Index

A

add_hashtag_in_first_line() (in module cifkit.utils.cif_editor)

C

calc_dist_two_cart_points() (in module cifkit.utils.distance) calculate_normalized_dist_diffs() (in module cifkit.preprocessors.environment_util) calculate_normalized_distances() (in module cifkit.preprocessors.environment_util) check_file_exists() (in module cifkit.utils.folder) check_file_not_empty() (in module cifkit.utils.folder) check_unique_atom_site_labels() (in module cifkit.utils.cif_parser) Cif (class in cifkit.models.cif) CifEnsemble (class in cifkit.models.cif_ensemble) CifEnsembleLog (class in cifkit.utils.log_messages) cifkit module cifkit.coordination module cifkit.coordination.bond_distance module cifkit.coordination.composition module cifkit.coordination.connection module cifkit.coordination.filter module cifkit.coordination.geometry module cifkit.coordination.method module cifkit.coordination.site module cifkit.coordination.site_distance module cifkit.data module cifkit.data.demo module cifkit.data.example module cifkit.data.mendeleev module cifkit.data.mendeleeve_handler module cifkit.data.radius module cifkit.data.radius_handler module cifkit.data.radius_optimization module cifkit.figures module cifkit.figures.histogram module cifkit.figures.polyhedron module cifkit.models module cifkit.models.cif module cifkit.models.cif_ensemble module cifkit.occupancy module cifkit.occupancy.mixing module cifkit.preprocessors module cifkit.preprocessors.environment module cifkit.preprocessors.environment_util module cifkit.preprocessors.error module cifkit.preprocessors.format module cifkit.preprocessors.supercell module

cifkit.preprocessors.supercell_util module cifkit.utils module cifkit.utils.bond_pair module cifkit.utils.cif_editor module cifkit.utils.cif_parser module cifkit.utils.cif_sourcer module cifkit.utils.distance module cifkit.utils.error_messages module cifkit.utils.folder module cifkit.utils.formula module cifkit.utils.log_messages module cifkit.utils.prompt module cifkit.utils.random module cifkit.utils.sort module cifkit.utils.string_parser module cifkit.utils.unit module cifkit.version module CifLog (class in cifkit.utils.log_messages) CifParserError (class in cifkit.utils.error_messages) clean_parsed_structure() (in module cifkit.utils.string_parser) CN_avg_by_best_methods (cifkit.models.cif.Cif property) CN_avg_by_min_dist_method (cifkit.models.cif.Cif property) CN_best_methods (cifkit.models.cif.Cif property) CN_bond_count_by_best_methods (cifkit.models.cif.Cif property) CN_bond_count_by_best_methods_sorted_by_mendeleev (cifkit.models.cif.Cif property) CN_bond_count_by_min_dist_method (cifkit.models.cif.Cif property) CN_bond_count_by_min_dist_method_sorted_by_mendeleev (cifkit.models.cif.Cif property) CN_bond_fractions_by_best_methods (cifkit.models.cif.Cif property) CN_bond_fractions_by_best_methods_sorted_by_mendeleev (cifkit.models.cif.Cif property) CN_bond_fractions_by_min_dist_method (cifkit.models.cif.Cif property) CN_bond_fractions_by_min_dist_method_sorted_by_mendeleev (cifkit.models.cif.Cif property) CN_connections_by_best_methods (cifkit.models.cif.Cif property) CN_connections_by_min_dist_method (cifkit.models.cif.Cif property) CN_max_by_best_methods (cifkit.models.cif.Cif property) CN_max_by_min_dist_method (cifkit.models.cif.Cif property) CN_max_gap_per_site (cifkit.models.cif.Cif property) CN_min_by_best_methods (cifkit.models.cif.Cif property) CN_min_by_min_dist_method (cifkit.models.cif.Cif property) CN_unique_values_by_best_methods (cifkit.models.cif.Cif property) (cifkit.models.cif_ensemble.CifEnsemble property) CN_unique_values_by_min_dist_method (cifkit.models.cif.Cif property) (cifkit.models.cif_ensemble.CifEnsemble property) composition_type_stats (cifkit.models.cif_ensemble.CifEnsemble property) compute_avg_CN() (in module cifkit.coordination.composition) compute_center_of_mass_and_distance() (in module cifkit.coordination.geometry) compute_CN_max_gap_per_site() (in module cifkit.coordination.method) COMPUTE_CONNECTIONS (cifkit.utils.log_messages.CifLog attribute) compute_connections() (cifkit.models.cif.Cif method) compute_coord_occupancy_sum() (in module cifkit.occupancy.mixing) compute_normalized_value() (in module cifkit.coordination.method) compute_polyhedron_metrics() (in module cifkit.coordination.geometry) compute_radius_sum() (in module cifkit.data.radius_handler) connections_flattened (cifkit.models.cif.Cif property) constraint() (in module cifkit.data.radius_optimization) copy_cif_files() (cifkit.models.cif_ensemble.CifEnsemble method) copy_files() (in module cifkit.utils.folder) count_connections_per_site() (in module cifkit.coordination.composition)

D

DUPLICATE_LABELS (cifkit.utils.error_messages.CifParserError attribute)

E

edit_cif_file_based_on_db() (in module cifkit.utils.cif_editor) EMPTY_STRING_INPUT (cifkit.utils.error_messages.GeneralError attribute) ensure_connections() (in module cifkit.models.cif) Er10Co9In20_file_path (cifkit.data.example.Example attribute)

Er5In3_file_path (cifkit.data.example.Example attribute) ErCoIn5_file_path (cifkit.data.example.Example attribute) ErCoIn_folder_path (cifkit.data.example.Example attribute) Example (class in cifkit.data.example)

F

FILE_IS_EMPTY (cifkit.utils.error_messages.FileError attribute) FILE_NOT_FOUND (cifkit.utils.error_messages.FileError attribute) FileError (class in cifkit.utils.error_messages) filter_by_CN_best_methods_containing() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_CN_best_methods_exact_matching() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_CN_min_dist_method_containing() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_CN_min_dist_method_exact_matching() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_composition_types() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_elements_containing() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_elements_exact_matching() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_formulas() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_min_distance() (cifkit.models.cif_ensemble.CifEnsemble method)

filter_by_site_mixing_types() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_space_group_names() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_space_group_numbers() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_structures() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_supercell_count() (cifkit.models.cif_ensemble.CifEnsemble method) filter_by_tags() (cifkit.models.cif_ensemble.CifEnsemble method) find_best_polyhedron() (in module cifkit.coordination.filter) find_symmetry_operations() (in module cifkit.preprocessors.supercell) flat_site_connections() (in module cifkit.preprocessors.environment_util) flatten_original_coordinates() (in module cifkit.preprocessors.supercell) formula_stats (cifkit.models.cif_ensemble.CifEnsemble property) frac_coordinates() (in module cifkit.occupancy.mixing) fractional_to_cartesian() (in module cifkit.utils.unit)

G

GeneralError (class in cifkit.utils.error_messages) generate_adjacent_pairs() (in module cifkit.data.radius_optimization) generate_CN_by_best_methods_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_CN_by_min_dist_method_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_color_mapping() (in module cifkit.figures.polyhedron) generate_composition_type_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_contrasting_colors() (in module cifkit.figures.polyhedron) generate_elements_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_formula_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_histogram() (in module cifkit.figures.histogram) generate_random_numbers() (in module cifkit.utils.random) generate_site_mixing_type_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_space_group_name_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_space_group_number_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_structure_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_supercell_size_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) generate_tag_histogram() (cifkit.models.cif_ensemble.CifEnsemble method) get_atom_type_from_label() (in module cifkit.utils.string_parser) get_bond_counts() (in module cifkit.coordination.composition) get_bond_fractions() (in module cifkit.coordination.composition) get_bond_pairs() (in module cifkit.utils.bond_pair) get_cell_atom_count() (in module cifkit.preprocessors.supercell_util) get_cif_block() (in module cifkit.utils.cif_parser) get_cif_db_source() (in module cifkit.utils.cif_sourcer) get_CIF_pauling_radius() (in module cifkit.data.radius_handler) get_CN_connections_by_best_methods() (in module cifkit.coordination.connection) get_CN_connections_by_min_dist_method() (in module cifkit.coordination.filter) get_file_count() (in module cifkit.utils.folder) get_file_path() (in module cifkit.utils.folder) get_file_paths() (in module cifkit.utils.folder) get_formula_structure_weight_s_group() (in module cifkit.utils.cif_parser) get_is_radius_data_available() (in module cifkit.data.radius_handler) get_label_occupancy_coordinates() (in module cifkit.utils.cif_parser) get_line_content_from_tag() (in module cifkit.utils.cif_parser) get_loop_tags() (in module cifkit.utils.cif_parser) get_loop_value_dict() (in module cifkit.utils.cif_parser) get_loop_values() (in module cifkit.utils.cif_parser) get_mendeleev_numbers() (in module cifkit.data.mendeleev) get_mendeleev_nums_from_pair_tuple() (in module cifkit.data.mendeleeve_handler) get_min_distance_pair() (in module cifkit.coordination.site)

get_min_distance_pair_per_site_label() (in module cifkit.coordination.site) get_mixing_type_per_pair_dict() (in module cifkit.occupancy.mixing) get_most_connected_point_per_site() (in module cifkit.preprocessors.environment) get_nearest_dists_per_site() (in module cifkit.preprocessors.environment) get_normalized_formula() (in module cifkit.utils.formula) get_pairs_sorted_by_mendeleev() (in module cifkit.utils.bond_pair) get_parsed_formula() (in module cifkit.utils.formula) get_parsed_norm_formula() (in module cifkit.utils.formula) get_path() (cifkit.data.example.Example static method) get_polyhedron_coordinates_labels() (in module cifkit.coordination.geometry) get_polyhedron_labels_by_CN_best_methods() (cifkit.models.cif.Cif method) get_polyhedron_labels_by_CN_min_dist_method() (cifkit.models.cif.Cif method) get_rad_sum_value() (in module cifkit.coordination.method) get_radians_from_degrees() (in module cifkit.utils.unit) get_radius_data() (in module cifkit.data.radius) get_radius_values_per_element() (in module cifkit.data.radius_handler) get_refined_CIF_radius() (in module cifkit.data.radius_optimization) get_shortest_distance() (in module cifkit.coordination.site_distance) get_shortest_distance_per_bond_pair() (in module cifkit.coordination.bond_distance) get_shortest_distance_per_site() (in module cifkit.coordination.site_distance) get_site_connections() (in module cifkit.preprocessors.environment) get_site_mixing_type() (in module cifkit.occupancy.mixing) get_start_end_line_indexes() (in module cifkit.utils.cif_parser) get_string_to_formatted_float() (in module cifkit.utils.string_parser) get_subscripted_formula() (in module cifkit.utils.formula) get_supercell_points() (in module cifkit.preprocessors.supercell) get_tag_from_third_line() (in module cifkit.utils.cif_parser) get_unique_CN_values() (in module cifkit.coordination.composition) get_unique_element_count() (in module cifkit.utils.formula) get_unique_elements() (in module cifkit.utils.formula) get_unique_elements_from_formulas() (in module cifkit.utils.formula) get_unique_elements_from_loop() (in module cifkit.utils.cif_parser) get_unique_formulas_structures_weights_s_groups() (in module cifkit.utils.cif_parser) get_unique_label_count() (in module cifkit.utils.cif_parser) get_unique_site_labels() (in module cifkit.utils.cif_parser) get_unitcell_angles_rad() (in module cifkit.utils.cif_parser) get_unitcell_coords_after_sym_operations_per_label() (in module cifkit.preprocessors.supercell) get_unitcell_coords_for_all_labels() (in module cifkit.preprocessors.supercell) get_unitcell_lengths() (in module cifkit.utils.cif_parser) get_validated_formula_label() (in module cifkit.utils.formula) getting-started

I

INVALID_CIF_BLOCK (cifkit.utils.error_messages.GeneralError attribute) INVALID_LOOP_TAGS (cifkit.utils.error_messages.CifParserError attribute)

INVALID_MIXING_TYPE (cifkit.utils.error_messages.OccupancyError attribute) INVALID_PARSED_ELEMENT (cifkit.utils.error_messages.CifParserError attribute) INVALID_TYPE (cifkit.utils.error_messages.GeneralError attribute)

L

license LOADING_DATA (cifkit.utils.log_messages.CifLog attribute)

log_connected_points() (in module cifkit.utils.prompt) log_save_file_message() (in module cifkit.utils.prompt)

M

make_output_folder() (in module cifkit.utils.folder) minimum_distances (cifkit.models.cif_ensemble.CifEnsemble property) MISSING_COORDINATES (cifkit.utils.error_messages.CifParserError attribute) MISSING_LOOP_VALUES (cifkit.utils.error_messages.CifParserError attribute) module cifkit cifkit.coordination cifkit.coordination.bond_distance cifkit.coordination.composition cifkit.coordination.connection cifkit.coordination.filter cifkit.coordination.geometry cifkit.coordination.method cifkit.coordination.site cifkit.coordination.site_distance cifkit.data cifkit.data.demo cifkit.data.example cifkit.data.mendeleev cifkit.data.mendeleeve_handler cifkit.data.radius cifkit.data.radius_handler cifkit.data.radius_optimization cifkit.figures cifkit.figures.histogram cifkit.figures.polyhedron cifkit.models cifkit.models.cif cifkit.models.cif_ensemble cifkit.occupancy cifkit.occupancy.mixing cifkit.preprocessors cifkit.preprocessors.environment cifkit.preprocessors.environment_util cifkit.preprocessors.error cifkit.preprocessors.format cifkit.preprocessors.supercell cifkit.preprocessors.supercell_util cifkit.utils cifkit.utils.bond_pair cifkit.utils.cif_editor cifkit.utils.cif_parser cifkit.utils.cif_sourcer cifkit.utils.distance cifkit.utils.error_messages cifkit.utils.folder cifkit.utils.formula cifkit.utils.log_messages cifkit.utils.prompt cifkit.utils.random cifkit.utils.sort cifkit.utils.string_parser cifkit.utils.unit cifkit.version

move_cif_files() (cifkit.models.cif_ensemble.CifEnsemble method) move_files() (in module cifkit.utils.folder) move_files_based_on_errors() (in module cifkit.preprocessors.error)

N

NON_ALPHABETIC_START (cifkit.utils.error_messages.GeneralError attribute)

NON_MATCHING_ELEMENT (cifkit.utils.error_messages.GeneralError attribute)

O

objective() (in module cifkit.data.radius_optimization)

OccupancyError (class in cifkit.utils.error_messages) order_tuple_pair_by_mendeleev() (in module cifkit.utils.bond_pair)

P

parse_atom_site_occupancy_info() (in module cifkit.utils.cif_parser) plot() (in module cifkit.figures.polyhedron) plot_histogram() (in module cifkit.figures.histogram)

plot_polyhedron() (cifkit.models.cif.Cif method) preprocess_label_element_loop_values() (in module cifkit.preprocessors.format) PREPROCESSING (cifkit.utils.log_messages.CifEnsembleLog attribute) (cifkit.utils.log_messages.CifLog attribute)

R

radius_sum (cifkit.models.cif.Cif property) radius_values (cifkit.models.cif.Cif property) release notes

remove_author_loop() (in module cifkit.utils.cif_editor) remove_duplicate_connections() (in module cifkit.preprocessors.environment) round_dict_values() (in module cifkit.utils.unit) round_float() (in module cifkit.utils.unit)

S

shift_and_append_points() (in module cifkit.preprocessors.supercell) shortest_bond_pair_distance (cifkit.models.cif.Cif property) shortest_distance (cifkit.models.cif.Cif property) shortest_site_pair_distance (cifkit.models.cif.Cif property) site_mixing_type_stats (cifkit.models.cif_ensemble.CifEnsemble property) sort_element_pair_tuples() (in module cifkit.utils.sort)

space_group_name_stats (cifkit.models.cif_ensemble.CifEnsemble property) space_group_number_stats (cifkit.models.cif_ensemble.CifEnsemble property) strip_numbers_and_symbols() (in module cifkit.utils.string_parser) structure_stats (cifkit.models.cif_ensemble.CifEnsemble property) supercell_atom_counts (cifkit.models.cif_ensemble.CifEnsemble property) supercell_size_stats (cifkit.models.cif_ensemble.CifEnsemble property) SYMMETRY_OPERATION_ERROR (cifkit.utils.error_messages.CifParserError attribute)

T

tag_stats (cifkit.models.cif_ensemble.CifEnsemble property)

trim_string() (in module cifkit.utils.string_parser)

U

unique_CN_values_by_method_methods_stat (cifkit.models.cif_ensemble.CifEnsemble property) unique_CN_values_by_min_dist_method_stat (cifkit.models.cif_ensemble.CifEnsemble property) unique_composition_types (cifkit.models.cif_ensemble.CifEnsemble property) unique_elements (cifkit.models.cif_ensemble.CifEnsemble property) unique_elements_stats (cifkit.models.cif_ensemble.CifEnsemble property)

unique_formulas (cifkit.models.cif_ensemble.CifEnsemble property) unique_site_mixing_types (cifkit.models.cif_ensemble.CifEnsemble property) unique_space_group_names (cifkit.models.cif_ensemble.CifEnsemble property) unique_space_group_numbers (cifkit.models.cif_ensemble.CifEnsemble property) unique_structures (cifkit.models.cif_ensemble.CifEnsemble property) unique_tags (cifkit.models.cif_ensemble.CifEnsemble property)