i7#ldZddlZddlmZddlmZddZGd d eZ Gd d e Z dS)a Base classes for the selection writers ====================================== Specialized SelectionWriters are derived from :class:`SelectionWriterBase`. Override the :meth:`~SelectionWriterBase._write_head`, :meth:`~SelectionWriterBase._translate`, and :meth:`~SelectionWriterBase._write_tail` methods. .. autoclass:: SelectionWriterBase :members: __init__, write, _translate, _write_head, _write_tail, comment .. autofunction:: join N)util)_SELECTION_WRITERScddfd|ddD|dgzS)zCreate a list from sequence. *string* is appended to each element but the last. *func* is applied to every element before appending *string*. Nc|SN)xs d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/selections/base.pyzjoin..6sc,g|]}|zSr r ).0r funcstrings r zjoin..7s& / / /DDGGf  / / /rr )seqrrs ``r joinr.sJ |{ / / / / /c#2#h / / /44B==/ AArceZdZdZdS)_Selectionmetactt||| tj|d}|D]#}||}|t |<$dS#t $rYdSwxYw)Nformat)type__init__r asiterableupperrKeyError)clsnamebases classdictfmtfs r rz_Selectionmeta.__init__<s dD%333 ,/)H"566C , ,9GGII(+"1%%  , ,    DD sA&& A43A4N)__name__ __module__ __qualname__rr rr rr:s# , , , , ,rrcheZdZdZdZdZdZdZdZ ddZ dZ dZ dd Z d Z d Zd Zd ZdZdZdS)SelectionWriterBasea'Export a selection in MDAnalysis to a format usable in an external package. The :class:`SelectionWriterBase` writes a selection string to a file that can be used in another package such as `VMD`_, `PyMOL`_, `Gromacs`_ or `CHARMM`_. In this way, analysis and visualization can be done with the best or most convenient tools at hand. :class:`SelectionWriterBase` is a base class and child classes are derived with the appropriate customizations for the package file format. .. _VMD: http://www.ks.uiuc.edu/Research/vmd/ .. _PyMol: http://www.pymol.org/ .. _CHARMM: http://www.charmm.org/ .. _Gromacs: http://www.gromacs.org/ .. versionchanged:: 0.11.0 Can now also write to a :class:`~MDAnalysis.lib.util.NamedStream` instead of a normal file (using :class:`~MDAnalysis.lib.util.openany`). .. versionchanged:: 0.16.0 Remove the `wa` mode. The file is now open when the instance is created and closed with the :meth:`close` method or when exiting the `with` statement. Nrwc tj||j|_|dvr"td|||_|d|_||dkr |j|_n|durd|_n||_||_ ||_ d|_ tj |j|j|_ |dS)aNSet up for writing to *filename*. Parameters ---------- filename: output file mode: create a new file ("w"), or append ("a") to existing file ["w"] numterms: number of individual index numbers per line for output formats that write multiple entries in one line. If set to 0 or ``False`` then no special formatting is done [8] preamble: string that is written as a comment at the top of the file [] kwargs: use as defaults for :meth:`write` )ext)ar-z'mode must be one of 'w', 'a', not {0!r}rNF)mode)rfilenamer/ ValueErrorrr1 _current_modedefault_numtermsnumtermspreamble otherargsnumberanyopen_outfilewrite_preamble)selfr2r1r6r7kwargss r rzSelectionWriterBase.__init__os( hDH=== z!!9@@FF  !!W  x!|| 1DMM   DMM$DM    T]9KLLL  rc.|jdS|j|zdzS)a:Return string *s* interpolated into the comment format string. If no :attr:`SelectionWriterBase.commentfmt` is defined (None) then the empty string is returned because presumably there is no way to enter comments into the file. A newline is appended to non-empty strings. Nr ) commentfmt)r=ss r commentzSelectionWriterBase.comments# ? "2"T))rc||jdS|j||jdS)z-Write a header, depending on the file format.N)r7r;writerCr=s r r<z"SelectionWriterBase.write_preambles9 = F DLL7788888rc|j}||j|n% |jjj}n#t$rd}YnwxYw|p|jdd}|2||xjdz c_|j}djd it}| |j }|j pt|j }|j} || |t!dt|j |D]} || | |z} | d| t| |kr;| |zt|j ks | d|jzdz| d|| | ddS) aWrite selection to the output file. Parameters ---------- selection: a :class:`MDAnalysis.core.groups.AtomGroup` number: selection will be named "mdanalysis" (``None`` auto increments between writes; useful when appending) [``None``] name: selection will be named *name* (instead of numbered) [``None``] frame: write selection of this frame (or the current one if ``None`` [``None``] Nrr"zmdanalysis{number:03d})r"r r@r )universe trajectorytsframeAttributeErrorr8getr9rvars _translateatomsr6lenr; _write_headrangerEr continuation _write_tail) r= selectionr9r"rLr1uselection_termsstepoutiatomlines r rEzSelectionWriterBase.writes"     L     -!    7t~))&$77 <~ q 2+2<s r rPzSelectionWriterBase._translates "!rc dS)z)Initial output to open file object *out*.Nr r=r[r>s r rSzSelectionWriterBase._write_head rc dS)z&Last output to open file object *out*.Nr rcs r rVzSelectionWriterBase._write_tailrdrc|Sr r rFs r __enter__zSelectionWriterBase.__enter__s rc.|dSr )r_)r=excs r __exit__zSelectionWriterBase.__exit__s r)r-NN)NNNN)r'r(r)__doc__rr/rUrAr5rrCr<rEr_rPrSrVrgrjr rr r+r+Js6F CLJ;?''''R * * *999 0000d " " "      rr+) metaclass)rN) rkos.pathoslibrrrrrrr+r rr rps2  B B B B , , , , ,T , , , vvvvvNvvvvvvr