i^dZddlZddlZddlmZddlmZmZddlm Z Gdd eZ dS) aYNo Jump Trajectory Unwrapping --- :mod:`MDAnalysis.transformations.nojump` ======================================================================================= Unwraps the trajectory such that atoms never move more than half a periodic box length. The consequence of this is that particles will diffuse across periodic boundaries when needed. This unwrapping method is suitable as a preprocessing step to calculate molecular diffusion, or more commonly to keep multi-domain proteins whole during trajectory analysis. The algorithm used is based on :footcite:p:`Kulke2022`. .. autoclass:: NoJump N)TransformationBase)dueDoi) NoDataErrorcreZdZdZejedde d fd ZdZxZ S) NoJumpa Returns transformed coordinates for the given timestep so that an atom does not move more than half the periodic box size between two timesteps, and will move across periodic boundary edges. The algorithm used is based on :footcite:p:`Kulke2022`, equation B6 for non-orthogonal systems, so it is general to most applications where molecule trajectories should not "jump" from one side of a periodic box to another. Note that this transformation depends on a periodic box dimension being set for every frame in the trajectory, and that this box dimension can be transformed to an orthonormal unit cell. If not, an error is emitted. Since it is typical to transform all frames sequentially when unwrapping trajectories, warnings are emitted if non-sequential timesteps are transformed using NoJump. Example ------- Suppose you had a molecular trajectory with a protein dimer that moved across a periodic boundary. This will normally appear to make the dimer split apart. This transformation uses the molecular motions between frames in a wrapped trajectory to create an unwrapped trajectory where molecules never move more than half a periodic box dimension between subsequent frames. Thus, the normal use case is to apply the transformation to every frame of a trajectory, and to do so sequentially. .. code-block:: python transformation = NoJump() u.trajectory.add_transformations(transformation) for ts in u.trajectory: print(ts.positions) In this case, ``ts.positions`` will return the NoJump unwrapped trajectory, which would keep protein dimers together if they are together in the inital timestep. The unwrapped trajectory may also be useful to compute diffusion coefficients via the Einstein relation. To reverse the process, wrap the coordinates again. Returns ------- MDAnalysis.coordinates.timestep.Timestep References ---------- .. footbibliography:: z10.1021/acs.jctc.2c00327z[Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach.) descriptionpathTNct|dd|_d|_d|_||_dS)NF) max_threadsparallelizablerA)super__init__prev old_frame older_framecheck_c)selfcheck_continuityr __class__s k/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/transformations/nojump.pyrzNoJump.__init__\sC [GGG ' cV|j}|d|j}t| tj|}n1#tjj$rd|j}t|wxYw|jdkr|j|z|_d|_ d|_ |S|j ri|j dkr^|j |j z |j|j z kr>tj dt|j|z|_|j|_ d|_ |S|j r?tj|j |jz dkrtj dt|j|z}|j}|tj||z z }||z|_||_|j |_ |j|_ |S) Nz-Periodic box dimensions not provided at step z3Periodic box dimensions are not invertible at step rrzyNoJump detected that the interval between frames is unequal.We are resetting the reference frame to the current timestep.rzNoJump transform is only accurate when positionsdo not move by more than half a box length.Currently jumping between frames with a step of more than 1.This might be fine, but depending on the trajectory stride,this might be inaccurate.)triclinic_dimensionsframernplinalginv LinAlgError positionsrrrrwarningswarn UserWarningabsround)rtsLmsgLinversefcurrentfprev newpositionss r _transformzNoJump._transformos  # 9L"(LLCc"" " #y}}Q''HHy$ # # #RRRCc"" " # 8q== x/DIDN!D I L  C''$"224>)++ MP     x/DIXDN"D I < BF4>BH#<==BB M,     <(* I  "(8e+;"<"<< #a'    > s A.A2)TN) __name__ __module__ __qualname____doc__rdciterrr1 __classcell__)rs@rr r .s++ZSY  &''4   ( ( ( ( (  (AAAAAAArr ) r5numpyr r%baserrr exceptionsrr rrr<s0  $$$$$$$$$$$$BBBBB BBBBBr