API reference
+This section contains the automatic API reference for Cif and CifEnsemble modules in the cifkit package.
+ cifkit
+
+
+
+
+
+ Cif
+
+
+
+
+
+
+ CN_best_methods
+
+
+ property
+
+
+
+
+
+ Determines the optimal coordination method for each atomic site.
+For each atomic site, the coordination polyhedron is generated for each method
+in self.CN_max_gap_per_site. The method with the smallest value of
+polyhedron_metrics["distance_from_avg_point_to_center"], indicating the highest
+symmetry of the polyhedron, is selected as the "best method" among the four
+methods used to determine the CN gap in self.CN_max_gap_per_site.
Returns:
+| Type | +Description | +
|---|---|
+ dict[str, dict[str, float | int | str]]]
+ |
+
+
+
+ Dictionary where each key represents an atomic site, and the corresponding +value is a dictionary containing: +
|
+
Examples:
+>>> CN_best_methods = cif_URhIn.CN_best_methods
+>>> CN_best_methods["In1"]["number_of_vertices"] == 14
+>>> CN_best_methods["Rh2"]["number_of_vertices"] == 9
+>>> CN_best_methods["In1"]["method_used"] == "dist_by_shortest_dist"
+>>> CN_best_methods["Rh2"]["method_used"] == "dist_by_shortest_dist"
+
+ CN_max_gap_per_site
+
+
+ property
+
+
+
+
+
+ Determines the maximum gap in coordination number (CN) for each +atomic site.
+For each atomic site, considers the first 20 nearest neighbors. The distances +to these neighbors are normalized based on four methods:
+-
+
dist_by_shortest_dist: Normalization by the shortest distance from the site.
+dist_by_CIF_radius_sum: Normalization by the sum of CIF radii.
+dist_by_CIF_radius_refined_sum: Normalization by the sum of refined CIF radii.
+dist_by_Pauling_radius_sum: Normalization by the sum of Pauling radii.
+
The radius sums are calculated for each element pair involved. For each +normalization method, the maximum gap is determined as the largest difference +between consecutive normalized distances (i.e., the difference between the nth +and (n-1)th neighbors).
+This CN gap provides insight into the bonding relevance for each site.
+ + +Returns:
+| Type | +Description | +
|---|---|
+ dict of dict of dict
+ |
+
+
+
+ A dictionary where each key represents an atomic site, mapping to another +dictionary with normalization methods as keys. Each normalization method +contains a dictionary with: +
|
+
Examples:
+>>> cif.CN_max_gap_per_site
+{
+ "In1": {
+ "dist_by_shortest_dist": {"max_gap": 0.306, "CN": 14},
+ "dist_by_CIF_radius_sum": {"max_gap": 0.39, "CN": 14},
+ "dist_by_CIF_radius_refined_sum": {"max_gap": 0.341, "CN": 12},
+ "dist_by_Pauling_radius_sum": {"max_gap": 0.398, "CN": 14},
+ },
+ "U1": {
+ "dist_by_shortest_dist": {"max_gap": 0.197, "CN": 11},
+ "dist_by_CIF_radius_sum": {"max_gap": 0.312, "CN": 11},
+ "dist_by_CIF_radius_refined_sum": {"max_gap": 0.27, "CN": 17},
+ "dist_by_Pauling_radius_sum": {"max_gap": 0.256, "CN": 17},
+ },
+ "Rh1": {
+ "dist_by_shortest_dist": {"max_gap": 0.315, "CN": 9},
+ "dist_by_CIF_radius_sum": {"max_gap": 0.347, "CN": 9},
+ "dist_by_CIF_radius_refined_sum": {"max_gap": 0.418, "CN": 9},
+ "dist_by_Pauling_radius_sum": {"max_gap": 0.402, "CN": 9},
+ },
+ "Rh2": {
+ "dist_by_shortest_dist": {"max_gap": 0.31, "CN": 9},
+ "dist_by_CIF_radius_sum": {"max_gap": 0.324, "CN": 9},
+ "dist_by_CIF_radius_refined_sum": {"max_gap": 0.397, "CN": 9},
+ "dist_by_Pauling_radius_sum": {"max_gap": 0.380, "CN": 9},
+ },
+}
+
+ connections_flattened
+
+
+ property
+
+
+
+
+
+ Transform site connections into a sorted list of tuples, each +containing a pair of alphabetically sorted element symbols and the +distance between them.
+ + +Returns:
+| Type | +Description | +
|---|---|
+ list[tuple[tuple[str, str], float]]
+ |
+
+
+
+ A sorted list of tuples, each containing a pair of alphabetically +sorted element symbols and the distance between them. + |
+
Examples:
+ +
+ radius_sum
+
+
+ property
+
+
+
+
+
+ Retrieve the sum of CIF radius, CIF_refined radius, and Pauling C12 +radius for the shortest bonding pairs of elements.
+ + +Returns:
+| Type | +Description | +
|---|---|
+ dict[str:dict[str:float]]
+ |
+
+
+
+ Dictionary where each key is a radius type and the value is a dictionary +with the key being a bond pair of elements and the value being the total +radius in Angstroms. + |
+
Examples:
+>>> cif.radius_values
+>>> {
+ "CIF_radius_sum": {
+ "In-In": 3.248,
+ "In-Rh": 2.969,
+ "In-U": 3.001,
+ "Rh-Rh": 2.69,
+ "Rh-U": 2.722,
+ "U-U": 2.754,
+ },
+ "CIF_radius_refined_sum": {
+ "In-In": 2.657,
+ "In-Rh": 2.697,
+ "In-U": 2.943,
+ "Rh-Rh": 2.737,
+ "Rh-U": 2.983,
+ "U-U": 3.229,
+ },
+ "Pauling_radius_sum": {
+ "In-In": 3.32,
+ "In-Rh": 3.002,
+ "In-U": 3.176,
+ "Rh-Rh": 2.684,
+ "Rh-U": 2.858,
+ "U-U": 3.032,
+ },
+}
+
+ radius_values
+
+
+ property
+
+
+
+
+
+ Retrieve CIF radius, CIF_refined radius, and Pauling C12 radius for +each element.
+This property uses lazy loading to compute or retrieve radius values only when
+needed, optimizing performance. The CIF radius and Pauling C12 radius are standard
+values sourced from data/radius.py for each element. In contrast, the
+CIF_refined radius is calculated based on bonding distances to ensure accuracy
+across different environments.
-
+
- CIF_radius: The standard radius value commonly determined from +elemental .cif files, the approximate size of an atom within a crystal structure. +
- CIF_radius_refined: An optimized radius calculated to ensure that, across +all bonding pairs, the sum of the two radii in a bonded pair attempts to +matches the shortest unique observed bond distances. This refinement is designed +to improve packing efficiency within a coordination polyhedron. +
- Pauling_radius_CN12: The Pauling radius of the element, calculated with a +coordination number (CN) of 12, providing a basis for comparison with other radius +types. +
Returns:
+| Type | +Description | +
|---|---|
+ dict[str, dict[str, float]]
+ |
+
+
+
+ A dictionary where each key is an atomic label (e.g., "In", "Rh", "U"), and +the corresponding value is a dictionary with radius information in Angstroms: +
|
+
Examples:
+>>> cif.radius_values
+{
+ "In": {
+ "CIF_radius": 1.624,
+ "CIF_radius_refined": 1.328,
+ "Pauling_radius_CN12": 1.66,
+ },
+ "Rh": {
+ "CIF_radius": 1.345,
+ "CIF_radius_refined": 1.369,
+ "Pauling_radius_CN12": 1.342,
+ },
+ "U": {
+ "CIF_radius": 1.377,
+ "CIF_radius_refined": 1.614,
+ "Pauling_radius_CN12": 1.516,
+ },
+}
+
+ shortest_bond_pair_distance
+
+
+ property
+
+
+
+
+
+ Determine the minimum distance for all possible unique pair of +elements. This property uses lazily loaded connections to compute the +distance if they are not already available.
+ + +Returns:
+| Type | +Description | +
|---|---|
+ dict[tuple[str, str], float]
+ |
+
+
+
+ Dictionary where each key is a tuple of element symbols and the float value +is the distance between pair of elements in Angstroms. + |
+
Examples:
+ +
+ shortest_distance
+
+
+ property
+
+
+
+
+
+ Lazily retrieve the shortest atomic distance within the crystal
+structure. This property is lazily loaded and ensures all necessary
+connections are computed beforehand using the @ensure_connections
+decorator. The computation calculates the minimum distance between any
+pairs of atoms based on the connection data.
Returns:
+| Type | +Description | +
|---|---|
+ float
+ |
+
+
+
+ The shortest distance between any two connected atoms in the +crystal structure, in Angstroms. + |
+
+ shortest_site_pair_distance
+
+
+ property
+
+
+
+
+
+ Retrieves the shortest distance from each unique atomic site in the +crystal structure. This property uses lazily loaded connections to +compute these distances if they are not already available.
+ + +Returns:
+| Type | +Description | +
|---|---|
+ dict[str, tuple[str, float]]
+ |
+
+
+
+ dictionary where each key is an atomic label and the value is a +tuple containing the label of the closest atomic site and the +shortest distance to it in Angstroms + |
+
Examples:
+ +
+ __init__(file_path, is_formatted=False, logging_enabled=False)
+
+
+
+
+ Initializes an object from a .cif file.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ file_path
+ |
+
+ str
+ |
+
+
+
+ Path to the .cif file. + |
+ + required + | +
+ is_formatted
+ |
+
+ bool
+ |
+
+
+
+ If False, preprocess the .cif file to ensure compatibility with the +gemmi library. Default is False. + |
+
+ False
+ |
+
+ logging_enabled
+ |
+
+ bool
+ |
+
+
+
+ Enables detailed logging during initialization and for distance +calculations. Default is False. + |
+
+ False
+ |
+
Attributes:
+| Name | +Type | +Description | +
|---|---|---|
file_path |
+
+ str
+ |
+
+
+
+ Path to the CIF file from which data is loaded. + |
+
logging_enabled |
+
+ bool
+ |
+
+
+
+ Enables detailed logging for initialization and distance +alculations if set to True. + |
+
file_name |
+
+ str
+ |
+
+
+
+ Base name of the CIF file, extracted from |
+
file_name_without_ext |
+
+ str
+ |
+
+
+
+ File name without its extension, useful for referencing or +generating derivative files. + |
+
db_source |
+
+ str
+ |
+
+
+
+ Source database (e.g., ICSD, MP, CCDC, PCD) from which the CIF file +originates, determined at runtime. + |
+
unitcell_lengths |
+
+ list[float]
+ |
+
+
+
+ List of unit cell lengths for the crystal structure, typically in +Angstroms. + |
+
unitcell_angles |
+
+ list[float]
+ |
+
+
+
+ List of unit cell angles in radians, ordered by alpha, beta, gamma. + |
+
site_labels |
+
+ list[str]
+ |
+
+
+
+ Lists all unique atomic site labels. + |
+
unique_elements |
+
+ set[str]
+ |
+
+
+
+ Set of unique chemical elements present in the CIF file. + |
+
atom_site_info |
+
+ dict[str, any]
+ |
+
+
+
+ Dictionary containing detailed information about each atomic site +including element, site occupancy, +fractional coordinates, symmetry, and multiplicity. + |
+
composition_type |
+
+ int
+ |
+
+
+
+ Number of unique elements present in the .cif file, e.g., 1 for +unary, 2 for binary, etc. + |
+
tag |
+
+ str
+ |
+
+
+
+ Additional tag associated with the CIF data, parsed from the third +line of PCD .cif files. + |
+
bond_pairs |
+
+ set[tuple[str, str]]
+ |
+
+
+
+ Set of tuples representing bonded pairs of elements. + |
+
site_label_pairs |
+
+ set[tuple[str, str]]
+ |
+
+
+
+ Set of tuples representing pairs of atomic site labels. + |
+
bond_pairs_sorted_by_mendeleev |
+
+ set[tuple[str, str]]
+ |
+
+
+
+ Set of bonded pairs sorted according to Mendeleev Numbers. + |
+
site_label_pairs_sorted_by_mendeleev |
+
+ set[tuple[str, str]]
+ |
+
+
+
+ Set of site label pairs sorted by Mendeleev Numbers. + |
+
site_mixing_type |
+
+ str
+ |
+
+
+
+ Descriptor of the mixing type, categorized into four types: +Full occupancy is assigned when a single atomic site occupies +the fractional coordinate with an occupancy value of 1. +Full occupancy with mixing is assigned when multiple atomic sites +collectively occupy the fractional coordinate to a sum of 1. +Deficiency without mixing is assigned when a single atomic site occupying +the fractional coordinate with a sum less than 1. +Deficiency with atomic mixing is assigned when multiple atomic sites occupy +the fractional coordinate with a sum less than 1. + |
+
is_radius_data_available |
+
+ bool
+ |
+
+
+
+ Indicates whether Pauling and CIF atomic radii are available for +all elements in the .cif file. + |
+
mixing_info_per_label_pair |
+
+ dict
+ |
+
+
+
+ Dictionary mapping pairs of labels to their mixing information. + |
+
mixing_info_per_label_pair_sorted_by_mendeleev |
+
+ dict
+ |
+
+
+
+ Same as |
+
unitcell_points |
+
+ list[list[tuple[float, float, float, str]]]
+ |
+
+
+
+ List of points defining the unit cell; each point contains +fractional coordinates and a site label. + |
+
supercell_points |
+
+ list[list[tuple[float, float, float, str]]]
+ |
+
+
+
+ List of points defining the supercell of the cell For each .cif file, +a unit cell is generated by applying the symmetry operations. +A supercell is generated by applying ±1 shifts from the unit cell. + |
+
unitcell_atom_count |
+
+ int
+ |
+
+
+
+ Total count of atoms within the unit cell. + |
+
supercell_atom_count |
+
+ int
+ |
+
+
+
+ Total count of atoms within the generated supercell +incorporating ±1, ±1, ±1 translations. + |
+
connections |
+
+ None or dict
+ |
+
+
+
+ Initially None, intended to store connection data related to +the crystal structure. Connections are computed lazily and are +only calculated when first needed by a method or property requiring them. + |
+
+ compute_connections(cutoff_radius=10.0)
+
+
+
+
+ Compute onnection network, shortest distances, bond counts, and +coordination numbers (CN). These prperties are lazily loaded to avoid +unnecessary computation during the initialization and pre-processing +step.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ cutoff_radius
+ |
+
+ float
+ |
+
+
+
+ The distance threshold in Angstroms used to consider two atoms as connected, +by default 10.0 + |
+
+ 10.0
+ |
+
+ plot_polyhedron(site_label, show_labels=True, is_displayed=False, output_dir=None)
+
+
+
+
+ Function to plot a polyhedron structure and optionally saves it.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ site_label
+ |
+
+ str
+ |
+
+
+
+ Central site label for the polyhedron + |
+ + required + | +
+ show_labels
+ |
+
+ bool
+ |
+
+
+
+ Whether to display vertex labels, by default True + |
+
+ True
+ |
+
+ is_displayed
+ |
+
+ bool
+ |
+
+
+
+ Display plot interactively, by default False + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ Directory to save the plot, by default None + |
+
+ None
+ |
+
+ CifEnsemble
+
+
+
+
+
+
+ CN_unique_values_by_best_methods: set[str]
+
+
+ property
+
+
+
+
+
+ Returns:
+| Type | +Description | +
|---|---|
+ set[str]
+ |
+
+
+
+ Unique coordination number by best methods from all .cif files. + |
+
+ CN_unique_values_by_min_dist_method: set[str]
+
+
+ property
+
+
+
+
+
+ Returns:
+| Type | +Description | +
|---|---|
+ set[str]
+ |
+
+
+
+ Unique coordination number values by minimum distance method from all .cif +files. + |
+
+ unique_composition_types: set[int]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_elements: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_formulas: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_site_mixing_types: set[int]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_space_group_names: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_space_group_numbers: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_structures: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ unique_tags: set[str]
+
+
+ property
+
+
+
+
+
+
+
+
+ __init__(cif_dir_path, add_nested_files=False, preprocess=True, logging_enabled=False)
+
+
+
+
+ Initialize a CifEnsemble object, containing a collection of Cif +objects.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ cif_dir_path
+ |
+
+ str
+ |
+
+
+
+ Path to the folder path containing .cif file(s). + |
+ + required + | +
+ add_nested_files
+ |
+
+ bool
+ |
+
+
+
+ Option to include .cif files contained in sub-directories within cif_dir_path +, by default False + |
+
+ False
+ |
+
+ preprocess
+ |
+
+ bool
+ |
+
+
+
+ Option to edit .cif files before initializing each into a Cif object, +by default True. Preprocess modifies atomic site labels in +atom_site_label. Some site labels may contain a comma or a symbol like M +due to atomic mixing. It reformats each atom_site_label so it can be +parsed into an element type matching atom_site_type_symbol. For PCD +databases, addresses in publ_author_address often have an incorrect +format requiring manual modifications. It also relocates any ill-formatted +files, such as those with duplicate labels in atom_site_label, missing +fractional coordinates, or files requiring supercell generation. + |
+
+ True
+ |
+
+ logging_enabled
+ |
+
+ bool
+ |
+
+
+
+ Option to log while pre-processing Cif objects, by default False + |
+
+ False
+ |
+
Attributes:
+| Name | +Type | +Description | +
|---|---|---|
dir_path |
+
+ str
+ |
+
+
+
+ Path to the folder containing .cif files + |
+
file_paths |
+
+ list[str]
+ |
+
+
+
+ List of file paths to .cif files + |
+
cifs |
+
+ list[Cif]
+ |
+
+
+
+ List of Cif objects + |
+
file_count |
+
+ int
+ |
+
+
+
+ Number of .cif files in the folder + |
+
logging_enabled |
+
+ bool
+ |
+
+
+
+ Option to log while pre-processing Cif objects + |
+
+ copy_cif_files(file_paths, to_directory_path)
+
+
+
+
+ Copy a set of CIF files to a destination directory.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ file_paths
+ |
+
+ set[str]
+ |
+
+
+
+ Set of file paths to CIF files. + |
+ + required + | +
+ to_directory_path
+ |
+
+ str
+ |
+
+
+
+ Destination directory path. + |
+ + required + | +
Examples:
+ + +
+ generate_CN_by_best_methods_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'CN_by_best_methods' property from CIF +files.
+This method creates a histogram based on the 'CN_by_best_methods' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_CN_by_min_dist_method_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'CN_by_min' property from CIF files.
+This method creates a histogram based on the 'CN_by_min' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_composition_type_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'composition_type' property from CIF +files.
+This method creates a histogram based on the 'composition_type' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_elements_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'unique_elements' property from CIF +files.
+This method creates a histogram based on the 'unique_elements' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_formula_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'formula' property from CIF files.
+This method creates a histogram based on the 'formula' statistics of the CIF +files. If 'output_dir' is specified, the histogram image (.png) will be saved to +that directory. If 'output_dir' is not specified, the image will be saved to the +directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_site_mixing_type_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'site_mixing_type' property from CIF +files.
+This method creates a histogram based on the 'site_mixing_type' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_space_group_name_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'space_group_name' property from CIF +files.
+This method creates a histogram based on the 'space_group_name' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_space_group_number_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'space_group_number' property from CIF +files.
+This method creates a histogram based on the 'space_group_number' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_structure_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'structure' property from CIF files.
+This method creates a histogram based on the 'structure' statistics of the CIF +files. If 'output_dir' is specified, the histogram image (.png) will be saved to +that directory. If 'output_dir' is not specified, the image will be saved to the +directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_supercell_size_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'supercell_count' property from CIF +files.
+This method creates a histogram based on the 'supercell_count' statistics of +the CIF files. If 'output_dir' is specified, the histogram image (.png) will be +saved to that directory. If 'output_dir' is not specified, the image will be saved +to the directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ generate_tag_histogram(display=False, output_dir=None)
+
+
+
+
+ Generate a histogram of the 'tag' property from CIF files.
+This method creates a histogram based on the 'tag' statistics of the CIF +files. If 'output_dir' is specified, the histogram image (.png) will be saved to +that directory. If 'output_dir' is not specified, the image will be saved to the +directory specified by 'self.dir_path'.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ display
+ |
+
+ bool
+ |
+
+
+
+ If True, the plot is displayed using plt.show(). Default is False. + |
+
+ False
+ |
+
+ output_dir
+ |
+
+ str
+ |
+
+
+
+ The directory path where the histogram should be saved. If None, +the histogram is saved in the directory defined by 'self.dir_path'. + |
+
+ None
+ |
+
+ move_cif_files(file_paths, to_directory_path)
+
+
+
+
+ Move a set of CIF files to a destination directory.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ file_paths
+ |
+
+ set[str]
+ |
+
+
+
+ Set of file paths to CIF files. + |
+ + required + | +
+ to_directory_path
+ |
+
+ str
+ |
+
+
+
+ Destination directory path. + |
+ + required + | +
Examples:
+ + +