iIdZddlZddlmZmZddlZddlmZddl m Z ddl m Z ddl mZdd lmZmZ ddlZd Zn #e$rd ZYnwxYwGd d ejZdS)a TNG trajectory files --- :mod:`MDAnalysis.coordinates.TNG` ========================================================== The TNG format :footcite:p:`Lundborg2014` is a format used in `GROMACS`_ for storage of trajectory and topology information. The TNG format allows a wide range of compression algorithms and unlike the compressed XTC format can also store velocities and forces in addition to positions. The classes in this module are based on the `pytng`_ package for reading TNG files. The reader is directed to the `pytng documentation`_ for further reading about how pytng works under the hood. Pytng is an optional dependency and must be installed to use this Reader. Use of the reader without pytng installed will raise an `ImportError`. The variable `HAS_PYTNG` indicates whether this module has pytng availble. In addition to particle-dependent trajectory information like positions, forces and velocities, the TNG format can store trajectory metadata and other arbitrary time dependent data. Additional information can range from the virial and pressure components to the molecular topology of the system. This is enabled by a block based system in which binary flags indicate the presence or absence of various data blocks. The structure of a TNG file is provided in the `TNG specification`_. The TNG paper :footcite:p:`Lundborg2014` and the `pytng documentation`_ are also good resources. The user is encouraged to read the full list of `TNG blocks`_ to understand the full power of the TNG format. Current Limitations ------------------- Currently there is only a Reader for TNG files and no Writer. This will depend on upstream changes in pytng. Additionally, it is not currently possible to read the molecular topology from a TNG file. There are also some limitations to reading TNG files with pytng. Currently we do not allow data to be read *off stride*. In essence this means that all of the critical trajectory data (positions, box, velocities (if present), forces (if present)) must share the same stride in trajectory integrator steps. These critical blocks in the TNG file are henceforth called *special blocks*. Optional blocks (all blocks that are not special blocks) will not be read if they do not share an integrator step with, or are not divisible by the shared integrator step of the special blocks. References ---------- .. footbibliography:: .. Links .. _GROMACS: https://www.gromacs.org/ .. _pytng: https://github.com/MDAnalysis/pytng .. _pytng documentation: https://www.mdanalysis.org/pytng/ .. _TNG blocks: https://www.mdanalysis.org/pytng/documentation_pages/Blocks.html .. _TNG specification: https://gitlab.com/hugomacdermott/tng/-/blob/master/Trajectoryformatspecification.mk N)ListOptional)base)Timestep) triclinic_box)store_init_arguments)DoidueTFceZdZdZdZdddddZdZd Zd Zd Z eeee gZ e j e d d eed)dedeffd ZdZdZededefdZedefdZedeefdZedeefdZedeefdZdZdedefdZdedefdZ d*d!e!edefd"Z"d#d$d!edefd%Z#d&Z$d'Z%d(Z&xZ'S)+ TNGReaderaReader for the TNG format The TNG format :footcite:p:`Lundborg2014` is a format used in `GROMACS`_ for storage of trajectory and topology information. This reader is are based on the `pytng`_ package for reading TNG files. The reader is directed to the `pytng documentation`_ and `TNG specification`_ for further reading. The TNG format allows a wide range of compression algorithms and unlike the compressed XTC format can also store velocities and forces in addition to positions. The contents of the *special blocks* (positions, box, velocities, forces) are read into the timestep if present. Additional blocks are read into the `ts.data` dictionary if they are available at the current frame. .. versionadded:: 2.4.0 TNGsecondnmznm/psz kJ/(mol*nm))timelengthvelocityforceTNG_TRAJ_BOX_SHAPETNG_TRAJ_POSITIONSTNG_TRAJ_VELOCITIESTNG_TRAJ_FORCESz10.1002/jcc.23495z The TNG paper) descriptionpathTfilename convert_unitsc tstdttj|fi||_|_tjjd_ j j _ j j _ tj j_j j_j j_j j_djD_jj fij_jjv_jr9djj<t;jdt:jj_ j!jv_"j"r8djj!<j #j!j_$j%jv_&j&r8djj%<j #j%j_'j(jv_)j)r8djj(<j #j(j_*fdjD_+,d_-j #j_.d _-/d S) zInitialize a TNG trajectory Parameters ---------- filename : str filename of the trajectory convert_units : bool (optional) convert into MDAnalysis units 1TNGReader: To read TNG files please install pytngrci|]}|dS)F).0ks d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/TNG.py z&TNGReader.__init__..s&N&N&NAq%&N&N&NT)dtypec&g|] }|jv |Sr!)_special_blocks)r"blockselfs r$ z&TNGReader.__init__..s1# # # D000 000r&rN)0 HAS_PYTNG ImportErrorsuperr __init__rrpytngTNGFileIterator_file_iteratorn_atomsn_steps_n_stepslist block_idskeys _block_names_block_dictionary block_strides_block_strides n_data_frames _data_framesr*_special_block_present _Timestep _ts_kwargsts_box_blockname_has_boxnpzerosfloat32 dimensions_positions_blockname_has_positions make_ndarray_for_block_from_name positions_velocities_blockname_has_velocities velocities_forces_blockname _has_forcesforces_additional_blocks_check_strides_and_frames_frame _box_temp_read_next_timestep)r,rrkwargs __class__s` r$r2zTNGReader.__init__s C  (i';;F;;;  *#3DM3GG*2 +3 !!4!>!C!C!E!EFF!%!4!>"1? /=&N&N9M&N&N&N# $.AAAA+t/@@ = ??CD '(; !>!>DG "74;LL   EID '(A B#DD- G  $9T=NN   FJD '(B C#DD. G   1T5FF   BFD '(> ?#DD* GN# # # # *# # #  &&((( ,MM        """""r&c|gg|jD]F}|j|}||j|}|Gt fdD}t fdD}|r|st dd|_ddz|_g|_|j D]r}|j|}||jkr>||jzrtj d|d=|j|X|j|sdS) z Check that the strides and frame numbers of the blocks in the TNG file match up so that the file can be iterated over retrieving data at each integrator step c30K|]}|dkVdSrNr!)r"vstridess r$ z6TNGReader._check_strides_and_frames..s+::Qgaj::::::r&c30K|]}|dkVdSr_r!)r"r`r@s r$rbz6TNGReader._check_strides_and_frames..s-EE!]1--EEEEEEr&z >E,U3JT000 33 M////3::/66u==== > >r&c8|jdS)zclose the readerN)r5_closer,s r$closezTNGReader.closes ""$$$$$r&returnctstdtj|d5}|j}dddn #1swxYwY|S)aparse the number of atoms in the TNG trajectory file Parameters ---------- filename : str The name of the TNG file Returns ------- n_atoms : int The number of atoms in the TNG file rrN)r/r0r3r4r6)rtngr6s r$ parse_n_atomszTNGReader.parse_n_atoms"s C  "8S 1 1 "SkG " " " " " " " " " " " " " " "sAAAc|jS)znumber of frames in trajectory Returns ------- n_frames : int The number of data containing frames in the trajectory )rjrus r$n_frameszTNGReader.n_frames9s ~r&c|jS)zlist of the blocks that are in the file Returns ------- blocks : list The block names present in the TNG trajectory )r<rus r$blockszTNGReader.blocksDs   r&cHd|jDS)zlist of the special blocks that are in the file Returns ------- special_blocks : list The special block names (positions, box, velocities, forces) present in the TNG trajectory cg|] \}}|| Sr!r!)r"r#r`s r$r-z,TNGReader.special_blocks..[s!GGGdaQGGGGr&)rBitemsrus r$rezTNGReader.special_blocksPs(HGd9??AAGGGGr&c|jS)a|list of the additional (non-special) blocks that are being read from the trajectory. This may be exclude some blocks present in the file if they do not fall on the same trajectory stride as the positions and velocities. Returns ------- additional_blocks : list The additional block names in the TNG trajectory )rkrus r$additional_blockszTNGReader.additional_blocks]s ..r&cd|j_d|_|j|j|jddS)zreopen the trajectoryrr.rN)rEframerXr5rt_openrrus r$_reopenzTNGReader._reopenlsH   ""$$$ !!$-55555r&rc||jzS)a Convert a frame number to an integrator step Parameters ---------- frame : int The frame number Returns ------- integrators_step : int The integrator step of the frame in the TNG file )ri)r,rs r$_frame_to_stepzTNGReader._frame_to_stepsst***r&icB|dz |_|}|S)zread frame i Parameters ---------- i : int The trajectory frame to be read Returns ------- ts : Timestep Data from frame i encapsulated in an MDA `:class:Timestep` rd)rXrZ)r,rrEs r$ _read_framezTNGReader._read_frames%!e  % % ' ' r&NrEc|j|jdz krtd||j}||jdz}|j|}|xjdz c_|||}|S)a Read next frame into a timestep Parameters ---------- ts : Timestep The timestep to read the data into Returns ------- ts : Timestep The timestep filled with data from the next step rdz"trying to go over trajectory limit)rXr|rhrErr5 read_step _frame_to_ts)r,rEstep iterator_steps r$rZzTNGReader._read_next_timesteps ;$-!+ + +>?? ? :B""4;?33+55d;;  q   }b 1 1 r& curr_stepzpytng.TNGCurrentIntegratorStepc|j|_|}|jr||}||_|j|jd<|jr| |j t|j dd|_ |jstd|jr"||j dd|jrQ||j|jstd|jr||j|jrQ||j|jstd|jr||j|jrV||j|jstd|jr||jj|jD]v}|j|}||jzs]|j !|}|"|j#|||j|<|jstd|d w|S) a;convert a TNGCurrentIteratorStep to an MDA Timestep Parameters ---------- curr_step : pytng.TNGCurrentIntegratorStep The current timestep in the TNG trajectory ts : Timestep The current timestep in the MDA trajectory Returns ------- ts: Timestep The current timestep in the MDA trajectory with data from TNG trajectory integrator step Raises ------ IOError The reading of one of the attributes from the TNG file failed rz Failed to read box from TNG fileNz&Failed to read positions from TNG filez'Failed to read velocities from TNG filez#Failed to read forces from TNG filez Failed to read additional block z from TNG file)$rXrget_timerconvert_time_from_nativerrdatarGget_boxrYrreshaperK read_successrhconvert_pos_from_nativerM get_positionsrOrQget_velocitiesrRconvert_velocities_from_nativerT get_forcesrUconvert_forces_from_nativerErkr?rir5rN get_blockidr=)r,rrErr+add_block_stride block_datas r$rzTNGReader._frame_to_tss2;!!##   70066D#. = @   dn - - -)4>+A+A!Q+G+GHBM) B@AAA! @,,R]2A2->???   ;  # #BL 1 1 1) HFGGG! ;,,R\:::   C  $ $R] 3 3 3) IGHHH! C33BMBBB   @   + + +) ECDDD! @//???4  E#259 $t':: 'HHOO"+!6!6*51:""!-!P5PPP r&c>|j}|d=|S)zMake a dictionary of the class state to pickle Reader instance. Must be done manually as pytng uses a non-trivial`__cinit__`. r5)__dict__copy)r,states r$ __getstate__zTNGReader.__getstate__s%  ""$$ " # r&c||_tj|jd|_||j}|j|}dS)zWRestore class from `state` dictionary in unpickling of Reader instance rN)rr3r4rr5rrXr)r,rr_s r$ __setstate__zTNGReader.__setstate__sS #3DM3GG""4;//   ) )$ / /r&c td)zWriter for TNG files Raises ------ NotImplementedError Currently there is not writer for TNG files pending implementation upstream in pytng. z*There is currently no writer for TNG files)NotImplementedErrorrus r$WriterzTNGReader.Writers""NOOOr&)T)N)(__name__ __module__ __qualname____doc__formatunitsrFrLrPrSr*r dciter rstrboolr2rWrv staticmethodintrzpropertyr|rr~rerrrrrrrZrrrr __classcell__)r\s@r$r r ps$F   E*N/1) OSY    oHS#S#S#TS#S#S#S#S#S#j,>,>,>\%%%\,#X !S ! ! !X ! HS H H HX H /49 / / /X /666+C+C++++ SX"hx&8H0I9I?GI IIIIV000" P P P P P P Pr&r )rrltypingrrnumpyrHMDAnalysis.coordinatesrMDAnalysis.coordinates.timesteprMDAnalysis.lib.mdamathrMDAnalysis.lib.utilrr r r3r/r0 ReaderBaser r!r&r$rs(0AAF!!!!!!!!''''''444444000000444444LLL II IIIkPkPkPkPkPkPkPkPkPkPs;AA