Index

A

actual_length() (nomodeco_classes.Molecule method) add_element_to_all_entries() (in module topology) append() (nomodeco_classes.Molecule method)

are_two_elements_same() (in module icsel) arguments module Atom (class in gaussian_parser)

B

b_matrix() (in module bmatrix) B_Matrix_Entry_Angle_AtomA() (in module bmatrix) B_Matrix_Entry_Angle_AtomB() (in module bmatrix) B_Matrix_Entry_Angle_AtomC() (in module bmatrix) B_Matrix_Entry_BondLength() (in module bmatrix) B_Matrix_Entry_LinearAngleFirstPlane_AtomA() (in module bmatrix) B_Matrix_Entry_LinearAngleFirstPlane_AtomB() (in module bmatrix) B_Matrix_Entry_LinearAngleFirstPlane_AtomC() (in module bmatrix) B_Matrix_Entry_LinearAngleSecondPlane_AtomA() (in module bmatrix) B_Matrix_Entry_LinearAngleSecondPlane_AtomB() (in module bmatrix) B_Matrix_Entry_LinearAngleSecondPlane_AtomC() (in module bmatrix) B_Matrix_Entry_OutOfPlane_AtomA() (in module bmatrix) B_Matrix_Entry_OutOfPlane_AtomB() (in module bmatrix)

B_Matrix_Entry_OutOfPlane_AtomC() (in module bmatrix) B_Matrix_Entry_OutOfPlane_AtomD() (in module bmatrix) B_Matrix_Entry_Torsion_AtomA() (in module bmatrix) B_Matrix_Entry_Torsion_AtomB() (in module bmatrix) B_Matrix_Entry_Torsion_AtomC() (in module bmatrix) B_Matrix_Entry_Torsion_AtomD() (in module bmatrix) bmatrix module bond_angle() (in module bmatrix) (nomodeco_classes.Molecule method) bond_dict() (nomodeco_classes.Molecule method) bond_length() (in module bmatrix) bound_to_atom() (in module specifications)

C

calculation_specification() (in module specifications) can_be_float() (in module molpro_parser) combine_dictionaries() (in module topology)

coordinates (gaussian_parser.Atom attribute) count_connected_components() (nomodeco_classes.Molecule static method) covalent_bonds() (nomodeco_classes.Molecule method)

D

degree_of_covalance() (nomodeco_classes.Molecule method) detect_submolecules() (nomodeco_classes.Molecule method)

dfs() (nomodeco_classes.Molecule static method) distribute_elements() (in module topology)

E

eliminate_symmetric_tuples() (in module topology)

F

find_optimal_coordinate_set() (in module icset_opt)

fully_linear_molecule() (in module topology)

G

gaussian_parser module general_acyclic_linunit_molecule() (in module topology) general_acyclic_nolinunit_molecule() (in module topology) general_cyclic_linunit_molecule() (in module topology) general_cyclic_nolinunit_molecule() (in module topology) get_args() (in module arguments)

get_atom_coords_by_symbol() (nomodeco_classes.Molecule method) get_bond_information() (in module nomodeco.nomodeco) get_different_elements() (in module icsel) get_donor_atoms() (nomodeco_classes.Molecule method) get_linear_bonds() (in module specifications) get_mass_information() (in module nomodeco.nomodeco) get_sets() (in module icsel) graph_rep() (nomodeco_classes.Molecule method)

I

icsel module icset_opt module idof_general() (nomodeco_classes.Molecule method) idof_linear() (nomodeco_classes.Molecule method) intermolecular_general_acyclic_linunit_molecule() (in module topology) intermolecular_general_acyclic_nolinunit_molecule() (in module topology) intermolecular_general_cyclic_linunit_molecule() (in module topology)

intermolecular_general_cyclic_nolinsub() (in module topology) intermolecular_planar_acyclic_linunit_molecule() (in module topology) intermolecular_planar_acyclic_nolinunit_molecule() (in module topology) intermolecular_planar_cyclic_linunit_molecule() (in module topology) intermolecular_planar_cyclic_nolinunit_molecule() (in module topology) is_connected() (nomodeco_classes.Molecule static method) is_donor() (nomodeco_classes.Molecule.Atom method) is_hydrogen() (nomodeco_classes.Molecule.Atom method) is_string_in_tuples() (in module specifications) is_system_planar() (in module specifications)

K

Kemalian_metric() (in module icsel)

L

list_of_atom_symbols() (nomodeco_classes.Molecule method)

list_of_atom_symbols_xyz() (nomodeco_classes.Molecule method)

M

module arguments bmatrix gaussian_parser icsel icset_opt molpro_parser nomodeco.nomodeco nomodeco_classes orca_parser specifications topology

Molecule (class in nomodeco_classes) Molecule.Atom (class in nomodeco_classes) molecule_is_not_split() (in module topology) molpro_parser module

N

nomodeco.nomodeco module nomodeco_classes module

num_atoms() (nomodeco_classes.Molecule method) numerate_strings() (in module gaussian_parser) (in module molpro_parser) (in module orca_parser)

O

orca_parser module

P

parse_Cartesian_F_Matrix_from_start_of_matrix() (in module molpro_parser) parse_cartesian_force_constants() (in module gaussian_parser) (in module orca_parser) parse_xyz() (in module gaussian_parser) parse_xyz_from_inputfile() (in module molpro_parser) (in module orca_parser)

planar_acyclic_linunit_molecule() (in module topology) planar_acyclic_nolinunit_molecule() (in module topology) planar_cyclic_linunit_molecule() (in module topology) planar_cyclic_nolinunit_molecule() (in module topology) print_welcome_message() (in module nomodeco.nomodeco)

R

read_and_enumerate_xyz() (in module nomodeco.nomodeco)

reciprocal_massvector() (in module nomodeco.nomodeco) reciprocal_square_massvector() (in module nomodeco.nomodeco)

S

specifications module strip_numbers() (in module nomodeco.nomodeco) (in module topology)

swap_deuterium() (nomodeco_classes.Molecule.Atom method) symbol (gaussian_parser.Atom attribute)

T

theoretical_length() (nomodeco_classes.Molecule method) theoretical_length_vdw() (nomodeco_classes.Molecule method) topology module

torsion_angle() (in module bmatrix) Total_IC_dict (in module topology)

U

update_internal_coordinates_cyclic() (in module topology)

V

valide_atoms_to_cut() (in module topology)