i%DdZddlZddlZddlZddlZddlZddlZejdZ ddl m Z ddl m Z ddlmZdd lmZmZdd lmZdd lmZGd d e jZGdde jZdS)aXYZ trajectory reader --- :mod:`MDAnalysis.coordinates.XYZ` ============================================================== The :ref:`XYZ format ` is a loosely defined, simple coordinate trajectory format. The implemented format definition was taken from the `VMD xyzplugin`_ and is therefore compatible with VMD. Note the following: * Comments are not allowed in the XYZ file (we neither read nor write them to remain compatible with VMD). * The atom name (first column) is ignored during reading. * The coordinates are assumed to be space-delimited rather than fixed width (this may cause issues - see below). * All fields to the right of the z-coordinate are ignored. * The unitcell information is all zeros since this is not recorded in the XYZ format. .. rubric:: Units * Coordinates are in Angstroms. * The length of a timestep can be set by passing the *dt* argument, it's assumed to be in ps (default: 1 ps). There appears to be no rigid format definition so it is likely users will need to tweak this class. .. _xyz-format: XYZ File format --------------- Definition used by the :class:`XYZReader` and :class:`XYZWriter` (and the `VMD xyzplugin`_ from whence the definition was taken):: [ comment line ] !! NOT IMPLEMENTED !! DO NOT INCLUDE [ N ] # of atoms, required by this xyz reader plugin line 1 [ molecule name ] name of molecule (can be blank) line 2 atom1 x y z [optional data] atom name followed by xyz coords line 3 atom2 x y z [ ... ] and (optionally) other data. ... atomN x y z [ ... ] line N+2 Note ---- * comment lines not implemented (do not include them) * molecule name: the line is required but the content is ignored at the moment * optional data (after the coordinates) are presently ignored .. Links .. _`VMD xyzplugin`: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html Classes ------- NzMDAnalysis.coordinates.XYZ)base)Timestep)util)cachedstore_init_arguments) NoDataError) __version__cNeZdZdZdZdZdddZ dd Zd Zd Z d Z dd Z dS) XYZWriteraWrites an XYZ file The XYZ file format is not formally defined. This writer follows the VMD implementation for the molfile `xyzplugin`_. Notes ----- By default, the XYZ writer will attempt to use the input :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` ``elements`` record to assign atom names in the XYZ file. If the ``elements`` record is missing, then the ``name`` record will be used. In the event that neither of these are available, the atoms will all be named ``X``. Please see, the `User Guide`_ for more information on how to add topology attributes if you wish to add your own elements / atom names to a :class:`~MDAnalysis.core.universe.Universe`. .. Links .. _xyzplugin: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html .. _User Guide: https://userguide.mdanalysis.org/examples/constructing_universe.html#Adding-topology-attributes .. versionchanged:: 1.0.0 Use elements attribute instead of names attribute, if present. .. versionchanged:: 2.0.0 Support for passing timestep to the writer was deprecated in 1.0 and has now been removed. As a consequence, custom names can no longer be passed to the writer, these should be added to the :class:`~MDAnalysis.core.universe.Universe`, or :class:`~MDAnalysis.core.groups.AtomGroup` before invoking the writer. XYZTpsAngstromtimelengthNc ||_||_||_||_||_t j|jd|_dS)aInitialize the XYZ trajectory writer Parameters ---------- filename: str filename of trajectory file. If it ends with "gz" then the file will be gzip-compressed; if it ends with "bz2" it will be bzip2 compressed. n_atoms: int (optional) Number of atoms in trajectory. By default assume that this is None and that this file is used to store several different models instead of a single trajectory. If a number is provided each written TimeStep has to contain the same number of atoms. convert_units : bool (optional) convert quantities to default MDAnalysis units of Angstrom upon writing [``True``] remark: str (optional) single line of text ("molecule name"). By default writes MDAnalysis version and frame precision: int (optional) set precision of saved trjactory to this number of decimal places. .. versionadded:: 2.9.0 .. versionchanged:: 1.0.0 Removed :code:`default_remark` variable (Issue #2692). .. versionchanged:: 2.0.0 Due to the removal of timestep as an input for writing, the atoms parameter is no longer relevant and has been removed. If passing an empty universe, please use ``add_TopologyAttr`` to add in the required elements or names. wtN)filenameremarkn_atoms convert_units precisionranyopen_xyz)selfrrrrrkwargss d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/XYZ.py__init__zXYZWriter.__init__sDT!   *"L55 c |jjS#ttf$rS |jjcYS#ttf$r/d}t j|tjdcYcYSwxYwwxYw)zEReturn a list of atom elements (if present) or fallback to atom nameszrInput AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X')X) atomselementsAttributeErrorr nameswarningswarn itertoolscycle)rr%wmsgs r _get_atoms_elements_or_namesz&XYZWriter._get_atoms_elements_or_namess /;' ' , / / / /{(((("K0 / / /(  d### v....... / /s) A2 .A2;A.)A2-A..A2c|j3|jd|jd|_dS)z2Close the trajectory file and finalize the writingN )rwriteclosers r r2zXYZWriter.closes; 9 IOOD ! ! ! IOO    r"c |j}t|dr?|jjj}|j|jkr|}n7||j}nt|dr |jj}|||_ n #t$rd}t|dwxYw| |dS)akWrite object `obj` at current trajectory frame to file. Atom elements (or names) in the output are taken from the `obj` or default to the value of the `atoms` keyword supplied to the :class:`XYZWriter` constructor. Parameters ---------- obj : Universe or AtomGroup The :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` to write. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. universe trajectoryz-Input obj is neither an AtomGroup or UniverseN) r%hasattrr5r6tsr copy_sliceindicesr. atomnamesr' TypeError_write_next_frame)robjr%ts_fullr8errmsgs r r1zXYZWriter.writes, FIE sJ'' ',14?em33 BB!++EM::BBl++ '^&!>>uEEDNN! . . .DFF## - .$ r"""""s BB,c |&t|dstd|j}|j>|j|jkr-t d|j|jnt |jtj st|j|jkrrt dt|j|jtj|jdg|jz|_|jr||jd}n|j}|jd |j|jFd |j|jjt0}|j|n4|j|jd zt5|j|D]@\}\}}}|jd |||||j AdS)a Write coordinate information in *ts* to the trajectory .. versionchanged:: 1.0.0 Print out :code:`remark` if present, otherwise use generic one (Issue #2692). Renamed from `write_next_timestep` to `_write_next_frame`. Nr8z9XYZWriter: no coordinate data to write to trajectory filezn_atoms keyword was specified indicating that this should be a trajectory of the same model. But the provided TimeStep has a different number ({}) then expected ({})zTrying to write a TimeStep with unknown atoms. Expected {} atoms, got {}. Try using "write" if you are using "_write_next_frame" directlyrF)inplacez{0:d} z1frame {} | Written by MDAnalysis {} (release {}) r0z.{0!s:>8} {1:10.{p}f} {2:10.{p}f} {3:10.{p}f} )p)r7r r8r ValueErrorformat isinstancer;r+r,lenloggerinfonparrayrconvert_pos_to_native positionsrr1rframe __class____name__r stripzipr)rr8 coordinatesratomxyzs r r=zXYZWriter._write_next_framesK :4&& !& W < #|rz)) vbj$,77 *t~y?? L''2:55 99?DN++RZ::"$4>!+<*= *J!K!K   '44 e5KK,K  ((44555 ; DKKHdn5{  IOOF # # # # IOODK--//$6 7 7 7 #4>;??  OD)1a IOO6$1a4>6::      r")NTNrN) rP __module__ __qualname____doc__rE multiframeunitsr!r.r2r1r=r"r r r es##JFJZ 0 0E  16161616f/// *#*#*#XDDDDDDr"r ceZdZdZdZdddZeZefdZ e e ddZ e e d d Z d Zd ZddZdZdZddZdZxZS) XYZReaderaReads from an XYZ file :Data: :attr:`ts` Timestep object containing coordinates of current frame :Methods: ``len(xyz)`` return number of frames in xyz ``for ts in xyz:`` iterate through trajectory .. Note: this can read both compressed (foo.xyz) and compressed (foo.xyz.bz2 or foo.xyz.gz) files; uncompression is handled on the fly and also reads streams via :class:`~MDAnalysis.lib.util.NamedStream`. The XYZ file format follows VMD's xyzplugin_ and is also described under :ref:`XYZ format `. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based. Added *dt* and *time_offset* keywords (passed to :class:`Timestep`) rrrrc tt|j|fi|tj|j\}}tj|j|_ |dddkr |ddnd|_ t|_ |j |jfi|j|_|dS)Nrxyz)superr`r!ospathsplitextrrrxyzfile compressiondict_cache _Timestepr _ts_kwargsr8_read_next_timestep)rrrrootextrOs r r!zXYZReader.__init__rs'i';;F;;; G$$T]33 c|DM22 &)!""g&6&63qrr77Dff  $.AAAA   """""r"rctj|j5}|}dddn #1swxYwYt |S)znumber of atoms in a frameN)rrrreadlineint)rfns r rzXYZReader.n_atomss\$- ( ( A A               1vv s ;??n_framescN |S#t$rYdSwxYw)Nr)_read_xyz_n_framesIOErrorr3s r ruzXYZReader.n_framess; **,, ,   11 s  $$cL|jdz}d}g}tj|j5}d}|rG||zs'|||}|dz }|Gdddn #1swxYwYt||z }||_|S)NrrTr) rrrrappendtellrqrr_offsets)r linesPerFramecounteroffsetsrslinerus r rwzXYZReader._read_xyz_n_framess q(  \$- ( ( AD .-NN16688,,,zz||1                  w.// sA BBBc|j|j||dz |j_|S)Nr)rgseekr|r8rNrm)rrNs r _read_framezXYZReader._read_frames> $-.///  '')))r"Nc||j}|j} ||g}t|jD]C}||ddD||_|xjdz c_|S#ttf$r}t|dd}~wwxYw)Nr) r8rgrqrangerrzsplitrMrNrD IndexErrorEOFError)rr8rstmp_bufierrs r rmzXYZReader._read_next_timesteps :B L * JJLLL JJLLLG4<(( : :qzz||1133AaC89999"BL HHMHHIJ' * * *3--T ) *sBB--C>CCcV||dSrX)r2open_trajectoryr3s r _reopenzXYZReader._reopens'  r"c|j ttjd|jt j|j|_|j}d|_|jS)NzXYZ file already opened) rgrxerrnoEALREADYrrrr8rN)rr8s r rzXYZReader.open_trajectorysU < # 94= |DM22 W|r"c 2||j}t|fd|i|S)a>Returns a XYZWriter for *filename* with the same parameters as this XYZ. Parameters ---------- filename: str filename of the output trajectory n_atoms: int (optional) number of atoms. If none is given use the same number of atoms from the reader instance is used **kwargs: See :class:`XYZWriter` for additional kwargs Returns ------- :class:`XYZWriter` (see there for more details) See Also -------- :class:`XYZWriter` Nr)rr )rrrrs r WriterzXYZReader.Writers+, ?lG==7=f===r"cX|jdS|jd|_dS)z)Close xyz trajectory file if it was open.N)rgr2r3s r r2zXYZReader.closes. <  F  r"rX)rPrYrZr[rEr]rrkr r!propertyrrrurwrrmrrrr2 __classcell__)rOs@r r`r`Ms9>FZ 0 0EI#####$ VIX VJX (*** *****   >>>>4r"r`)r[r+rdrnumpyrJr)logging getLoggerrHrtimesteprlibrlib.utilrr exceptionsr versionr WriterBaser ReaderBaser`r^r"r rsH2::v   7 8 833333333$$$$$$!!!!!!eeeeeeeePhhhhhhhhhhr"