i,dZddlZddlZddlZddlmZddlmZddl m Z Gdd e j Z Gd d e j ZdS) aCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.CRD` =========================================================================== Read and write coordinates in CHARMM CARD coordinate format (suffix "crd"). The CHARMM "extended format" is handled automatically. N) NoDataError)util)basec,eZdZdZdZdddZdZdZdS) CRDReaderzCRD reader that implements the standard and extended CRD coordinate formats .. versionchanged:: 0.11.0 Now returns a ValueError instead of FormatError. Frames now 0-based instead of 1-based. CRDNAngstromtimelengthc `g}tj|j5}d}d}t|D]k\}}|ds|dkrF|}t|dkr"t|d}|ddk} |rQ| tj |dd dd t nP| tj |d d dd t 5#t$r+d|d|}t|dwxYw dddn #1swxYwYt||_|jjtj |fi|j|_d|j_|j|krtd|j|j|fzdS)NFr*rEXT-ddtype2zCheck CRD format at line z: zUFound %d coordinates in %r but the header claims that there should be %d coordinates.)ropenanyfilename enumeratestrip startswithsplitlenintappendnparrayfloat Exceptionrstrip ValueErrorn_atoms _Timestepfrom_coordinates _ts_kwargstsframe) self coords_listcrdfileextendednatomslinenumlinefieldserrmsgs d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/CRD.py_read_first_framezCRDReader._read_first_frame4s \$- ( ( 7GHF!*7!3!3 7 7 ::<<**3//4::<<23E3Ev;;!## ^^F%bzU2H7#**HT"S&\%7%7%9%9!A#%>eLLL$**HT"R%[%6%6%8%81%=UKKK!777+G++;;==++%V,,$6 7' 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7:;'' 1$.1 H[ ! !  %)_   <6 ! !,<78  " !s+B#F*B#E%#F*%5FF**F.1F.c t|fi|S)zReturns a CRDWriter for *filename*. Parameters ---------- filename: str filename of the output CRD file Returns ------- :class:`CRDWriter` ) CRDWriterr0rkwargss r9WriterzCRDReader.Writerls,,V,,,)__name__ __module__ __qualname____doc__formatunitsr:r?r@r9r r )sQFZ 0 0E666p - - - - -r@r c>eZdZdZdZdddZdddd d d Zd Zdd ZdS)r<aCRD writer that implements the CHARMM CRD coordinate format. It automatically writes the CHARMM EXT extended format if there are more than 99,999 atoms. Requires the following attributes to be present: - resids - resnames - names - chainIDs - tempfactors .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 2.2.0 CRD extended format can now be explicitly requested with the `extended` keyword .. versionchanged:: 2.6.0 Files are now written in `wt` mode, and keep extensions, allowing for files to be written under compressed formats r Nr r z{serial:10d}{totRes:10d} {resname:<8.8s} {name:<8.8s}{pos[0]:20.10f}{pos[1]:20.10f}{pos[2]:20.10f} {chainID:<8.8s} {resSeq:<8d}{tempfactor:20.10f} z {0:10d} EXT z{serial:5d}{totRes:5d} {resname:<4.4s} {name:<4.4s}{pos[0]:10.5f}{pos[1]:10.5f}{pos[2]:10.5f} {chainID:<4.4s} {resSeq:<4d}{tempfactor:10.5f} z* FRAME {frame} FROM {where} z{0:5d} )ATOM_EXT NUMATOMS_EXTATOMTITLENUMATOMSc tj|dd|_d|_|dd|_dS)a4 Parameters ---------- filename : str or :class:`~MDAnalysis.lib.util.NamedStream` name of the output file or a stream extended : bool (optional) By default, noextended CRD format is used [``False``]. However, extended CRD format can be forced by specifying `extended` ``=True``. Note that the extended format is *always* used if the number of atoms exceeds 99,999, regardless of the setting of `extended`. .. versionadded:: 2.2.0 crdT)extkeepNr3F)rrrOpopr3r=s r9__init__zCRDWriter.__init__s>" hEEEE  :u55 r@c |j}n #t$rd}t|dwxYw||j|n% |jjj}n#t$rd}YnwxYw|j}|j}t|}|j s|dkr|j d}d} d} d} n|j d}d } d } d } i} g} d tj d fd tj|tfdtj dfdtj dffD]J\}} t!||| |<#t"tf$r|| |<| |YGwxYw |j| d<nf#t"tf$rR |j| d<nC#t"tf$r/tj d| d<| |YnwxYwYnwxYw| r;t+jdd| t3j|jd5}||j d||jj|d|j s|dkr4||j d|n3||j d|d}| d }t;t=||| d | d| d| d | dD]\}}}}}}}|dks||||dz kr|dz }t3j|dz| }t3j|| }t3j|| }|||||||||| ddddS#1swxYwYdS) a1Write selection at current trajectory frame to file. Parameters ---------- selection : AtomGroup group of atoms to be written frame : int (optional) Move the trajectory to frame `frame`; by default, write the current frame. z-Input obj is neither an AtomGroup or UniverseNrirI rKresnames)UNKresidsrnames)X tempfactors)gchainIDs)rzlSupplied AtomGroup was missing the following attributes: {miss}. These will be written with default values. z, )misswtrL)r/wherez* rJrMr)serialtotResresnamenameposchainIDresSeq tempfactor) universeAttributeError TypeError trajectoryr.r/atoms positionsr!r3fmt itertoolscycler$onesr"getattrrr#r_segidswarningswarnrEjoinrrrwriteziprange ltruncate_int)r0 selectionr/ur8rocoorr*at_fmt serial_len resid_len totres_lenattrsmissing_topologyattrdefaultrO current_residr[irgrerfrhresidrjrcs r9rzzCRDWriter.writes ."AA . . .DFF## - .   L     -!     O e** = GeOOXj)FJIJJXf%FJIJ 22 3 rwwc222 3 iof-- . IOF33 4  . .MD' .%eT22d 0 . . .%d  ''----- . . %E*  ^, . . . .$)Lj!!0 . . .$-OE$:$:j! ''----- .  .   M6tyy)9::6;;    \$- . ./ # II!((q|'<)    IIe   } @% $(>299'BBCCCC $(:.55g>>???M8_FEHgj!gj!hm$FF  A3wzAvv&)va!e}"<"<!Q&M+AE:>>*5)<< $ 2=* M M  MM%, '! '$#-"      # '/ / / / / / / / / / / / / / / / / / st 'A AAD+++EE E((G : FG =GG GG  G %F0O##O'*O')N) rArBrCrDrErFrqrSrzrGr@r9r<r<|s,FZ 0 0E  A( ?2#  C(666.}}}}}}r@r<)rDrrnumpyr$rw exceptionsrlibrrrSingleFrameReaderBaser WriterBaser<rGr@r9rs2$$$$$$P-P-P-P-P-*P-P-P-fBBBBBBBBBBr@