Function qsym2::bindings::python::molecule_symmetrisation::symmetrise_molecule

pub fn symmetrise_molecule(
    py: Python<'_>,
    inp_xyz: Option<PathBuf>,
    inp_mol: Option<PyMolecule>,
    out_target_sym: Option<PathBuf>,
    loose_moi_threshold: f64,
    loose_distance_threshold: f64,
    target_moi_threshold: f64,
    target_distance_threshold: f64,
    use_magnetic_group: bool,
    reorientate_molecule: bool,
    max_iterations: usize,
    consistent_target_symmetry_iterations: usize,
    verbose: u8,
    infinite_order_to_finite: Option<u32>,
) -> PyResult<PyMolecule>

Python-exposed function to perform molecule symmetrisation by bootstrapping and log the result via the qsym2-output logger at the INFO level.

See crate::drivers::molecule_symmetrisation_bootstrap for more information.

Arguments

• inp_xyz - An optional string providing the path to an XYZ file containing the molecule to be symmetrised. Only one of inp_xyz or inp_mol can be specified. Python type: Optional[str].
• inp_mol - An optional PyMolecule structure containing the molecule to be symmetrised. Only one of inp_xyz or inp_mol can be specified. Python type: PyMolecule.
• out_target_sym - An optional path for a QSym2FileType::Sym file to be saved that contains the symmetry-group detection results of the symmetrised molecule at the target thresholds. Python type: Optional[str].
• loose_moi_threshold - The loose MoI threshold. Python type: float.
• loose_distance_threshold - The loose distance threshold. Python type: float.
• target_moi_threshold - The target (tight) MoI threshold. Python type: float.
• target_distance_threshold - The target (tight) distance threshold. Python type: float.
• use_magnetic_group - A boolean indicating if the magnetic group (i.e. the group including time-reversed operations) is to be used for the symmetrisation. Python type: bool.
• reorientate_molecule - A boolean indicating if the molecule is also reoriented to align its principal axes with the Cartesian axes. Python type: bool.
• max_iterations - The maximum number of iterations for the symmetrisation process. Python type: int.
• consistent_target_symmetry_iterations - The number of consecutive iterations during which the symmetry group at the target level of threshold must be consistently found for convergence to be reached, if this group cannot become identical to the symmetry group at the loose level of threshold. Python type: int.
• verbose - The print-out level. Python type: int.
• infinite_order_to_finite - The finite order with which infinite-order generators are to be interpreted to form a finite subgroup of the prevailing infinite group. This finite subgroup will be used for the symmetrisation. Python type: Optional[int].

Returns

The symmetrised molecule.

Python type: PyMolecule

Errors

Errors if any intermediate step in the symmetrisation procedure fails.