molsysmt.structure.center#

molsysmt.structure.center(molecular_system, selection='all', center_of_selection='all', weights=None, center_coordinates=None, structure_indices='all', syntax='MolSysMT', engine='MolSysMT', in_place=False, skip_digestion=False)[source]#

Translate a selection of atoms so that a reference center lies at a target point.

The function computes the center of center_of_selection (optionally weighted), then applies a translation to selection so that the reference center moves to center_coordinates. If center_coordinates is None the reference center is moved to the origin. A second-pass correction is applied when floating-point residuals exceed 1e-12 nm.

Parameters:

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

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms that are physically moved by the translation.

  • center_of_selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms whose center defines the reference point to be relocated.

  • weights (array-like, optional) – Per-atom weights for computing the center of center_of_selection. When None, all atoms have equal weight (centroid).

  • center_coordinates (quantity or None, default None) – Target position for the center. Must be a PyUnitWizard length quantity with shape compatible with (n_structures, 1, 3). When None the center is moved to the origin.

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

  • syntax (str, default 'MolSysMT') – Selection syntax used when selection or center_of_selection are strings.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend used for center computation and translation.

  • 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:

  • NotImplementedMethodError – If an unsupported engine is requested.

  • .. versionadded: – 1.0.0:

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