i]^dZddlZddlmZddlmZddlmZddl m Z Gd d e Z dS) zTrajectory rotation --- :mod:`MDAnalysis.transformations.rotate` ================================================================ Rotates the coordinates by a given angle arround an axis formed by a direction and a point. .. autoclass:: rotateby N)partial)rotation_matrix) get_weights)TransformationBasec6eZdZdZ dfd ZdZxZS) rotatebya 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. Note ---- ``max_threads`` is set to 1 for this transformation with which it performs better. 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 from MDAnalysis import transformations ts = u.trajectory.ts angle = 90 ag = u.atoms d = [0,0,1] rotated = transformations.rotate.rotateby(angle, direction=d, ag=ag)(ts) e.g. rotate the coordinates by a custom axis: .. code-block:: python from MDAnalysis import transformations ts = u.trajectory.ts angle = 90 p = [1,2,3] d = [0,0,1] rotated = transformations.rotate.rotateby(angle, direction=d, point=p)(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.timestep.Timestep Warning ------- Wrapping/unwrapping the trajectory or performing PBC corrections may not be possible after rotating the trajectory. .. versionchanged:: 2.0.0 The transformation was changed from a function/closure to a class with ``__call__``. .. versionchanged:: 2.0.0 The transformation was changed to inherit from the base class for limiting threads and checking if it can be used in parallel analysis. NFrTc t||||_||_||_||_||_||_tj |j|_ tj |jtj |_|jj dkr7|jj dkr'td|j|jd|_n&#t$rt|jddwxYw|jtj |jtj |_|jj dkr7|jj dkr'td|j|jd|_dS|jr |jj|_ t#|j|j|_nM#tt$f$rd } t%| dwxYw#t&$rt|jd dwxYwt)|jj|j|j |_dStd ) N) max_threadsparallelizable))rrz{} is not a valid directionrz is not a valid directionz{} is not a valid point)weightszPweights must be {'mass', None} or an iterable of the same size as the atomgroup.z is not an AtomGroup object)wrapz)A point or an AtomGroup must be specified)super__init__angle directionpointagrrnpdeg2radasarrayfloat32shape ValueErrorformatreshapeatomsr TypeErrorAttributeErrorrcenter center_method) selfrrrrrrr r errmsg __class__s k/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/transformations/rotate.pyrzrotateby.__init__~s #N     "   Z ++  Z CCDN~#t++0D0N0N 188HH"^33DNN   ><<<   : !DJ ;;DJz4''DJ,<,F,F !:!A!A$*!M!MNNN++DJJJW J 6!W] 6#. DL$$$DLL#I.666=$F++5 6"    w;;; ") !4>#D!H G77$H#Ic|j|}n|j}t|j|j|}|ddddfj}|dddf}t j|j||_|xj|z c_|S)Nr) rr#rrrTrdot positions)r$tspositionmatrixrotation translations r' _transformzrotateby._transforms : ))++HHzH T^XFF"1"bqb&>#RaRUm vblH55  #  )NNNFrT)__name__ __module__ __qualname____doc__rr1 __classcell__)r&s@r'r r +szPPl  AJAJAJAJAJAJF       r2r ) r6numpyr functoolsrlib.transformationsrlib.utilrbaserr r2r'r>s0  111111""""""$$$$$$`````!`````r2