iL-dZddlZddlZddlZddlmZddlmZdZ Gdd ej Z Gd d ej Z Gd d ejZdS)a  XVG auxiliary reader --- :mod:`MDAnalysis.auxiliary.XVG` ======================================================== xvg files are produced by Gromacs during simulation or analysis, formatted for plotting data with Grace. Data is column-formatted; time/data selection is enabled by providing column indices. Note ---- By default, the time of each step is assumed to be stored in the first column, in units of ps. .. autoclass:: XVGStep :members: XVG Readers ----------- The default :class:`XVGReader` reads and stores the full contents of the .xvg file on initialisation, while a second reader (:class:`XVGFileReader`) that reads steps one at a time as required is also provided for when a lower memory footprint is desired. Note ---- Data is assumed to be time-ordered. Multiple datasets, separated in the .xvg file by '&', are currently not supported (the readers will stop at the first line starting '&'). .. autoclass:: XVGReader :members: .. autoclass:: XVGFileReader :members: .. autofunction:: uncomment N)base)anyopenc#K|D]d}|}|s|ddkr&|d}|dkr|d|r |d|VX|dkr|r|VedS)zRemove comments from lines in an .xvg file Parameters ---------- lines : list of str Lines as directly read from .xvg file Yields ------ str The next non-comment line, with any trailing comments removed r@#N)stripfind)linesline stripped_linecomment_positions b/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/auxiliary/XVG.py uncommentrLs        s " " (--c22 a  M2C3C2C$D  1!1 12 2 2 2 2  ! !m !      c0eZdZdZdfd ZdZdZxZS)XVGStepaAuxStep class for .xvg file format. Extends the base AuxStep class to allow selection of time and data-of-interest fields (by column index) from the full set of data read each step. Parameters ---------- time_selector : int | None, optional Index of column in .xvg file storing time, assumed to be in ps. Default value is 0 (i.e. first column). data_selector : list of int | None, optional List of indices of columns in .xvg file containing data of interest to be stored in ``data``. Default value is ``None``. **kwargs Other AuxStep options. See Also -------- :class:`~MDAnalysis.auxiliary.base.AuxStep` rNc Ntt|jd||d|dS)N) time_selector data_selector)superr__init__)selfrrkwargs __class__s rrzXVGStep.__init__sE%gt% '}  HN     rc|dSt|tjr||St d)Nz"Time selector must be single index) isinstancenumbersIntegral _select_data ValueError)rkeys r _select_timezXVGStep._select_timesE ; F c7+ , , C$$S)) )ABB Brc |dSt|tjrF j|S#t$r+|dt jd}t |dwxYwtjfd|DS)Nz! not a valid index for data with z columnsc:g|]}|Sr)r").0irs r z(XVGStep._select_data..s'???aT..q11???r) rr r!_data IndexErrorlenr#nparray)rr$errmsgs` rr"zXVGStep._select_datas ; F c7+ , , A 3z#& 3 3 3114:111!((d2  38????3???@@ @s .5A#)rN)__name__ __module__ __qualname____doc__rr%r" __classcell__rs@rrrjso,      CCCAAAAAAArrcBeZdZdZdZeZfdZdZdZ dZ dZ xZ S) XVGReaderaAuxiliary reader to read data from an .xvg file. Default reader for .xvg files. All data from the file will be read and stored on initialisation. Parameters ---------- filename : str Location of the file containing the auxiliary data. **kwargs Other AuxReader options. See Also -------- :class:`~MDAnalysis.auxiliary.base.AuxReader` Note ---- The file is assumed to be of a size such that reading and storing the full contents is practical. XVGc tj||_t |5}|}dddn #1swxYwYg}t t|D]\}}|ddkrn| d| Dt||t|dkr0td ||||dtj||_t|j|_t%t&|jdi|dS)Nr&c,g|]}t|Srfloat)r(vals rr*z&XVGReader.__init__..s"F"F"F#5::"F"F"Frz'Step {0} has {1} columns instead of {2}r)ospathabspath_auxdatar readlines enumeraterlstripappendsplitr-r#formatr.r/_auxdata_values_n_stepsrr8r) rfilenamerxvg_filer auxdata_valuesr)r rs rrzXVGReader.__init__s11 X   )(&&((E ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) 5!1!122  GAt{{}}Q3&&  ! !"F"F"F"F"F G G G>!$%%^A->)?)???  &N1$5~a7HII@ "x77D011 'i'11&11111sAAAc|jjSN)rJnbytesrs r _memory_usagezXVGReader._memory_usages#**rc|j}|jdz}||jkr|j||_||_|S|t )aRead next auxiliary step and update ``auxstep``. Returns ------- AuxStep object Updated with the data for the new step. Raises ------ StopIteration When end of auxiliary data set is reached. r)auxstepstepn_stepsrJr+rewind StopIteration)rrUnew_steps r_read_next_stepzXVGReader._read_next_stepsQ,9q= dl " " 0:GM#GLN KKMMM rc||jks|dkr(td||j|dz |j_||jS)a-Move to and read i-th auxiliary step. Parameters ---------- i: int Step number (0-indexed) to move to Returns ------- :class:`XVGStep` Raises ------ ValueError If step index not in valid range. rz:Step index {0} is not valid for auxiliary (num. steps {1})r)rWr#rIrUrVnext)rr)s r _go_to_stepzXVGReader._go_to_stepsf"   A##)6!T\#:#: E  |rc.|jdd|jfS)zGet NumPy array of time at each step. Returns ------- NumPy array of float Time at each step. N)rJrrRs rread_all_timeszXVGReader.read_all_timess#AAAt'9$9::r) r1r2r3r4rIr_AuxsteprrSr[r^r`r5r6s@rr8r8s,FH22222*+++   .4;;;;;;;rr8c<eZdZdZdZeZfdZdZdZ dZ xZ S) XVGFileReadera/Auxiliary reader to read (one step at a time) from an .xvg file. An alternative XVG reader which reads each step from the .xvg file as needed (rather than reading and storing all from the start), for a lower memory footprint. Parameters ---------- filename : str Location of the file containing the auxiliary data. **kwargs Other AuxReader options. See Also -------- :class:`~MDAnalysis.auxiliary.base.AuxFileReader` Note ---- The default reader for .xvg files is :class:`XVGReader`. zXVG-Fc Jtt|j|fi|dSrP)rrcr)rrLrrs rrzXVGFileReader.__init__)s.+mT""+H???????rc t|j} |r2|r9|ddkr|tt |gD]}|j}|jdz|_d|D|_ |j n)#t$rt|j |_ YnwxYwt|j |j kr4td|jdt|j d|j |cSt|j}7) a'Read next recorded step in xvg file and update ``auxstep``. Returns ------- AuxStep object Updated with the data for the new step. Raises ------ StopIteration When end of file or end of first data set is reached. Trr;rc,g|]}t|Srr=)r(r)s rr*z1XVGFileReader._read_next_step..Es G G Gaq G G GrzStep z has z columns instead of )r]auxfiler rXrYrrUrVrHr+_n_colsAttributeErrorr-r#)rr uncommentedrUs rr[zXVGFileReader._read_next_step,siDL!! & $DJJLL $TZZ\\!_-C-C ##($00   ,#y1} G G;3D3D3F3F G G G 9OOO%999&)'-&8&8GOOO9w}%%88$0 00w}--00%o00  %%D5 &s1B99#CCc|js_ t|jS#t$r=||_t|cYSwxYw|d}|D]}|dz}|S)zIterate through all steps to count total number. Returns ------- int Total number of steps rr) constant_dtr-_timesrir`_restart)rcountrVs r_count_n_stepszXVGFileReader._count_n_stepsVs  24;'''! 2 2 2#1133 4..0011111  2 MMOOOE " " LsAA$#A$c|g}|D]}||jtj|S)zIterate through all steps to build times list. Returns ------- NumPy array of float Time of each step )rnrGtimer.r/)rtimesrVs rr`zXVGFileReader.read_all_timesosJ  $ $D LL # # # #xr) r1r2r3r4rIrrarr[rpr`r5r6s@rrcrcs.FH@@@@@(&(&(&T2       rrc)r4r r@numpyr.rlib.utilrrAuxStepr AuxReaderr8 AuxFileReaderrcrrrrzs0,,Z    <3A3A3A3A3Adl3A3A3Alk;k;k;k;k;k;k;k;\mmmmmD&mmmmmr