molsysmt.structure.translate#

molsysmt.structure.translate(molecular_system, translation=None, selection='all', structure_indices='all', syntax='MolSysMT', in_place=False, skip_digestion=False)[source]#

Apply a translation vector to atomic coordinates of a selection.

The function supports three translation broadcasting modes determined automatically from the shape of translation:

  • Single vector — shape (1, 1, 3): the same displacement is applied to all atoms in all frames.

  • Per-frame vector — shape (n_structures, 1, 3): each frame receives its own displacement; all atoms within a frame move by the same amount.

  • Per-atom-per-frame array — shape (n_structures, n_atoms, 3): each atom in each frame can have a different displacement.

Parameters:

  • molecular_system (molecular system) – Input system in any form supported by MolSysMT.

  • translation (quantity) – Displacement vector as a PyUnitWizard length quantity. Must have a shape compatible with one of the three broadcasting modes described above.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms whose coordinates are translated.

  • structure_indices ('all' or array-like, default 'all') – Frame indices over which the translation is applied.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selection is a string.

  • in_place (bool, default False) – If True the molecular system is modified in-place and None is returned. If False a new copy is returned with the translated coordinates.

  • skip_digestion (bool, default False) – Whether to skip argument digestion (for internal use on trusted hot paths).

Returns:

A new molecular system with the translated coordinates when in_place=False; None when in_place=True.

Return type:

molecular system or None

Raises:

  • StructuralInconsistencyError – If the shape of translation is not compatible with any of the supported broadcasting modes for the given coordinate array.

  • .. versionadded: – 1.0.0:

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