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) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • center_of_selection (str, list, tuple, or numpy.ndarray, or None, default='all') – Atoms whose center defines the translation reference.

  • weights (numpy.ndarray, list, or tuple, default=None) – Atomic mass weights array for center calculation.

  • center_coordinates (PyUnitWizard quantity or None, default=None) – Coordinates to which the selected center is translated, in units of length.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • engine (str, default='MolSysMT') – Backend used to perform the calculation.

  • in_place (bool, default=False) – Whether to modify the input molecular system in place.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

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.

Added in version 1.0.0.

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