iDdZddlZddlZddlZddlZGddejZGddejZGddej Z Gd d ej Z Gd d ej ZddZddZddZdS)a Picklable read-only I/O classes --- :mod:`MDAnalysis.lib.picklable_file_io` =========================================================================== Provide with an interface for pickling read-only IO file object. These classes are used for further pickling :class:`MDAnalysis.core.universe` in a object composition approach. .. autoclass:: FileIOPicklable :members: .. autoclass:: BufferIOPicklable :members: .. autoclass:: TextIOPicklable :members: .. autoclass:: BZ2Picklable :members: .. autoclass:: GzipPicklable :members: .. autofunction:: pickle_open .. autofunction:: bz2_pickle_open .. autofunction:: gzip_pickle_open .. versionadded:: 2.0.0 Nc0eZdZdZdfd ZdZdZxZS)FileIOPicklableaFile object (read-only) that can be pickled. This class provides a file-like object (as returned by :func:`open`, namely :class:`io.FileIO`) that, unlike standard Python file objects, can be pickled. Only read mode is supported. When the file is pickled, filename and position of the open file handle in the file are saved. On unpickling, the file is opened by filename, and the file is seeked to the saved position. This means that for a successful unpickle, the original file still has to be accessible with its filename. Note ---- This class only supports reading files in binary mode. If you need to open a file in text mode, use the :func:`pickle_open`. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode : str only reading ('r') mode works. It exists to be consistent with a wider API. Example ------- :: >>> import pickle >>> from MDAnalysis.tests.datafiles import PDB >>> file = FileIOPicklable(PDB) >>> _ = file.readline() >>> file_pickled = pickle.loads(pickle.dumps(file)) >>> print(file.tell(), file_pickled.tell()) 55 55 See Also --------- TextIOPicklable BufferIOPicklable .. versionadded:: 2.0.0 rcZ||_t||dSN)_modesuper__init__selfnamemode __class__s j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/lib/picklable_file_io.pyr zFileIOPicklable.__init__os*  t$$$$$c|d}||d ||ddS#t$rYdSwxYw)Nname_valr)rtell_valr seekKeyError)r stater s r __setstate__zFileIOPicklable.__setstate__ssfZ  d %%%  IIeJ' ( ( ( ( (    DD s> A  A c|jdkr'td|j|j|j|jf|j|dfSNrz;Can only pickle files that were opened in read mode, not {})rr)r RuntimeErrorformatrr tellr prots r __reduce_ex__zFileIOPicklable.__reduce_ex__{sg :  ''-vdj'9'9  N Y # < <  r)r__name__ __module__ __qualname____doc__r rr! __classcell__rs@rrr>sf..`%%%%%%        rrc.eZdZdZfdZdZdZxZS)BufferIOPicklableaA picklable buffer object for read-only FileIO object. This class provides a buffered :class:`io.BufferedReader` that can be pickled. Note that this only works in read mode. Parameters ---------- raw : FileIO object Example ------- :: file = FileIOPicklable('filename') buffer_wrapped = BufferIOPicklable(file) See Also --------- FileIOPicklable TextIOPicklable .. versionadded:: 2.0.0 cbt||j|_dSrr r r raw_classr rawrs rr zBufferIOPicklable.__init__( rc|d}|d}||}||||ddSNr-rrr r)r rr-r r/s rrzBufferIOPicklable.__setstate__sR+& Z ioo c % #$$$$$rcb|j|jf|j|j|dfSN)r-rr)r-r rrs rr!zBufferIOPicklable.__reduce_ex__s9 N YL!^ I IIKK    rr"r(s@rr*r*s`4'''''%%%        rr*c.eZdZdZfdZdZdZxZS)TextIOPicklableaCharacter and line based picklable file-like object. This class provides a file-like :class:`io.TextIOWrapper` object that can be pickled. Note that this only works in read mode. Parameters ---------- raw : FileIO object Example ------- :: file = FileIOPicklable('filename') text_wrapped = TextIOPicklable(file) See Also --------- FileIOPicklable BufferIOPicklable .. versionadded:: 2.0.0 .. versionchanged:: 2.8.0 The raw class instance instead of the class name that is wrapped inside will be serialized. After deserialization, the current position is no longer reset so `universe.trajectory[i]` is not needed to seek to the original position. cbt||j|_dSrr,r.s rr zTextIOPicklable.__init__r0rc|d}|d}|d}||}|||||dSdSr2r3)r argsr-r rr/s rrzTextIOPicklable.__setstate__sb% JJioo c   IIdOOOOO  rc |}n#t$rd}YnwxYw |j}n!#t$r|jjj}YnwxYw|jj|jf|j||dfSr5) rOSErrorr AttributeErrorbuffer_fpr__new__r-)r r curr_locr s rr!zTextIOPicklable.__reduce_ex__s yy{{HH   HHH  (9DD ( ( (;?'DDD ( N " ^ !^ $    s &&2AAr"r(s@rr7r7s`>'''''          rr7c0eZdZdZdfd ZdZdZxZS) BZ2PicklableaFile object (read-only) for bzip2 (de)compression that can be pickled. This class provides a file-like object (as returned by :func:`bz2.open`, namely :class:`bz2.BZ2File`) that, unlike standard Python file objects, can be pickled. Only read mode is supported. When the file is pickled, filename and position of the open file handle in the file are saved. On unpickling, the file is opened by filename, and the file is seeked to the saved position. This means that for a successful unpickle, the original file still has to be accessible with its filename. Note ---- This class only supports reading files in binary mode. If you need to open to open a compressed file in text mode, use :func:`bz2_pickle_open`. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode : str can only be 'r', 'rb' to make pickle work. Example ------- :: >>> import pickle >>> from MDAnalysis.tests.datafiles import XYZ_bz2 >>> file = BZ2Picklable(XYZ_bz2) >>> _ = file.readline() >>> file_pickled = pickle.loads(pickle.dumps(file)) >>> print(file.tell(), file_pickled.tell()) 5 5 See Also --------- FileIOPicklable BufferIOPicklable TextIOPicklable GzipPicklable .. versionadded:: 2.0.0 rbcZ||_t||dSr)_bz_moder r r s rr zBZ2Picklable.__init__3*  t$$$$$rc|jds'td|j|jj|dSr)rF startswithrrr?r rr s r __getstate__zBZ2Picklable.__getstate__7s\}'',, ''-vdm'<'< !HMtyy{{CCCrc|d}|d}|| ||dS#t$rYdSwxYwNrrrr r:r rs rrzBZ2Picklable.__setstate__?bJJ d  IIdOOOOO    DD > A  A rDr#r$r%r&r rKrr'r(s@rrCrCsi//b%%%%%%DDDrrCc0eZdZdZdfd ZdZdZxZS) GzipPicklableaGzip file object (read-only) that can be pickled. This class provides a file-like object (as returned by :func:`gzip.open`, namely :class:`gzip.GzipFile`) that, unlike standard Python file objects, can be pickled. Only read mode is supported. When the file is pickled, filename and position of the open file handle in the file are saved. On unpickling, the file is opened by filename, and the file is seeked to the saved position. This means that for a successful unpickle, the original file still has to be accessible with its filename. Note ---- This class only supports reading files in binary mode. If you need to open to open a compressed file in text mode, use the :func:`gzip_pickle_open`. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode : str can only be 'r', 'rb' to make pickle work. Example ------- :: >>> import pickle >>> from MDAnalysis.tests.datafiles import MMTF_gz >>> file = GzipPicklable(MMTF_gz) >>> _ = file.readline() >>> file_pickled = pickle.loads(pickle.dumps(file)) >>> print(file.tell(), file_pickled.tell()) 1218 1218 See Also --------- FileIOPicklable BufferIOPicklable TextIOPicklable BZ2Picklable .. versionadded:: 2.0.0 rDcZ||_t||dSr)_gz_moder r r s rr zGzipPicklable.__init__{rGrc|jds'td|j|j|dSr)rVrIrrr rrJs rrKzGzipPicklable.__getstate__sZ}'',, ''-vdm'<'< !I499;;???rc|d}|d}|| ||dS#t$rYdSwxYwrMrrNs rrzGzipPicklable.__setstate__rOrPrQrRr(s@rrTrTIsi//b%%%%%%@@@rrTrtc|dvrtdtj|}t|}|dkrt |S|dvrt |SdS)aOpen file and return a stream with pickle function implemented. This function returns a FileIOPicklable object wrapped in a BufferIOPicklable class when given the "rb" reading mode, or a FileIOPicklable object wrapped in a TextIOPicklable class with the "r" or "rt" reading mode. It can be used as a context manager, and replace the built-in :func:`open` function in read mode that only returns an unpicklable file object. In order to serialize a :class:`MDAnalysis.core.Universe`, this function can used to open trajectory/topology files. This object composition is more flexible and easier than class inheritance to implement pickling for new readers. Note ---- Can be only used with read mode. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode: {'r', 'rt', 'rb'} (optional) 'r': open for reading in text mode; 'rt': read in text mode (default); 'rb': read in binary mode; Returns ------- stream-like object: BufferIOPicklable or TextIOPicklable when mode is 'r' or 'rt', returns TextIOPicklable; when mode is 'rb', returns BufferIOPicklable Raises ------ ValueError if `mode` is not one of the allowed read modes Examples ------- open as context manager:: with pickle_open('filename') as f: line = f.readline() open as function:: f = pickle_open('filename') line = f.readline() f.close() See Also -------- :func:`MDAnalysis.lib.util.anyopen` :func:`io.open` .. versionadded:: 2.0.0 >rrDrY6Only read mode ('r', 'rt', 'rb') files can be pickled.rD>rrYN) ValueErrorosfspathrr*r7)r rr/s r pickle_openr_szz $$$ G    9T??D $  C t|| %%%   s###  rrDc|dvrtd|dd}t||}d|vrt|S|S)asOpen a bzip2-compressed file in binary or text mode with pickle function implemented. This function returns a BZ2Picklable object when given the "rb" or "r" reading mode, or a BZ2Picklable object wrapped in a TextIOPicklable class with the "rt" reading mode. It can be used as a context manager, and replace the built-in :func:`bz2.open` function in read mode that only returns an unpicklable file object. Note ---- Can be only used with read mode. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode: {'r', 'rt', 'rb'} (optional) 'r': open for reading in binary mode; 'rt': read in text mode; 'rb': read in binary mode; (default) Returns ------- stream-like object: BZ2Picklable or TextIOPicklable when mode is 'rt', returns TextIOPicklable; when mode is 'r' or 'rb', returns BZ2Picklable Raises ------ ValueError if `mode` is not one of the allowed read modes Examples ------- open as context manager:: with bz2_pickle_open('filename') as f: line = f.readline() open as function:: f = bz2_pickle_open('filename') line = f.readline() f.close() See Also -------- :func:`io.open` :func:`bz2.open` :func:`MDAnalysis.lib.util.anyopen` :func:`MDAnalysis.lib.picklable_file_io.pickle_open` :func:`MDAnalysis.lib.picklable_file_io.gzip_pickle_open` .. versionadded:: 2.0.0 >rrDrYr[t)r\replacerCr7)r rbz_mode binary_files rbz2_pickle_openrfsgz $$$ G   ll3##GtW--K d{{{+++rc|dvrtd|dd}t||}d|vrt|S|S)ayOpen a gzip-compressed file in binary or text mode with pickle function implemented. This function returns a GzipPicklable object when given the "rb" or "r" reading mode, or a GzipPicklable object wrapped in a TextIOPicklable class with the "rt" reading mode. It can be used as a context manager, and replace the built-in :func:`gzip.open` function in read mode that only returns an unpicklable file object. Note ---- Can be only used with read mode. Parameters ---------- name : str either a text or byte string giving the name (and the path if the file isn't in the current working directory) of the file to be opened. mode: {'r', 'rt', 'rb'} (optional) 'r': open for reading in binary mode; 'rt': read in text mode; 'rb': read in binary mode; (default) Returns ------- stream-like object: GzipPicklable or TextIOPicklable when mode is 'rt', returns TextIOPicklable; when mode is 'r' or 'rb', returns GzipPicklable Raises ------ ValueError if `mode` is not one of the allowed read modes Examples ------- open as context manager:: with gzip_pickle_open('filename') as f: line = f.readline() open as function:: f = gzip_pickle_open('filename') line = f.readline() f.close() See Also -------- :func:`io.open` :func:`gzip.open` :func:`MDAnalysis.lib.util.anyopen` :func:`MDAnalysis.lib.picklable_file_io.pickle_open` :func:`MDAnalysis.lib.picklable_file_io.bz2_pickle_open` .. versionadded:: 2.0.0 >rrDrYr[rarb)r\rcrTr7)r rgz_moderes rgzip_pickle_openri#sgz $$$ G   ll3##Gg..K d{{{+++r)rYrQ)r&ior]bz2gzipFileIOrBufferedReaderr* TextIOWrapperr7BZ2FilerCGzipFilerTr_rfrirrrss.@ G G G G G biG G G T1 1 1 1 1 )1 1 1 hB B B B B b&B B B JEEEEE3;EEEPEEEEEDMEEEPF$F$F$F$RFFFFRFFFFFFr