molsysmt.structure.rotate#

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

Rotate atomic coordinates of a selection by a given rotation.

The rotation is applied frame-by-frame. If a rotation_center is provided, the coordinates are first translated so that the center sits at the origin, rotated, then translated back.

Two rotation representations are accepted:

  • Array-like matrices of shape (3, 3), (n_structures, 3, 3), or (n_structures, n_atoms, 3, 3).

  • An object providing an apply(coordinates) method, such as scipy.spatial.transform.Rotation. SciPy is not required.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • rotation (array-like or rotation-like object, default=None) – Proper rotation matrices or an object providing an apply method.

  • rotation_center (PyUnitWizard quantity or None, default=None) – Point about which coordinates are rotated, in units of length.

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

  • 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’).

  • 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 rotated coordinates when in_place=False; None when in_place=True.

Return type:

molecular system or None

Raises:

  • ArgumentError – If a matrix has an invalid shape, non-finite values, is not orthonormal, or has a determinant other than +1.

  • NotImplementedMethodError – If rotation is not a supported type.

  • StructuralInconsistencyError – If the number of per-frame or per-atom matrices cannot be broadcast to the selected coordinates.

Notes

MolSysMT uses active proper rotations on row-vector coordinates. Distances and handedness are therefore preserved.

See also

molsysmt.structure.translate()

Translate selected coordinates.

molsysmt.structure.least_rmsd_fit()

Estimate and apply a least-RMSD rigid transformation.

Examples

>>> import molsysmt as msm
>>> coordinates = msm.pyunitwizard.quantity([[[1.0, 0.0, 0.0]]], 'nm')
>>> rotation = [[0.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]]
>>> rotated = msm.structure.rotate(coordinates, rotation=rotation)
>>> msm.pyunitwizard.get_value(rotated, to_unit='nm').round(12).tolist()
[[[0.0, 1.0, 0.0]]]

Tutorial with more examples

See Rotate.

Added in version 1.0.0.

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