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) – Input system in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms that will be physically displaced.

  • center_of_selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms whose center defines the starting point of the displacement vector (ignored when direction is provided).

  • weights (array-like, optional) – Per-atom weights for computing the center of center_of_selection.

  • structure_indices (int or array-like, default 0) – Frame index (or indices) of the system to operate on.

  • reference_molecular_system (molecular system or None, default None) – System that defines the reference center. When None, molecular_system itself is used.

  • reference_center_of_selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms in the reference system whose center serves as the origin of the displacement direction.

  • reference_weights (array-like, optional) – Per-atom weights for computing the reference center.

  • reference_structure_indices (int, array-like or None, default None) – Frame indices for the reference system. When None, the same value as structure_indices is used.

  • direction (array-like or None, default None) – Explicit unit displacement vector of shape (1, 3). When None, the direction is derived from the two centers.

  • distance (str or quantity, default '3 angstroms') – Distance by which the atoms are displaced. Accepts any PyUnitWizard-parseable length quantity (e.g. '3 angstroms', puw.quantity(0.3, 'nm')).

  • 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 updated coordinates.

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

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

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.

  • .. versionadded: – 1.0.0:

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