molsysmt.structure.align_principal_axes#

molsysmt.structure.align_principal_axes(molecular_system, selection='all', principal_axes_of_selection=None, principal_axes_type='inertia', structure_indices='all', weights=None, axes=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], center=False, syntax='MolSysMT', engine='MolSysMT', in_place=False)[source]#

Aligning selected atoms to reference principal axes.

Parameters:

  • molecular_system (molecular system) – System whose coordinates will be rotated.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms to rotate.

  • principal_axes_of_selection (str, list, tuple or numpy.ndarray, optional) – Atoms used to compute principal axes; defaults to selection.

  • principal_axes_type ({'inertia'}, default 'inertia') – Type of principal axes to compute.

  • structure_indices ('all' or array-like, default 'all') – Structures/frames to align.

  • weights (array-like, optional) – Weights for axis computation.

  • axes (array-like shape (3,3), default identity) – Target axes to align to.

  • center (bool, default False) – If True, recenter coordinates after rotation.

  • syntax (str, default 'MolSysMT') – Selection syntax when using strings.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend.

  • in_place (bool, default False) – If True, modify the input system; otherwise return a rotated copy.

Returns:

Rotated system when in_place=False, otherwise None.

Return type:

molecular system or None

Raises:
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