geom.gui.structure_generator
============================

.. py:module:: geom.gui.structure_generator

.. autoapi-nested-parse::

   Programmatic structure generation helpers used by the native GUI.



Attributes
----------

.. autoapisummary::

   geom.gui.structure_generator._GENERATION_LOCK
   geom.gui.structure_generator._CONVERSION_LOCK
   geom.gui.structure_generator.GUI_TMP_ROOT


Classes
-------

.. autoapisummary::

   geom.gui.structure_generator.AtomRecord
   geom.gui.structure_generator.StructureResult


Functions
---------

.. autoapisummary::

   geom.gui.structure_generator.supported_metals
   geom.gui.structure_generator.supported_atomistic_metals
   geom.gui.structure_generator.supported_fcc_metals
   geom.gui.structure_generator.generate_structure
   geom.gui.structure_generator.convert_molecule_to_xyz
   geom.gui.structure_generator.smiles_to_xyz
   geom.gui.structure_generator.manipulate_xyz
   geom.gui.structure_generator.translate_pair_controlled_distance
   geom.gui.structure_generator.cleanup_gui_tmp
   geom.gui.structure_generator._xyz_snapshot
   geom.gui.structure_generator._newest_generated_xyz
   geom.gui.structure_generator.read_xyz


Module Contents
---------------

.. py:data:: _GENERATION_LOCK

.. py:data:: _CONVERSION_LOCK

.. py:data:: GUI_TMP_ROOT

.. py:class:: AtomRecord

   .. py:attribute:: element
      :type:  str


   .. py:attribute:: x
      :type:  float


   .. py:attribute:: y
      :type:  float


   .. py:attribute:: z
      :type:  float


.. py:class:: StructureResult

   .. py:attribute:: xyz_path
      :type:  pathlib.Path


   .. py:attribute:: atoms
      :type:  tuple[AtomRecord, Ellipsis]


   .. py:attribute:: command
      :type:  tuple[str, Ellipsis]


   .. py:property:: atom_count
      :type: int



.. py:function:: supported_metals(arrangements: set[str] | None = None) -> list[str]

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


.. py:function:: supported_atomistic_metals() -> list[str]

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


.. py:function:: supported_fcc_metals() -> list[str]

   Return FCC metals used by the ASE cluster generators.


.. py:function:: generate_structure(command_args: list[str], output_root: pathlib.Path) -> StructureResult

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


.. py:function:: 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.


.. py:function:: smiles_to_xyz(smiles: str) -> pathlib.Path

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


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: cleanup_gui_tmp() -> None

   Remove GUI-generated temporary conversion files.


.. py:function:: _xyz_snapshot(results_dir: pathlib.Path) -> dict[pathlib.Path, int]

.. py:function:: _newest_generated_xyz(results_dir: pathlib.Path, before: dict[pathlib.Path, int]) -> pathlib.Path

.. py:function:: read_xyz(path: pathlib.Path) -> tuple[AtomRecord, Ellipsis]

   Read the atom records from an XYZ file.