Source code for MDAnalysis.transformations.rotate

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Trajectory rotation --- :mod:`MDAnalysis.transformations.rotate`

Rotates the coordinates by a given angle arround an axis formed by a direction and a

.. autofunction:: rotateby

from __future__ import absolute_import
from six import raise_from

import math
import numpy as np
from functools import partial

from ..lib.transformations import rotation_matrix
from ..lib.util import get_weights

[docs]def rotateby(angle, direction, point=None, ag=None, weights=None, wrap=False): ''' Rotates the trajectory by a given angle on a given axis. The axis is defined by the user, combining the direction vector and a point. This point can be the center of geometry or the center of mass of a user defined AtomGroup, or an array defining custom coordinates. Examples -------- e.g. rotate the coordinates by 90 degrees on a axis formed by the [0,0,1] vector and the center of geometry of a given AtomGroup: .. code-block:: python ts = u.trajectory.ts angle = 90 ag = u.atoms() d = [0,0,1] rotated = MDAnalysis.transformations.rotate(angle, direction=d, ag=ag)(ts) e.g. rotate the coordinates by a custom axis: .. code-block:: python ts = u.trajectory.ts angle = 90 p = [1,2,3] d = [0,0,1] rotated = MDAnalysis.transformations.rotate(angle, direction=d, point=point)(ts) Parameters ---------- angle: float rotation angle in degrees direction: array-like vector that will define the direction of a custom axis of rotation from the provided point. Expected shapes are (3, ) or (1, 3). ag: AtomGroup, optional use the weighted center of an AtomGroup as the point from where the rotation axis will be defined. If no AtomGroup is given, the `point` argument becomes mandatory point: array-like, optional list of the coordinates of the point from where a custom axis of rotation will be defined. Expected shapes are (3, ) or (1, 3). If no point is given, the `ag` argument becomes mandatory. weights: {"mass", ``None``} or array_like, optional define the weights of the atoms when calculating the center of the AtomGroup. With ``"mass"`` uses masses as weights; with ``None`` weigh each atom equally. If a float array of the same length as `ag` is provided, use each element of the `array_like` as a weight for the corresponding atom in `ag`. Default is None. wrap: bool, optional If `True`, all the atoms from the given AtomGroup will be moved to the unit cell before calculating the center of mass or geometry. Default is `False`, no changes to the atom coordinates are done before calculating the center of the AtomGroup. Returns ------- MDAnalysis.coordinates.base.Timestep Warning ------- Wrapping/unwrapping the trajectory or performing PBC corrections may not be possible after rotating the trajectory. ''' angle = np.deg2rad(angle) try: direction = np.asarray(direction, np.float32) if direction.shape != (3, ) and direction.shape != (1, 3): raise ValueError('{} is not a valid direction'.format(direction)) direction = direction.reshape(3, ) except ValueError: raise_from( ValueError('{} is not a valid direction'.format(direction)), None) if point is not None: point = np.asarray(point, np.float32) if point.shape != (3, ) and point.shape != (1, 3): raise ValueError('{} is not a valid point'.format(point)) point = point.reshape(3, ) elif ag: try: atoms = ag.atoms except AttributeError: raise_from(ValueError('{} is not an AtomGroup object'.format(ag)), None) else: try: weights = get_weights(atoms, weights=weights) except (ValueError, TypeError): raise_from( TypeError("weights must be {'mass', None} or an iterable of the " "same size as the atomgroup."), None) center_method = partial(, weights, pbc=wrap) else: raise ValueError('A point or an AtomGroup must be specified') def wrapped(ts): if point is None: position = center_method() else: position = point matrix = rotation_matrix(angle, direction, position) rotation = matrix[:3, :3].T translation = matrix[:3, 3] ts.positions=, rotation) ts.positions += translation return ts return wrapped