translation molorient module molorient.classes module molorient.classes.atom module molorient.classes.square_matrix module molorient.classes.vector module molorient.cli module molorient.helpers module molorient.helpers.diagonalization module molorient.helpers.precision module molorient.helpers.trig_helpers module molorient.orient_system module molorient.orientation module molorient.orientation.sort_atoms module molorient.orientation.standardize_axes module molorient.orientation.standardize_axes.axis_standardization module molorient.orientation.standardize_axes.nwchem_orientation module molorient.orientation.translation module moment_tol() (in module molorient.helpers.precision) multiply() (molorient.classes.square_matrix.SquareMatrix method) N negate() (molorient.classes.square_matrix.SquareMatrix method) (molorient.classes.vector.Vector method) norm() (molorient.classes.vector.Vector method) normalized() (molorient.classes.vector.Vector method) O OP_TOL (in module molorient.orientation.standardize_axes.nwchem_orientation) orient_asymm() (in module molorient.orientation.standardize_axes.axis_standardization) orient_atom() (in module molorient.orientation.standardize_axes.axis_standardization) orient_linear() (in module molorient.orientation.standardize_axes.axis_standardization) orient_mol() (in module molorient.orientation.standardize_axes.nwchem_orientation) orient_spherical() (in module molorient.orientation.standardize_axes.axis_standardization) (in module molorient.orientation.standardize_axes.nwchem_orientation) orient_symm() (in module molorient.orientation.standardize_axes.axis_standardization) orient_symmetric_or_linear() (in module molorient.orientation.standardize_axes.nwchem_orientation) orient_system() (in module molorient.orient_system) P parse_xyz() (in module molorient.cli) permute_positions() (in module molorient.orientation.standardize_axes.nwchem_orientation) PERP_TOL (in module molorient.orientation.standardize_axes.nwchem_orientation) pi_as_decimal() (in module molorient.helpers.trig_helpers) pick_canonical_atoms() (in module molorient.orientation.standardize_axes.nwchem_orientation) pick_canonical_frame() (in module molorient.orientation.standardize_axes.axis_standardization) pos_vector() (in module molorient.helpers.diagonalization) position() (molorient.classes.atom.Atom method) positive_int() (in module molorient.cli) prec_tol() (in module molorient.helpers.precision) Q quantized_atoms() (in module molorient.orientation.standardize_axes.nwchem_orientation) R rot_mat_from_axes() (in module molorient.helpers.diagonalization) rotate_atoms() (in module molorient.orientation.standardize_axes.nwchem_orientation) rotate_in_plane() (in module molorient.orientation.standardize_axes.nwchem_orientation) S scale() (molorient.classes.square_matrix.SquareMatrix method) (molorient.classes.vector.Vector method) set_precision() (in module molorient.cli) sign_variants() (in module molorient.orientation.standardize_axes.nwchem_orientation) sin_series() (in module molorient.helpers.trig_helpers) snap() (in module molorient.orientation.standardize_axes.nwchem_orientation) snap_moments() (in module molorient.orientation.standardize_axes.axis_standardization) sort_atoms() (in module molorient.orientation.sort_atoms) sorted_rows() (in module molorient.orientation.standardize_axes.nwchem_orientation) SquareMatrix (class in molorient.classes.square_matrix) standardize_axes() (in module molorient.orientation.standardize_axes.axis_standardization) subtract() (molorient.classes.vector.Vector method) swap() (in module molorient.orientation.standardize_axes.nwchem_orientation) symmetric_frames() (in module molorient.orientation.standardize_axes.axis_standardization) symmetrize() (in module molorient.orientation.standardize_axes.nwchem_orientation) T TENM04 (in module molorient.orientation.standardize_axes.nwchem_orientation) TENM05 (in module molorient.orientation.standardize_axes.nwchem_orientation) TENM05_DIST (in module molorient.orientation.standardize_axes.nwchem_orientation) THREQUIV (in module molorient.orientation.standardize_axes.nwchem_orientation) THREQUIV_MOMENT (in module molorient.orientation.standardize_axes.nwchem_orientation) translate_to_origin() (in module molorient.orientation.translation) translation_vector() (in module molorient.orientation.translation) transpose() (molorient.classes.square_matrix.SquareMatrix method) U unique_axis_frame() (in module molorient.orientation.standardize_axes.axis_standardization) V vec() (in module molorient.orientation.standardize_axes.nwchem_orientation) Vector (class in molorient.classes.vector) W write_xyz() (in module molorient.cli) X x (molorient.classes.atom.Atom attribute) Y y (molorient.classes.atom.Atom attribute) Z z (molorient.classes.atom.Atom attribute)