i}dZddlZddlmZddlmZmZddlmZddl m Z m Z Gd d eZ Gd d eZ dS) aA XTC trajectory files --- :mod:`MDAnalysis.coordinates.XTC` ========================================================== Read and write GROMACS XTC trajectories. See Also -------- MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files. MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats N)base) XDRBaseReader XDRBaseWriter)XTCFile)triclinic_vectors triclinic_boxcFeZdZdZdZdZdddZeZ d fd Z d Z xZ S) XTCWriteraWriter for the Gromacs XTC trajectory format. XTC is a compressed trajectory format from Gromacs. The trajectory is saved with reduced precision (3 decimal places by default) compared to other lossless formarts like TRR and DCD. The main advantage of XTC files is that they require significantly less disk space and the loss of precision is usually not a problem. XTCTpsnmtimelengthNc `tt|j||f||d|||_dS)aR Parameters ---------- filename : str filename of the trajectory n_atoms : int number of atoms to write convert_units : bool (optional) convert into MDAnalysis units dt : float (optional) timestep in MDAnalysis units to write trajectory with; if `dt` is ``None``, time for a frame is set from the timestep; else, the time for a frame is `dt` * frame precision : float (optional) set precision of saved trjactory to this number of decimal places. ) convert_unitsdtN)superr __init__ precision)selffilenamen_atomsrrrkwargs __class__s d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/XTC.pyrzXTCWriter.__init__9sO2 (i' g -:r  EK   #c( |j}n>#t$r1 |jj}n #t$rd}t|dwxYwYnwxYw|j}|j|j}n|j|jz}|j d|j}|j }|j r.| |d}||d}t|}d|jz} |j||||| dS)a5Write information associated with ``ag`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe See Also -------- .write(AtomGroup/Universe) The normal write() method takes a more general input .. versionchanged:: 1.0.0 Added ability to use either AtomGroup or Universe. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. z-Input obj is neither an AtomGroup or UniverseNstepF)inplaceg$@)tsAttributeError trajectory TypeError positionscopy_dtrframedataget dimensions_convert_unitsconvert_pos_to_nativeconvert_dimensions_to_unitcellr r_xdrwrite) ragr$errmsgxyzrr"r.boxrs r_write_next_framezXTCWriter._write_next_frameWs>& 2BB 2 2 2 2]%! 2 2 2H''T1 2 2l!! 8 7DD8bh&Dw{{628,,]   P,,S%,@@C<` for more information about offsets. r rrrNc>|j|jdz krttjd||j}|jr |j|j }n|j }|xjdz c_| |||S)a  copy next frame into timestep versionadded:: 2.4.0 XTCReader implements this method so that it can use read_direct_x method of XTCFile to read the data directly into the timestep rather than copying it from a temporary array. rz"trying to go over trajectory limit) _framen_framesIOErrorerrnoEIOr$ has_positionsr2 read_direct_xr(read _frame_to_ts)rr$r+s r_read_next_timestepzXTCReader._read_next_timesteps ;$-!+ + +%)%IJJ J :B  %I++BL99EEINN$$E q  %$$$ r c|j|_|jd}| |j|_n|j|z|_|j|jd<t |j|_|j |j |j |_ n |j |_ |j rC| |j |j"| |jdd|S)z%convert a xtc-frame to a mda TimeSteprNr"r)rEr+_kwargsrr"r,r r7r._subxr(rconvert_pos_from_native)rr+r$rs rrMzXTCReader._frame_to_tss; \$  :jBGGkB&BG*%uy1 9  749-BLL 7BL   @  ( ( 6 6 6}(,,R]2A2->??? r )N) r9r:r;r<r=r?r _writerrr@rNrMr rrCrCs_"FT * *EG E*r rC)r<rHrXDRrrlib.formats.libmdaxdrr lib.mdamathr r r rCrUr rrZs.   --------++++++::::::::\9\9\9\9\9 \9\9\9~@@@@@ @@@@@r