Index

A

add_adjacency_mat() (ocal.utils.cif_reader.FileIO method) add_coordinates() (ocal.utils.cif_reader.FileIO method) add_link() (ocal.utils.gjf_maker.GjfMaker method)

add_root() (ocal.utils.gjf_maker.GjfMaker method) add_symbols() (ocal.utils.cif_reader.FileIO method) ATOMIC_WEIGHTS (ocal.utils.cif_reader.CifReader attribute)

C

calc_cen_of_weight() (ocal.utils.cif_reader.CifReader method) calc_distance_matrix() (in module ocal.utils.cube_reader) calc_otf() (in module ocal.utils.cube_reader) (ocal.ocal.Ocal method) check_normal_termination() (in module ocal.utils.gaus_log_reader) (ocal.ocal.Ocal static method) CifReader (class in ocal.utils.cif_reader) close() (ocal.utils.gaus_log_reader.FileReader method)

convert_cart_to_frac() (ocal.utils.cif_reader.CifReader method) convert_frac_to_cart() (ocal.utils.cif_reader.CifReader method) COVALENT_RADII (ocal.utils.cif_reader.CifReader attribute) create_chk_file() (ocal.utils.gjf_maker.GjfMaker method) create_cube() (ocal.ocal.Ocal method) create_fchk() (ocal.ocal.Ocal method) create_gjf() (ocal.ocal.Ocal method) create_rwf_file() (ocal.utils.gjf_maker.GjfMaker method)

E

ELEMENT_PROP (ocal.utils.cif_reader.CifReader attribute) (ocal.utils.gjf_maker.GjfMaker attribute) ElementPropertiesIsNotDefinedError ELEMENTS_NUM (ocal.utils.gjf_maker.GjfMaker attribute)

expand_mols() (ocal.utils.cif_reader.CifReader method) export_gjf() (ocal.utils.gjf_maker.GjfMaker method) export_mol_file() (ocal.utils.cif_reader.FileIO method) export_unit_cell_file() (ocal.utils.cif_reader.CifReader method) export_xyz_file() (ocal.utils.cif_reader.FileIO method)

F

FileIO (class in ocal.utils.cif_reader)

FileReader (class in ocal.utils.gaus_log_reader)

G

GjfMaker (class in ocal.utils.gjf_maker)

L

load_element_tables() (in module ocal.utils.cube_reader)

M

main() (in module ocal.ocal) module ocal ocal.ocal ocal.utils ocal.utils.cif_reader ocal.utils.cube_reader ocal.utils.gaus_log_reader ocal.utils.gjf_maker ocal.utils.structure_reader

O

ocal module Ocal (class in ocal.ocal) ocal.ocal module ocal.utils module ocal.utils.cif_reader module

ocal.utils.cube_reader module ocal.utils.gaus_log_reader module ocal.utils.gjf_maker module ocal.utils.structure_reader module opt() (ocal.utils.gjf_maker.GjfMaker method) output_detail() (ocal.utils.gjf_maker.GjfMaker method)

P

parent_dir (ocal.utils.cif_reader.CifReader attribute) (ocal.utils.gjf_maker.GjfMaker attribute)

parse_args() (in module ocal.ocal) print_timestamp() (ocal.ocal.Ocal static method)

R

read_cif() (in module ocal.utils.structure_reader) read_cubefile() (in module ocal.utils.cube_reader) read_gjf() (in module ocal.utils.structure_reader) read_mol() (in module ocal.utils.structure_reader) read_mol2() (in module ocal.utils.structure_reader)

read_structure() (in module ocal.utils.structure_reader) read_xyz() (in module ocal.utils.structure_reader) remove_duplicates() (ocal.utils.cif_reader.CifReader method) reset_variable() (ocal.utils.gjf_maker.GjfMaker method) reversed_readline() (ocal.utils.gaus_log_reader.FileReader method) run_gaussian() (ocal.ocal.Ocal method)

S

set_charge_spin() (ocal.utils.gjf_maker.GjfMaker method) set_coordinates() (ocal.utils.gjf_maker.GjfMaker method) set_function() (ocal.utils.gjf_maker.GjfMaker method)

set_resource() (ocal.utils.gjf_maker.GjfMaker method) set_symbols() (ocal.utils.gjf_maker.GjfMaker method) set_title() (ocal.utils.gjf_maker.GjfMaker method) SymmetryIsNotDefinedError

Z

ZValueIsNotMatchError