idZddlmZddlZddlmZddlmZGdd ej Z Gd d ej Z dS) aNAMDBIN files format --- :mod:`MDAnalysis.coordinates.NAMDBIN` ================================================================================ Read/Write coordinates in `NAMD double-precision binary format`_ (suffix "coor" or "namdbin"). .. _`NAMD double-precision binary format` : https://www.ks.uiuc.edu/Research/namd/2.10/ug/node11.html#SECTION00061500000000000000 Classes ------- .. autoclass:: NAMDBINReader :members: .. autoclass:: NAMDBINWriter :members: )packN)base)utilcDeZdZdZddgZddiZdZedZdZ d S) NAMDBINReaderzKReader for NAMD binary coordinate files. .. versionadded:: 1.0.0 COORNAMDBINlengthAngstromct|jd5}tj|tjdd|_|j|jfi|j|_d|j_ tj|tj |jdz}tj |t |jd|jjdd<ddddS#1swxYwYdS)Nrbrdtypecountr)openfilenamenpfromfileint32n_atoms _Timestep _ts_kwargstsframefloat64arrayfloatreshape_pos)selfnamdbin coord_doubles h/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/NAMDBIN.py_read_first_framezNAMDBINReader._read_first_frame<s $- & & ';wbhaHHHKDL$dnT\EET_EEDGDGM;rz1AL!h|U;;CC aDGLO                  sCC$$C(+C(c t|d5}tj|tjdd}dddn #1swxYwY|S)Nrrrr)rrrr)rkwargsr$rs r& parse_n_atomszNAMDBINReader.parse_n_atomsIs (D ! ! GWk'CCCAFG G G G G G G G G G G G G G G Gs(AA  A c t|fi|S)zReturns a NAMDBINWriter for *filename*. Parameters ---------- filename: str filename of the output NAMDBIN file Returns ------- :class:`NAMDBINWriter` ) NAMDBINWriter)r#rr)s r&WriterzNAMDBINReader.WriterOsX00000N) __name__ __module__ __qualname____doc__formatunitsr' staticmethodr*r-r.r&r r 2sm i F z "E   \ 1 1 1 1 1r.r c2eZdZdZddgZdddZd dZdZdS) r,zWriter for NAMD binary coordinate files. Note ---- * Does not handle writing to bz2 or gz compressed file types. .. versionadded:: 1.0.0 r r Nr )timer c 8tj||_dS)z Parameters ---------- filename : str or :class:`~MDAnalysis.lib.util.NamedStream` name of the output file or a stream n_atoms : int number of atoms for the output coordinate N)rr)r#rrr)s r&__init__zNAMDBINWriter.__init__ns h// r.c t|dr4|j}t|}|j|dz}nd}t |dt j|jd5}| td|| td t|g|RddddS#1swxYwYdS)a<Write information associated with ``obj`` at current frame into trajectory Parameters ---------- obj : :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` write coordinate information associated with `obj` .. versionchanged:: 1.0.0 Renamed from `write` to `_write_next_frame`. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. atomsrz-Input obj is neither an AtomGroup or UniverseNwbiz{:d}d) hasattrr<len positionsr! TypeErrorropenanyrwriterr3)r#objr<rcoorerrmsgr$s r&_write_next_framezNAMDBINWriter._write_next_frameys0$ 3  .IE%jjG?**7Q;77DDDFF## - \$- . . B' MM$sG,, - - - MM$w~~c$ii88@4@@@ A A A  B B B B B B B B B B B B B B B B B Bs1A$C""C&)C&)N)r/r0r1r2r3r4r:rHr6r.r&r,r,_s_  i FZ 0 0E 0 0 0 0BBBBBr.r,) r2structrnumpyrrlibrSingleFrameReaderBaser WriterBaser,r6r.r&rOs2$*1*1*1*1*1D.*1*1*1Z8B8B8B8B8BDO8B8B8B8B8Br.