cifkit.utils.cif_parser module
Parses attributes from a .cif file.
- cifkit.utils.cif_parser.check_unique_atom_site_labels(file_path: str)[source]
Check whether all parsed atom site labels are unique.
- cifkit.utils.cif_parser.get_cif_block(file_path: str) Block[source]
Return CIF block from file path.
- cifkit.utils.cif_parser.get_formula_structure_weight_s_group(block: Block) tuple[str, str, float, int, str][source]
Return the unit cell lengths.
- cifkit.utils.cif_parser.get_label_occupancy_coordinates(loop_values: list, i) tuple[str, float, tuple[float, float, float]][source]
Return atom information (label, occupancy, coordinates) for the i-th atom.
- cifkit.utils.cif_parser.get_line_content_from_tag(file_path: str, start_keyword: str) list[str][source]
Returns a list containing file content with starting keyword.
This function only appropriate for PCD format for removing the author section.
- cifkit.utils.cif_parser.get_loop_tags() list[str][source]
Return tags commonly used for atomic description.
- cifkit.utils.cif_parser.get_loop_value_dict(loop_values: list) dict[str, dict[str, Any]][source]
Create a dictionary containing CIF loop values for each label.
- cifkit.utils.cif_parser.get_loop_values(block: Block) list[Column][source]
Retrieve a list of predefined loop tags for atomic site description.
If a tag is not found, None is inserted in its place in the list.
- cifkit.utils.cif_parser.get_start_end_line_indexes(file_path: str, start_keyword: str) tuple[int, int][source]
Find the starting and ending indexes of the lines in atom_site_loop.
- cifkit.utils.cif_parser.get_tag_from_third_line(file_path: str, db_source='PCD') str[source]
Extract the tag from the provided CIF file path appropriate for PCD db source only.
- cifkit.utils.cif_parser.get_unique_elements_from_loop(loop_values: list) set[str][source]
Return a list of alphabetically sorted unique elements from loop values.
- cifkit.utils.cif_parser.get_unique_formulas_structures_weights_s_groups(file_path_list: list[str]) tuple[set[str], set[str], set[float], set[int], set[str]][source]
Find all unique structures, formulas, weights, space groups.
This function requires no initialization and should be more efficient in analyzing and filtering a dataset.
- cifkit.utils.cif_parser.get_unique_label_count(loop_values: list) int[source]
Count the number of labels in the loop.
- cifkit.utils.cif_parser.get_unique_site_labels(loop_values: list) list[str][source]
Return a list of atom labels from loop values.
- cifkit.utils.cif_parser.get_unitcell_angles_rad(block: Block) list[float][source]
Return the unit cell angles.