rgpycrumbs.chemgp.match_atoms

Match atoms in structure file to target coordinates.

CLI for matching target coordinates to closest atoms in a structure file. Useful for identifying atom IDs in eOn calculations.

Added in version 1.7.0: Extracted from rgpycrumbs._aux to standalone CLI script.

Attributes

log

POSCON_FILENAME

_EXPECTED_COORD_COLS

DEFAULT_TARGET_COORDS

Functions

parse_target_coords(→ numpy.ndarray)

Parse multiline string of target coordinates.

match_atoms(→ list[dict])

Match target coordinates to closest atoms in structure.

main(structure_file, target_file, target_coords, output)

Match target coordinates to closest atoms in a structure.

Module Contents

rgpycrumbs.chemgp.match_atoms.log[source]
rgpycrumbs.chemgp.match_atoms.POSCON_FILENAME = 'pos.con'[source]
rgpycrumbs.chemgp.match_atoms._EXPECTED_COORD_COLS = 3[source]
rgpycrumbs.chemgp.match_atoms.DEFAULT_TARGET_COORDS = Multiline-String[source]
Show Value
"""
19.7267 23.4973 21.4053
21.6919 21.7746 21.7746
19.7274 21.4053 23.4968
21.6918 21.7752 25.2201
21.6915 25.2205 21.7761
18.0999 23.4978 23.4978
19.7265 25.5905 23.4985
21.6915 25.2206 25.2206
22.7758 23.4966 23.4983
20.6077 23.4982 23.4977
19.7268 23.4982 25.5902
23.6566 21.4042 23.4962
23.6566 23.4979 21.4058
23.6561 25.5897 23.4984
23.6566 23.4984 25.5906
25.2834 23.4976 23.4978
"""
rgpycrumbs.chemgp.match_atoms.parse_target_coords(text_block: str) → numpy.ndarray[source]

Parse multiline string of target coordinates.

Parameters

text_block

Multiline string with space-separated x y z coordinates

Returns

np.ndarray

Array of shape (n, 3) with target coordinates

rgpycrumbs.chemgp.match_atoms.match_atoms(structure_file: pathlib.Path, target_coords: numpy.ndarray) → list[dict][source]

Match target coordinates to closest atoms in structure.

Parameters

structure_file

Path to structure file (any ASE-readable format)

target_coords

Array of target coordinates to match

Returns

list[dict]

List of match results with atom info and distances

rgpycrumbs.chemgp.match_atoms.main(structure_file: pathlib.Path, target_file: pathlib.Path | None, target_coords: str, output: pathlib.Path | None)[source]

Match target coordinates to closest atoms in a structure.

Reads a structure file and finds the closest atoms to specified target coordinates. Useful for identifying atom IDs in eOn calculations.