izE\dZddlZddlZddlmZddlmZddlm Z  ddl Z dZ n5#e $r-d Z ddl Z Gd d Ze jd Z ee _YnwxYwed ZedZdZGddejZGddejZGdde jZdS)a Reading trajectories with *chemfiles* --- :mod:`MDAnalysis.coordinates.chemfiles` ================================================================================= MDAnalysis interoperates with the `chemfiles`_ library. The *chemfiles* C++ library supports an expanding set of file formats, some of which are not natively supported by MDAnalysis. Using the *CHEMFILES* reader you can use `chemfiles`_ for the low-level file reading. Check the list of `chemfile-supported file formats`_. .. _chemfiles: https://chemfiles.org .. _chemfile-supported file formats: https://chemfiles.org/chemfiles/latest/formats.html#list-of-supported-formats Using the CHEMFILES reader -------------------------- When reading, set the ``format="CHEMFILES"`` keyword argument and I/O is delegated to `chemfiles`_. For example:: >>> import MDAnalysis as mda >>> from MDAnalysis.tests import datafiles as data >>> u = mda.Universe(data.TPR, data.TRR, format="CHEMFILES") >>> print(u.trajectory) You can then use the :class:`~MDAnalysis.core.universe.Universe` as usual while chemfiles is handling the I/O transparently in the background. `chemfiles`_ can also *write* a number of formats for which there are no Writers in MDAnalysis. For example, to write a mol2 file:: >>> u = mda.Universe(data.mol2_ligand) >>> with mda.Writer("ligand.mol2", format="CHEMFILES") as W: ... W.write(u.atoms) Classes ------- Classes to read and write files using the `chemfiles`_ library. This library provides C++ implementation of multiple formats readers and writers. .. autoclass:: ChemfilesReader .. autoclass:: ChemfilesWriter .. autoclass:: ChemfilesPicklable Helper functions ---------------- .. autodata:: MIN_CHEMFILES_VERSION .. autodata:: MAX_CHEMFILES_VERSION .. autofunction:: check_chemfiles_version N)Version)base)store_init_argumentsTFceZdZdS)MockTrajectoryN)__name__ __module__ __qualname__j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/chemfiles.pyr r ^s rr chemfilesz0.10z0.11ctstjddSttj}|t ko |tkS)zCheck if an appropriate *chemfiles* is available Returns ``True`` if a usable chemfiles version is available, with :data:`MIN_CHEMFILES_VERSION` <= version < :data:`MAX_CHEMFILES_VERSION` .. versionadded:: 1.0.0 zKchemfiles package not found, try installing it with 'pip install chemfiles'F) HAS_CHEMFILESwarningswarnrr __version__MIN_CHEMFILES_VERSIONMAX_CHEMFILES_VERSION)versions rcheck_chemfiles_versionrmsS   =   ui+,,G + + O:O0OOrceZdZdZdZdddZedfd ZedZ d Z d Z e d Z e d Zd ZdZddZdZddZxZS)ChemfilesReaderaCoordinate reader using chemfiles. The file format to used is guessed based on the file extension. If no matching format is found, a ``ChemfilesError`` is raised. It is also possible to manually specify the format to use for a given file. .. versionadded:: 1.0.0 rfsAngstromtimelengthc Zts'tdtt t |j|fi|||_d|_| |j |j fi|j |_ |dS)a Parameters ---------- filename : chemfiles.Trajectory or str the chemfiles object to read or filename to read chemfiles_format : str (optional) if *filename* was a string, use the given format name instead of guessing from the extension. The `list of supported formats `_ and the associated names is available in the chemfiles documentation. **kwargs : dict General reader arguments. Please install Chemfiles > {}N)r RuntimeErrorformatrsuperr__init___format_cached_n_atoms_open _Timestepn_atoms _ts_kwargstsnext)selffilenamechemfiles_formatkwargs __class__s rr'zChemfilesReader.__init__s '(( 6/00  .ot$$-hAA&AAA' #  $.AAAA rcDtot|tjS)zCan this Reader read *thing*)r isinstancer Trajectory)things r _format_hintzChemfilesReader._format_hints HE93G!H!HHrcd|_d|_d|_t|jt jr|j|_dSt|jd|j |_dS)NFrr) _closed_step_framer6r1rr7_fileChemfilesPicklabler(r0s rr*zChemfilesReader._opensW   dmY%9 : : NDJJJ+DM3 MMDJJJrcX|js"|jd|_dSdS)z close readerTN)r=r@closerBs rrDzChemfilesReader.closes5| J     DLLL  rc|jjS)znumber of frames in trajectory)r@nstepsrBs rn_frameszChemfilesReader.n_framessz  rc|j1t|jdj|_|jS)z4number of atoms in the first frame of the trajectoryNr)r)lenr@ read_stepatomsrBs rr,zChemfilesReader.n_atomss9   '#&tz';';A'>'>'D#E#ED ##rcV||dS)zreopen trajectoryN)rDr*rBs r_reopenzChemfilesReader._reopens   rc8||_|S)z read frame i)r>_read_next_timestep)r0is r _read_framezChemfilesReader._read_frames '')))rNc|j|jkrtd||j}||_|j|j}||||j|_|xjdz c_|S)zcopy next frame into timestepz"trying to go over trajectory limitNr) r>rGIOErrorr.r@rJ _frame_to_tsstepframe)r0r.rVs rrOz#ChemfilesReader._read_next_timesteps} : & &>?? ? :B $$TZ00 %$$$: a  rcVt|j|jkrtdtj|jj|jjf|_ |j dd|j dd<| r"d|_ |j dd|j dd<dSdS)z0convert a chemfiles frame to a :class:`TimeStep`zRThe number of atom changed in the trajectory. This is not supported by MDAnalysis.NT) rIrKr,rSnpr_celllengthsangles dimensions positionshas_velocities velocities)r0rVr.s rrTzChemfilesReader._frame_to_tss u{  t| + +7  ej0%*2CCD /!!!, QQQ    ! ! 3 $B $/2BM!!!    3 3rc 0||j}t||fi|S)z#Return writer for trajectory format)r,ChemfilesWriter)r0r1r,r3s rWriterzChemfilesReader.Writers& ?lGx;;F;;;r)r!N)r r r __doc__r%unitsrr' staticmethodr9r*rDpropertyrGr,rMrQrOrTrc __classcell__r4s@rrrs0FZ 0 0E6II\I NNN   !!X!$$X$  ***     3 3 3<<<<<<<`_ and the associated names is available in chemfiles documentation. topology : Universe or AtomGroup (optional) use the topology from this :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` to write all the timesteps to the file **kwargs : dict General writer arguments. r#arlz.Expected 'a' or 'w' as mode in ChemfilesWriterFN)rr$r%rr1r,rSrr7r@r=r6str set_topology_topology_to_chemfiles)r0r1r,moder2topologyr3s rr'zChemfilesWriter.__init__sB'(( 6/00 !  3;;43;;JKK K) M4!1     (C(( 2 ''1111166xII ''11111 rc|t|dr)|js$|jd|_dSdSdS)z2Close the trajectory file and finalize the writingr=TN)hasattrr=r@rDrBs rrDzChemfilesWriter.closeEsP 4 # # DL J     DLLL    rc |j}t|dr?|jjj}|j|jkr|}nX||j}n=t|dr |jj}n #t$rd}t|dwxYw| |}| |t|j|_ |j|dS)a3Write information associated with ``obj`` at current frame into trajectory. Topology for the output is taken from the `obj` or default to the value of the `topology` keyword supplied to the :class:`ChemfilesWriter` constructor. If `obj` contains velocities, and the underlying format supports it, the velocities are written to the file. Writing forces is unsupported at the moment. Parameters ---------- obj : AtomGroup or Universe The :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` to write. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. universe trajectoryz-Input obj is neither an AtomGroup or UniverseN)rKrurwrxr.r, copy_sliceindicesAttributeError TypeError_timestep_to_chemfilesrqrIrsr@write)r0objrKts_fullr.errmsgrVs r_write_next_framez!ChemfilesWriter._write_next_frameKs. 'IE sJ'' ',14?em33 BB!++EM::BBl++ '^& . . .DFF## - . ++B//44S#ek:J:JKK s A55Bctj}||j|jr|jdd|jdd<|jr-||jdd|jdd<|j +tj dtj gd}}n|j dd}|j dd}tj |||_|S)z9 Convert a Timestep to a chemfiles Frame N)ZrgV@)rFrameresizer, has_positionsr^r_add_velocitiesr`r]rXzerosarrayUnitCellrZ)r0r.rVr[r\s rr}z&ChemfilesWriter._timestep_to_chemfilesys !! RZ    1!#aaaEOAAA   3  " " ""$-"2E QQQ  =  hqkk28NNN+C+CVGGmBQB'G]122&F'88  rctj}t|ds|||Si}|jD]}t |dd}t |d|}tj||}t|drt|j|d<t|drt|j |d<t|drt|j |d<t|d rt |d d} |j | vr"tj| |j ||j <||j } t|j} | j| t|d r|jd krd | d<nd| d<|j||D]} |j| t |dgD]8} || jdj| jdj9|S)zM Convert an AtomGroup or an Universe to a chemfiles Topology rKnamer!typealtLocaltlocsegidsegindexresidresname record_typeATOMTis_standard_pdbFbondsrr)rTopologyrurrKgetattrAtomrorrintrrkeysResiduerIappendrvaluesresiduesadd_bondix) r0rr,rsratomrrchemfiles_atomrresidueatom_idxbonds rrqz&ChemfilesWriter._topology_to_chemfilessX%''sG$$  OOG $ $ $OI 2 2D4,,D4..D&^D$77NtX&& <+.t{+;+;x(tW%% :*-dj//w'tZ(( @-0-?-?z*tW%% ;!$ 266:X]]__44+4+<,,HTZ(#4:.x~.. $$X...4//;'61159 1225: 12 N ! !. 1 1 1 1 (( . .G   $ $W - - - -C"-- B BD   djm. 1 0@ A A A Ar)rrlr!N) r r r rer% multiframerfr'rDrr}rqr rrrbrbs  FJZ 0 0E   32323232j   , , , \266666rrbc0eZdZdZdfd ZdZdZxZS)rAaChemfiles file object (read-only) that can be pickled. This class provides a file-like object (as returned by :class:`chemfiles.Trajectory`) that, unlike standard Python file objects, can be pickled. Only read mode is supported. When the file is pickled, path, mode, and format of the file handle are saved. On unpickling, the file is opened by path with mode, and saved format. This means that for a successful unpickle, the original file still has to be accessible with its filename. Note ---- Can only be used with reading ('r') mode. Upon pickling, the current frame is reset. `universe.trajectory[i]` has to be used to return to its original frame. Parameters ---------- filename : str a filename given a text or byte string. mode : 'r' , optional only 'r' can be used for pickling. format : '', optional guessed from the file extension if empty. Example ------- :: f = ChemfilesPicklable(XYZ, 'r', '') print(f.read()) f.close() can also be used as context manager:: with ChemfilesPicklable(XYZ) as f: print(f.read()) See Also --------- :class:`MDAnalysis.lib.picklable_file_io.FileIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.BufferIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.TextIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.GzipPicklable` :class:`MDAnalysis.lib.picklable_file_io.BZ2Picklable` .. versionadded:: 2.0.0 r<r!cz|dkrtdt|||dS)Nr<z*Only read mode ('r') files can be pickled.)pathrrr%) ValueErrorr&r')r0rrrr%r4s rr'zChemfilesPicklable.__init__s@ 3;;IJJ J df=====rc*|j|j|jfSrd)r_Trajectory__mode_Trajectory__formatrBs r __getstate__zChemfilesPicklable.__getstate__sy$0$2JJJrc|j|dSrd)r')r0argss r __setstate__zChemfilesPicklable.__setstate__ s tr)r<r!)r r r rer'rrrirjs@rrArAsi33j>>>>>> KKKrrA)renumpyrXrpackaging.versionrr!rlib.utilrrr ImportErrortypesr ModuleTyper7rrr ReaderBaser WriterBaserbrAr rrrs,88r%%%%%%++++++MM * * *MLLL        ! --I)I *  PPP&t<t<t<t<t