cryspy-extract-struc

Last updated: October 16, 2026

cryspy-extract-struc Command

From v1.5.0, cryspy-extract-struc extracts structures from init_struc_data.pkl or opt_struc_data.pkl and saves them as CIF files. This command integrates CrySPY Utility’s extract_struc.py into CrySPY. It can also print structure information without writing files.

Usage and Options

cryspy-extract-struc infile [options]

The input file can be specified with a relative or absolute path. CIF files are saved in the directory where the command is run. Specify exactly one of -i, -a, or -t; these options cannot be combined.

Argument or option	Description
`infile`	A structure-data pickle file, such as `init_struc_data.pkl` or `opt_struc_data.pkl`. Gzip-compressed files are also supported.
`-i INDEX [INDEX ...]`, `--index INDEX [INDEX ...]`	Structure IDs to extract. Multiple IDs can be specified.
`-a`, `--all_id`	Extract all structures in the input file.
`-t TOP`, `--top TOP`	Extract the specified number of structures in ascending order of `E_eV_atom` in `rslt_data.pkl`.
`-p`, `--print`	Print structure information without writing CIF files.
`-r`, `--rank`	Use with `-t` to prefix output filenames with the rank.
`-s`, `--symmetrized`	Write CIF files with symmetry information.
`--tolerance TOLERANCE`	Tolerance for symmetry detection with `-s`. The default is `0.01`.
`-h`, `--help`	Show help.

Examples

Extracting by Structure ID

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl -i 0 1

Structures with IDs 0 and 1 are saved as 0.cif and 1.cif in the current directory. Missing IDs are skipped with a warning.

Printing Structure Information

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl -i 0 1 -p

With -p, structure IDs and structure information are printed without creating CIF files.

Extracting the Lowest-Energy Structures

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl -t 3

This extracts the three lowest-energy structures. rslt_data.pkl must be in the same directory as the input file. Output filenames are {ID}.cif.

Adding -r produces filenames of the form {rank}_{ID}.cif. Ranks start from 1.

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl -t 3 -r

Extracting All Structures

cryspy-extract-struc ./data/pkl_data/init_struc_data.pkl -a

All initial structures are saved as {ID}.cif.

Writing Symmetry Information

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl -i 0 1 -s --tolerance 0.01

With -s, output CIF files include symmetry information such as the space group. --tolerance is optional. Adding symmetry information may change the cell representation and the number of atoms.

Extracting from Gzip-Compressed Files

cryspy-extract-struc ./data/pkl_data/opt_struc_data.pkl.gz -i 0 1

Gzip-compressed structure data can be read directly without decompression. Options such as -a, -t, -p, and -s can be used in the same way. When using -t, place rslt_data.pkl in the same directory as the compressed input file.