molsysmt.structure.move_away#

molsysmt.structure.move_away(molecular_system, selection='all', center_of_selection='all', weights=None, structure_indices=0, reference_molecular_system=None, reference_center_of_selection='all', reference_weights=None, reference_structure_indices=None, direction=None, distance='3 angstroms', in_place=False, syntax='MolSysMT', skip_digestion=False)[source]#

Translate a selection of atoms away from a reference center by a fixed distance.

Two operating modes are available depending on whether direction is provided:

  • Auto direction (direction=None): the displacement direction is computed automatically as the unit vector pointing from the center of reference_center_of_selection to the center of center_of_selection. The atoms in selection are then translated by distance along that direction.

  • Explicit direction: the selection is first centered on the reference center (via molsysmt.structure.center), then translated by distance along the supplied unit vector. Only single-frame / single-group use is supported in this mode.

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.

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

  • reference_molecular_system (molecular system or None, default=None) – Reference molecular system; None uses the input molecular system.

  • reference_center_of_selection (str, list, tuple, or numpy.ndarray, default='all') – Atoms whose center defines the reference position.

  • reference_weights (str, list, tuple, numpy.ndarray, or None, default=None) – Weights used to calculate the reference center.

  • reference_structure_indices (int, list, tuple, numpy.ndarray, or None, default=None) – Zero-based structures used to calculate the reference center.

  • direction (array-like or None, default=None) – Direction of displacement; None uses the vector between the two centers.

  • distance (PyUnitWizard quantity, default='3 angstroms') – Requested separation between the selected centers, in units of length.

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

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

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

Returns:

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

Return type:

molecular system or None

Raises:

NotImplementedMethodError – When called with an explicit direction and more than one frame or more than one group — not yet implemented for that case.

Added in version 1.0.0.

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