iZdZddlZddlZddlZddlmZddlZddl m Z ddl m Z m Z ddlmZdd lmZd Zd Zd ZGd dejZdS)a-ChainReader --- :mod:`MDAnalysis.coordinates.chain` =================================================== The :class:`ChainReader` is used by MDAnalysis internally to represent multiple trajectories as one virtual trajectory. Users typically do not need to use the :class:`ChainReader` explicitly and the following documentation is primarily of interest to developers. .. autoclass:: ChainReader :members: .. automethod:: _get_local_frame .. automethod:: _apply .. automethod:: _get .. automethod:: _get_same .. automethod:: _read_frame N)Tuple)util) asiterablestore_init_arguments)base)corecTdtt|dDS)a Return indices to sort a multi value tuple. Sorting is done on the first value of the tuple. Parameters ---------- l : list Returns ------- indices Example ------- >>> multi_level_argsort(((0, 2), (4, 9), (0, 4), (7, 9))) [0, 2, 1, 3] cg|] }|d S)r).0els f/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/chain.py z'multi_level_argsort..Ks H H HbBqE H H Hc|ddS)Nrrr )xs rz%multi_level_argsort..KsqtAwr)key)sorted enumerate)ls rmulti_level_argsortr8s0& I HF9Q<<5F5FGGG H H HHrc t|dkrdgSt|dkrU|dd|ddkrddgStj|dd|ddrdgSdgStj|jdkrt|dz gSdg}t t |dd|dd|dddD]\}\}}}tj|d|dr||d<0tj|d|dz |s:|d|dkr'|d|dkr|||d|dkr|||dd|ddkr%|t|dz |S)aBGiven a list of start and end times this function filters out any duplicate time steps preferring the last tuple. Parameters ---------- times : list sorted list of times dt : float timestep between two frames Returns ------- list: indices of times to be used with overlaps removed Example ------- >>> filter_times(((0, 3), (0, 3))) [1, ] >>> filter_times(((0, 3), (0, 4))) [1, ] >>> filter_times(((0, 3), (3, 4))) [0, 1] >>> filter_times(((0, 3), (2, 5), (4, 9))) [1, 2, 3] rrrN)start)lennpallcloseuniquesizerzipappend)timesdtused_idxifirstmiddlelasts r filter_timesr-Ns : 5zzQ    Uq 8A;q! $ $q6M [q!eAhqk 2 2     y!! JJN   H%. E#2#Jad U122Y//q%%%    E64 ;uQx + + HRLLVAY2B77 q U1X%%DGvay,@,@""" AY%( " " OOA    Ry|uRy|##E Q''' Orc4t|dtjfd|D}|s.d|D}td||dj|vr"t d|dS)z Make a check that all readers have the same filetype and are of the allowed files types. Throws Exception on failure. Parameters ---------- readers : list of MDA readers allowed : list of allowed formats rc0g|]}t|Sr ) isinstance)rr classnames rrz+check_allowed_filetypes..s#HHH1jI66HHHrc,g|]}t|Sr )type)rr1s rrz+check_allowed_filetypes..s0001tAww000rz_ChainReader: continuous=true only supported when all files are using the same reader. Found: {}z;ChainReader: continuous=True only supported for formats: {}N)r4r all ValueErrorformatNotImplementedError)readersallowedonly_one_reader readernamesr2s @rcheck_allowed_filetypesr=sWQZ  IfHHHHHHHIIO  00000  {++   qz''! ((.w   ('rc~eZdZdZdZe d"fd ZedZd e e e ffd Z d Z d Z d ZdZdZdZedZedZedZedZedZedZedZdZdZdZdZedZdZd#dZ dZ!d Z"d!Z#xZ$S)$ ChainReadera; Reader that concatenates multiple trajectories on the fly. The :class:`ChainReader` is used by MDAnalysis internally to represent multiple trajectories as one virtual trajectory. Users typically do not need to use the :class:`ChainReader` explicitly. Chainreader can also handle a continuous trajectory split over several files. To use this pass the ``continuous == True`` keyword argument. Setting ``continuous=True`` will make the reader choose frames from the set of trajectories in such a way that the trajectory appears to be as continuous in time as possible, i.e. that time is strictly monotonically increasing. This means that there will be no duplicate time frames and no jumps backwards in time. However, there can be gaps in time (e.g., multiple time steps can appear to be missing). Ultimately, it is the user's responsibility to ensure that the input trajectories can be virtually stitched together in a meaningful manner. As an example take the following trajectory that is split into three parts. The column represents the time and the trajectory segments overlap. With the continuous chainreader only the frames marked with a + will be read. :: part01: ++++-- part02: ++++++- part03: ++++++++ .. warning:: The order in which trajectories are given to the chainreader can change what frames are used with the continuous option. The default chainreader will read all frames. The continuous option is currently only supported for XTC, TRR, and LAMMPSDUMP files. Notes ----- The trajectory API attributes exist but most of them only reflect the first trajectory in the list; :attr:`ChainReader.n_frames`, :attr:`ChainReader.n_atoms`, and :attr:`ChainReader.fixed` are properly set, though .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 0.13.0 :attr:`time` now reports the time summed over each trajectory's frames and individual :attr:`dt`. .. versionchanged:: 0.19.0 added ``continuous`` trajectory option .. versionchanged:: 0.19.0 limit output of __repr__ .. versionchanged:: 2.0.0 Now ChainReader can be (un)pickled. Upon unpickling, current timestep is retained. CHAINrNFTc v ttjdd||dt|}||d<fd|D_g_|D]}t |tjrj d7t |tr!j |dmj |tj j_d_ |_ d_d}tjdg|z_tj|_tj d_j|z_|rt/jgd tjtj |d krt3d d}tjd}tjjj|z_g} jD]A} | d| jj} | d | jj} | | | fBt?| } fd | D_j| _j|| z_tAjd krhtCtj | | |}fd|D_j|_j|||z_dg}d}tEjdd jd dD]\}}|d|df|j}|j}|d |j|krtGj$dtJ|d ||cxkr |jkrnnt3d|ddd D]}|j|krn| |d |j&zd z||j&d zz }|jd jz }|_|_|_'d_(dS)aSet up the chain reader. Parameters ---------- filenames : str or list or sequence file name or list of file names; the reader will open all file names and provide frames in the order of trajectories from the list. Each trajectory must contain the same number of atoms in the same order (i.e. they all must belong to the same topology). The trajectory format is deduced from the extension of each file name. Extension: `filenames` are either a single file name or list of file names in either plain file names format or ``(filename, format)`` tuple combination. This allows explicit setting of the format for each individual trajectory file. skip : int (optional) skip step (also passed on to the individual trajectory readers); must be same for all trajectories dt : float (optional) Passed to individual trajectory readers to enforce a common time difference between frames, in MDAnalysis time units. If not set, each reader's `dt` will be used (either inferred from the trajectory files, or set to the reader's default) when reporting frame times; note that this might lead an inconsistent time difference between frames. continuous : bool (optional) treat all trajectories as one single long trajectory. Adds several checks; all trajectories have the same dt, they contain at least 2 frames, and they are all of the same file-type. Not implemented for all trajectory formats! This can be used to analyze GROMACS simulations without concatenating them prior to analysis. **kwargs : dict (optional) all other keyword arguments are passed on to each trajectory reader unchanged r@)filenameskip convert_unitsr'Nr'c8g|]}tj|fdiS)rD)r reader)rrBrDkwargss rrz(ChainReader.__init__..(s@    K H H H H H   rrn_atomsn_frames)XTCTRR LAMMPSDUMPTRCrzNChainReader: Need at least two frames in every trajectory with continuous=Truerc*g|]}j|Sr r9rr)selfs rrz(ChainReader.__init__..ps>>>DLO>>>rc*g|]}j|Sr rOrPs rrz(ChainReader.__init__..xsBBBA QBBBrz!Missing frame in continuous chainz=ChainReader: Interleaving not supported with continuous=True.r ))superr?__init__rr9 filenamesr0r ndarrayr%tuplearray!_ChainReader__active_reader_indexrC _get_samerH_getcumsum _start_framessumrIdts total_timesr=any RuntimeErrorasarrayonesshapetstimerrr-r$warningswarn UserWarningframe_sfrewind)rQrUrCr' continuousrDrGfnrIr&r1rendsort_idxr(sfr1r2 r1_start_time start_timerf __class__s` `` rrTzChainReader.__init__s \ *k4  ) '       y))  >F4L     %     * *B"bj)) *%%d++++B&& *%%be,,,,%%b))))$.11&'" ~~i00 99Z(( YsX~66x(( 8DIIdOO,,8h. L  # AAA   vbhx((A-.. "< %%Bz$))J"7"788Hwtx~..3DHE\ + +! "di eS\*****511H>>>>X>>>DL!^H5DN#x(8*<= 0rz.Cannot find trajectory for virtual frame {0:d}) IndexErrorbisect bisect_rightr]r7)rQkr)fs r_get_local_framezChainReader._get_local_frames> q55DEE E   2A 6 6 : q55@GGJJ  "1% %!t rc|j}|j|d<|dd|jdzD]}||d|_|S)Nrfr9r)__dict__copyrf __deepcopy__rYrm)rQstaterFs r __getstate__zChainReader.__getstate__sv ""$$g**,,d I&'G)Ca)G'GH  F MMOOOO+ rc\|j||j|j_dSN)rupdate_ChainReader__current_framerfrk)rQrs r __setstate__zChainReader.__setstate__s( U###, rc6|j|Sr) active_readerconvert_time_from_nativerQts rrz$ChainReader.convert_time_from_natives!::1===rc6|j|Sr)rconvert_time_to_nativers rrz"ChainReader.convert_time_to_natives!88;;;rc6|j|Sr)rconvert_from_nativerQrs rconvert_pos_from_nativez#ChainReader.convert_pos_from_natives!55a888rc6|j|Sr)rconvert_pos_to_nativers rrz!ChainReader.convert_pos_to_natives!77:::rc|jjSr)r skip_timesteprQs rrzChainReader.skip_timesteps!//rc|jjSr)rdeltars rrzChainReader.deltas!''rc|jjS)z;:attr:`periodic` attribute of the currently read trajectory)rperiodicrs rrzChainReader.periodics!**rc|jjS)z8:attr:`units` attribute of the currently read trajectory)runitsrs rrzChainReader.units s!''rc> |jjS#t$rYdSwxYw)z=:attr:`compressed` attribute of the currently read trajectoryN)r compressedAttributeErrorrs rrzChainReader.compresseds5 %0 0   44 s  c|jjS)z1Cumulative frame number of the current time step.)rfrkrs rrkzChainReader.framesw}rc||j\}}|jd|||j|zzS)zMCumulative time of the current frame in MDAnalysis time units (typically ps).N)rrkr`r^r_)rQ trajindexsubframes rrgzChainReader.timesO#33DJ?? 8  ZiZ ( , , . .DHY.,sG    ,F # #F + + 5 5f 5 5   rrO)rQrrGs ``r_applyzChainReader._apply*s6     ,    rc*fd|jDS)z$Get value of `attr` for all readers.c:g|]}|Sr r)rrFattrs rrz$ChainReader._get..3s'III&''--IIIrrO)rQrs `rr[zChainReader._get1sIIIIDLIIIIrctj||}|d}tj||sGtj|j||k}t d||||S)axVerify that `attr` has the same value for all readers and return value. Parameters ---------- attr : str attribute name Returns ------- value : int or float or str or object common value of the attribute Raises ------ ValueError if not all readers have the same value rzBThe following trajectories do not have the correct {0} ({1}): {2})r rXr[r!rUr6r7)rQrvaluesvaluebad_trajs rrZzChainReader._get_same5s$$))D//**q {65)) x//%@H%vdE8<<  rcd|cxkrt|jks6ntdt|j||_|j||_dS)z"Make reader `i` the active reader.rz#Reader index must be 0 <= i < {0:d}N)rr9rr7rYrUrB)rQr)s r__activate_readerzChainReader.__activate_readerQsvQ****T\******5<d|_|ddS)z@Internal method: Rewind trajectories themselves and trj pointer.rrmN)rrrs r_reopenzChainReader._reopens"! Hrc0|ddS)Nclose)rrs rrzChainReader.closes Grct|jdkrf|jdr*tj|jdnd}d|t|jdz }n$dd|jD}d |jj||j |j S) Nr numpy.ndarrayz{fname} and {nfnames} morer)fnamenfnamesz, cTg|]%}|rtj|nd&S)r)ospathbasename)rros rrz(ChainReader.__repr__..sB-/CBG$$R(((OrzF<{clsname} containing {fname} with {nframes} frames of {natoms} atoms>)clsnamernframesnatoms) rrUrrrr7joinrw__name__rIrH)rQrfnamess r__repr__zChainReader.__repr__s t~   " ">!$%  !2333$  288S%8%81%<9FFYY"nF v/ |  r)rNFTr)%r __module__ __qualname____doc__r7rrT staticmethodr|rintrrrrrrrpropertyrrrrrrkrgrr[rZrrrrrrr __classcell__)rws@rr?r?so77rF  uuuuuun   \  )U38_))))V   --- >>><<<999;;; 00X0((X(++X+((X(XX   X     JJJ8***88X88 " " " "        rr?)rrhos.pathrrtypingrnumpyr librlib.utilrrr r rr-r= ReaderBaser?r rrrs 0& 77777777III,FFFR   4z z z z z $/z z z z z r