i30dZddlZddlZddlmZmZmZmZm Z ddl Z ddl m Z ddl mZddlmZdd lmZdd Zd ZGd dejZGddejZdS)aXDR based trajectory files --- :mod:`MDAnalysis.coordinates.XDR` ================================================================ This module contains helper function and classes to read the XTC and TRR file formats. See Also -------- MDAnalysis.coordinates.XTC: Read and write GROMACS XTC trajectory files. MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files. MDAnalysis.lib.formats.libmdaxdr: Low level xdr format reader N)getctimegetsizeisfilesplitjoin)FileLock)base) triclinic_box)store_init_argumentsnpzcRt|\}}t|d|d|S)a>Return offset or its lock filename for XDR files. For this the filename is appended with `_offsets.{ending}`. Parameters ---------- filename : str filename of trajectory ending : str (optional) fileending of offsets file Returns ------- offset_filename : str .z _offsets.)rr)filenameendingheadtails d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/XDR.pyoffsets_filenamer0s4"xJD$ 1$1111 2 22c dtj|DS#ttf$rt jd|dYdSwxYw)zread offsets into dictionary. This assume offsets have been saved using numpy Parameters ---------- filename : str filename of offsets Returns ------- offsets : dict dictionary of offsets information ci|]\}}|| Sr).0kvs r z&read_numpy_offsets..Vs;;;A1;;;rzFailed to load offsets file  F)nploaditems ValueErrorIOErrorwarningswarn)rs rread_numpy_offsetsr'Esv ;;!2!2!8!8!:!:;;;;   AXAAABBBuus/2)AAceZdZdZe dfd ZedZdZdZ dd Z e d Z d Z d Zdd ZxZS) XDRBaseReaderaDBase class for libmdaxdr file formats xtc and trr This class handles integration of XDR based formats into MDAnalysis. The XTC and TRR classes only implement `_write_next_frame` and `_frame_to_ts`. .. _offsets-label: Notes ----- XDR based readers store persistent offsets on disk. The offsets are used to enable access to random frames efficiently. These offsets will be generated automatically the first time the trajectory is opened. Generally offsets are stored in hidden `*_offsets.npz` files. Afterwards opening the same file again is fast. It sometimes can happen that the stored offsets get out off sync with the trajectory they refer to. For this the offsets also store the number of atoms, size of the file and last modification time. If any of them change the offsets are recalculated. Writing of the offset file can fail when the directory where the trajectory file resides is not writable or if the disk is full. In this case a warning message will be shown but the offsets will nevertheless be used during the lifetime of the trajectory Reader. However, the next time the trajectory is opened, the offsets will have to be rebuilt again. .. versionchanged:: 1.0.0 XDR offsets read from trajectory if offsets file read-in fails .. versionchanged:: 2.0.0 Add a InterProcessLock when generating offsets .. versionchanged:: 2.4.0 Use a direct read into ts attributes .. versionchanged:: 2.9.0 Changed fasteners.InterProcessLock() to filelock.FileLock TNFc tt|j|fd|i|||j|_||_|jt|j|_n|jj|_|s| n| d|j } |j }||j |j z }n ||j d<|jdn#t$rd}YnwxYw|j|jfi|j |_d|_|||j||j_t+|j|j_|jr5|jj+||jjdddSdSdS) a Parameters ---------- filename : str trajectory filename convert_units : bool (optional) convert units to MDAnalysis units sub : array_like (optional) `sub` is an array of indices to pick out the corresponding coordinates and load only them; this requires that the topology itself is that of the sub system. refresh_offsets : bool (optional) force refresh of offsets dt : float (optional) timestep in MDAnalysis units to load trajectory with; if `dt` is ``None``, the time is taken from the xdr file; else, the time is set to `dt` * frame **kwargs : dict General reader arguments. convert_unitsNTstoredtr r)superr)__init___filer_xdr_sublenn_atoms _load_offsets _read_offsetsreadtime _ts_kwargsseek StopIteration _Timestepts_frame _frame_to_tsr.r box dimensionsr+convert_pos_from_native) selfrr+subrefresh_offsetsr.kwargsframe xdr_frame __class__s rr1zXDRBaseReader.__init__s> ,mT""+   $1 5;   JJt}--  9 ty>>DLL9,DL +      T  * * *     ((Iz^ej0(*% INN1       BBB !$.AAAA  %))) *EI6   Ew!-,,TW-?-CDDDDD E E--sAD D#"D#c n||5}|j}dddn #1swxYwY|SN)r2r6)clsrrHfr6s r parse_n_atomszXDRBaseReader.parse_n_atomssr YYx  AiG               s *..c8|jdS)z close readerNr3closerEs rrSzXDRBaseReader.close rc`t|j}t|jd} t|5} dddn #1swxYwYnv#t$ri}t |t s|jt jkr9tj d|jd| dYd}~dSd}~wwxYwt|5}t|s$| d ddddSt|}|ss- ?lGt|H@@g@@@@r)TNFN)FrM)__name__ __module__ __qualname____doc__r r1 classmethodrPrSr7r8propertyrnrur{r~ __classcell__)rKs@rr)r)^s  D   @E@E@E@E@E@ED[ =7=7=7~EEEE$X + + +   AAAAAAAArr)c(eZdZdZ ddZdZdZdS) XDRBaseWriterz1Base class for libmdaxdr file formats xtc and trrTNc ~||_||_||_||jd|_||_dS)a5 Parameters ---------- filename : str filename of trajectory n_atoms : int number of atoms to be written convert_units : bool (optional) convert from MDAnalysis units to format specific 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 **kwargs : dict General writer arguments wN)r_convert_unitsr6r2r3_dt)rErr6r+r.rHs rr1zXDRBaseWriter.__init__Hs<&! + JJt}c22 rc8|jdS)zclose trajectoryNrRrTs rrSzXDRBaseWriter.closearUrc.|dSrM)rSrTs r__del__zXDRBaseWriter.__del__es r)TN)rrrrr1rSrrrrrrEsQ;;9=2rr)r)rr^numpyr os.pathrrrrrr%rdrr lib.mdamathr lib.utilr rr' ReaderBaser) WriterBaserrrrrs7.   ::::::::::::::''''''++++++3333*2dAdAdAdAdADOdAdAdAN!!!!!DO!!!!!r