cifkit package

Subpackages

• cifkit.coordination package
  • Submodules
    • cifkit.coordination.bond_distance module
      • get_shortest_distance_per_bond_pair()
    • cifkit.coordination.composition module
      • compute_avg_CN()
      • count_connections_per_site()
      • get_bond_counts()
      • get_bond_fractions()
      • get_unique_CN_values()
    • cifkit.coordination.connection module
      • get_CN_connections_by_best_methods()
    • cifkit.coordination.filter module
      • find_best_polyhedron()
      • get_CN_connections_by_min_dist_method()
    • cifkit.coordination.geometry module
      • compute_center_of_mass_and_distance()
      • compute_polyhedron_metrics()
      • get_polyhedron_coordinates_labels()
    • cifkit.coordination.method module
      • compute_CN_max_gap_per_site()
      • compute_normalized_value()
      • get_rad_sum_value()
    • cifkit.coordination.site module
      • get_min_distance_pair()
      • get_min_distance_pair_per_site_label()
    • cifkit.coordination.site_distance module
      • get_shortest_distance()
      • get_shortest_distance_per_site()
  • Module contents
• cifkit.data package
  • Subpackages
    • cifkit.data.demo package
      • Module contents
  • Submodules
    • cifkit.data.example module
      • Example
    • cifkit.data.mendeleev module
      • get_mendeleev_numbers()
    • cifkit.data.mendeleeve_handler module
      • get_mendeleev_nums_from_pair_tuple()
    • cifkit.data.radius module
      • get_radius_data()
    • cifkit.data.radius_handler module
      • compute_radius_sum()
      • get_CIF_pauling_radius()
      • get_is_radius_data_available()
      • get_radius_values_per_element()
    • cifkit.data.radius_optimization module
      • constraint()
      • generate_adjacent_pairs()
      • get_refined_CIF_radius()
      • objective()
  • Module contents
• cifkit.figures package
  • Submodules
    • cifkit.figures.histogram module
      • generate_histogram()
      • plot_histogram()
    • cifkit.figures.polyhedron module
      • generate_color_mapping()
      • generate_contrasting_colors()
      • plot()
  • Module contents
• cifkit.models package
  • Submodules
    • cifkit.models.cif module
      • Cif
      • ensure_connections()
    • cifkit.models.cif_ensemble module
      • CifEnsemble
  • Module contents
• cifkit.occupancy package
  • Submodules
    • cifkit.occupancy.mixing module
      • compute_coord_occupancy_sum()
      • frac_coordinates()
      • get_mixing_type_per_pair_dict()
      • get_site_mixing_type()
  • Module contents
• cifkit.preprocessors package
  • Submodules
    • cifkit.preprocessors.environment module
      • get_most_connected_point_per_site()
      • get_nearest_dists_per_site()
      • get_site_connections()
      • remove_duplicate_connections()
    • cifkit.preprocessors.environment_util module
      • calculate_normalized_dist_diffs()
      • calculate_normalized_distances()
      • flat_site_connections()
    • cifkit.preprocessors.error module
      • move_files_based_on_errors()
    • cifkit.preprocessors.format module
      • preprocess_label_element_loop_values()
    • cifkit.preprocessors.supercell module
      • find_symmetry_operations()
      • flatten_original_coordinates()
      • get_supercell_points()
      • get_unitcell_coords_after_sym_operations_per_label()
      • get_unitcell_coords_for_all_labels()
      • shift_and_append_points()
    • cifkit.preprocessors.supercell_util module
      • get_cell_atom_count()
  • Module contents
• cifkit.utils package
  • Submodules
    • cifkit.utils.bond_pair module
      • get_bond_pairs()
      • get_pairs_sorted_by_mendeleev()
      • order_tuple_pair_by_mendeleev()
    • cifkit.utils.cif_editor module
      • add_hashtag_in_first_line()
      • edit_cif_file_based_on_db()
      • remove_author_loop()
    • cifkit.utils.cif_parser module
      • check_unique_atom_site_labels()
      • get_cif_block()
      • get_formula_structure_weight_s_group()
      • get_label_occupancy_coordinates()
      • get_line_content_from_tag()
      • get_loop_tags()
      • get_loop_value_dict()
      • get_loop_values()
      • get_start_end_line_indexes()
      • get_tag_from_third_line()
      • get_unique_elements_from_loop()
      • get_unique_formulas_structures_weights_s_groups()
      • get_unique_label_count()
      • get_unique_site_labels()
      • get_unitcell_angles_rad()
      • get_unitcell_lengths()
      • parse_atom_site_occupancy_info()
    • cifkit.utils.cif_sourcer module
      • get_cif_db_source()
    • cifkit.utils.distance module
      • calc_dist_two_cart_points()
    • cifkit.utils.error_messages module
      • CifParserError
      • FileError
      • GeneralError
      • OccupancyError
    • cifkit.utils.folder module
      • check_file_exists()
      • check_file_not_empty()
      • copy_files()
      • get_file_count()
      • get_file_path()
      • get_file_paths()
      • make_output_folder()
      • move_files()
    • cifkit.utils.formula module
      • get_normalized_formula()
      • get_parsed_formula()
      • get_parsed_norm_formula()
      • get_subscripted_formula()
      • get_unique_element_count()
      • get_unique_elements()
      • get_unique_elements_from_formulas()
      • get_validated_formula_label()
    • cifkit.utils.log_messages module
      • CifEnsembleLog
      • CifLog
    • cifkit.utils.prompt module
      • log_connected_points()
      • log_save_file_message()
    • cifkit.utils.random module
      • generate_random_numbers()
    • cifkit.utils.sort module
      • sort_element_pair_tuples()
    • cifkit.utils.string_parser module
      • clean_parsed_structure()
      • get_atom_type_from_label()
      • get_string_to_formatted_float()
      • strip_numbers_and_symbols()
      • trim_string()
    • cifkit.utils.unit module
      • fractional_to_cartesian()
      • get_radians_from_degrees()
      • round_dict_values()
      • round_float()
  • Module contents

Submodules

• cifkit.version module

Module contents

Python package for doing science.