geom.gui.structure_generator

Programmatic structure generation helpers used by the native GUI.

Attributes

_GENERATION_LOCK
_CONVERSION_LOCK
GUI_TMP_ROOT

Classes

AtomRecord
StructureResult

Functions

supported_metals(→ list[str])	Return metals supported by GEOM, optionally filtered by crystal arrangement.
supported_atomistic_metals(→ list[str])	Return FCC/BCC metals supported by the bulk-lattice atomistic generators.
supported_fcc_metals(→ list[str])	Return FCC metals used by the ASE cluster generators.
generate_structure(→ StructureResult)	Run GEOM's existing CLI generator and return the newest generated XYZ file.
convert_molecule_to_xyz(→ pathlib.Path)	Convert a PDB/SMI-like molecule file to XYZ through GEOM's RDKit command path.
smiles_to_xyz(→ pathlib.Path)	Write a SMILES string into GEOM's GUI temp folder and convert it to XYZ.
manipulate_xyz(→ pathlib.Path)	Run an existing GEOM manipulation command in the GUI temp folder.
translate_pair_controlled_distance(...)	Run GEOM -t for two XYZ files, translating the second to a controlled distance.
cleanup_gui_tmp(→ None)	Remove GUI-generated temporary conversion files.
_xyz_snapshot(→ dict[pathlib.Path, int])
_newest_generated_xyz(→ pathlib.Path)
read_xyz(→ tuple[AtomRecord, Ellipsis])	Read the atom records from an XYZ file.

Module Contents

geom.gui.structure_generator._GENERATION_LOCK

geom.gui.structure_generator._CONVERSION_LOCK

geom.gui.structure_generator.GUI_TMP_ROOT

class geom.gui.structure_generator.AtomRecord

element: str

x: float

y: float

z: float

class geom.gui.structure_generator.StructureResult

xyz_path: pathlib.Path

atoms: tuple[AtomRecord, Ellipsis]

command: tuple[str, Ellipsis]

property atom_count: int

geom.gui.structure_generator.supported_metals(arrangements: set[str] | None = None) → list[str]

Return metals supported by GEOM, optionally filtered by crystal arrangement.

geom.gui.structure_generator.supported_atomistic_metals() → list[str]

Return FCC/BCC metals supported by the bulk-lattice atomistic generators.

geom.gui.structure_generator.supported_fcc_metals() → list[str]

Return FCC metals used by the ASE cluster generators.

geom.gui.structure_generator.generate_structure(command_args: list[str], output_root: pathlib.Path) → StructureResult

Run GEOM’s existing CLI generator and return the newest generated XYZ file.

geom.gui.structure_generator.convert_molecule_to_xyz(input_path: pathlib.Path) → pathlib.Path

Convert a PDB/SMI-like molecule file to XYZ through GEOM’s RDKit command path.

geom.gui.structure_generator.smiles_to_xyz(smiles: str) → pathlib.Path

Write a SMILES string into GEOM’s GUI temp folder and convert it to XYZ.

geom.gui.structure_generator.manipulate_xyz(input_path: pathlib.Path, command_args: Callable[[str], list[str]]) → pathlib.Path

Run an existing GEOM manipulation command in the GUI temp folder.

geom.gui.structure_generator.translate_pair_controlled_distance(fixed_path: pathlib.Path, moving_path: pathlib.Path, distance: float, axis: str) → tuple[pathlib.Path, pathlib.Path]

Run GEOM -t for two XYZ files, translating the second to a controlled distance.

geom.gui.structure_generator.cleanup_gui_tmp() → None

Remove GUI-generated temporary conversion files.

geom.gui.structure_generator._xyz_snapshot(results_dir: pathlib.Path) → dict[pathlib.Path, int]

geom.gui.structure_generator._newest_generated_xyz(results_dir: pathlib.Path, before: dict[pathlib.Path, int]) → pathlib.Path

geom.gui.structure_generator.read_xyz(path: pathlib.Path) → tuple[AtomRecord, Ellipsis]

Read the atom records from an XYZ file.