i52dZddlZddlZddlZddlmZddlmZGddej Z Gd d ej Z dS) u PQR file format --- :mod:`MDAnalysis.coordinates.PQR` ===================================================== Read atoms with charges from a PQR_ file (as written by PDB2PQR_). The following is adopted from the description of the PQR_ format as used by APBS_: *MDAnalysis* reads very loosely-formatted PQR files: all fields are **whitespace-delimited** rather than the strict column formatting mandated by the PDB_ format. This more liberal formatting allows coordinates which are larger/smaller than ±999 Å. MDAnalysis reads data on a per-line basis from PQR files using the following format:: recordName serial atomName residueName chainID residueNumber X Y Z charge radius If this fails it is assumed that the *chainID* was omitted and the shorter format is read:: recordName serial atomName residueName residueNumber X Y Z charge radius Anything else will raise a :exc:`ValueError`. The whitespace is the most important feature of this format: fields *must* be separated by at least one space or tab character. The fields are: *recordName* A string which specifies the type of PQR entry and should either be ATOM or HETATM. *serial* An integer which provides the atom index (but note that MDAnalysis renumbers atoms so one cannot rely on the *serial*) *atomName* A string which provides the atom name. *residueName* A string which provides the residue name. *chainID* An optional string which provides the chain ID of the atom. *residueNumber* An integer which provides the residue index. *X Y Z* Three floats which provide the atomic coordiantes. *charge* A float which provides the atomic charge (in electrons). *radius* A float which provides the atomic radius (in Å). Clearly, this format can deviate wildly from PDB_ due to the use of whitespaces rather than specific column widths and alignments. This deviation can be particularly significant when large coordinate values are used. Output should look like this (although the only real requirement is *whitespace* separation between *all* entries). The chainID is optional and can be omitted:: ATOM 1 N MET 1 -11.921 26.307 10.410 -0.3000 1.8500 ATOM 36 NH1 ARG 2 -6.545 25.499 3.854 -0.8000 1.8500 ATOM 37 HH11 ARG 2 -6.042 25.480 4.723 0.4600 0.2245 .. Warning:: Fields *must be white-space separated* or data are read incorrectly. PDB formatted files are *not* guaranteed to be white-space separated so extra care should be taken when quickly converting PDB files into PQR files using simple scripts. For example, PQR files created with PDB2PQR_ and the `--whitespace` option are guaranteed to conform to the above format:: pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr Notes ----- The PQR format does not provide a means by which to provide box information. In all cases the `dimensions` attribute will be set to `None`. .. _PQR: https://apbs.readthedocs.io/en/latest/formats/pqr.html .. _APBS: https://apbs.readthedocs.io/en/latest/ .. _PDB2PQR: https://pdb2pqr.readthedocs.io/en/latest/ .. _PDB: http://www.wwpdb.org/documentation/file-format N)util)basec8eZdZdZdZdddZddddZd Zd ZdS) PQRReaderzRead a PQR_ file into MDAnalysis. .. _PQR: https://apbs.readthedocs.io/en/latest/formats/pqr.html .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based PQRNAngstromtimelength))i)ORIGINAL NO_CHAINIDGROMACSc,ddlm}d}g}tj|j5}|D]o}|drX|%||}|j|\}}|}| |||p dddn #1swxYwYt||_ |j j |fi|j|_d|j_|jr!||jjdSdS)Nr) PQRParser)ATOMHETATMr)topology.PQRParserrropenanyfilename startswith guess_flavour_SLICE_INDICESsplitappendlenn_atoms _Timestepfrom_coordinates _ts_kwargstsframe convert_unitsconvert_pos_from_native_pos) selfrflavourcoordspqrfilelinexyfieldss d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/PQR.py_read_first_framezPQRReader._read_first_framesg222222 \$- ( ( /G / /??#566/"+"9"9$"?"?#27;1!ZZ\\FMM&1+... / / / / / / / / / / / / / / / /6{{ 1$.1&LLDOLL   7  ( ( 6 6 6 6 6 7 7sA3B$$B(+B(c t|fi|S)zReturns a PQRWriter for *filename*. Parameters ---------- filename : str filename of the output PQR file Returns ------- :class:`PQRWriter` ) PQRWriter)r*rkwargss r2WriterzPQRReader.Writers,,V,,,) __name__ __module__ __qualname____doc__formatunitsrr3r7r8r2rrtsgFZ 0 0EN 7770 - - - - -r8rc8eZdZdZdZdddZdZdZd d Zd d Z dS) r5aWrite a single coordinate frame in whitespace-separated PQR format. Charges ("Q") are taken from the :attr:`MDAnalysis.core.groups.Atom.charge` attribute while radii are obtaine from the :attr:`MDAnalysis.core.groups.Atom.radius` attribute. * If the segid is 'SYSTEM' then it will be set to the empty string. Otherwise the first letter will be used as the chain ID. * The serial number always starts at 1 and increments sequentially for the atoms. The output format is similar to ``pdb2pqr --whitespace``. .. versionadded:: 0.9.0 .. 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 zATOM {serial:6d} {name:<4} {resname:<3} {chainid:1.1} {resid:4d} {pos[0]:-8.3f} {pos[1]:-8.3f} {pos[2]:-8.3f} {charge:-7.4f} {radius:6.4f} zREMARK {0} {1} Tc tj|dd|_||_|dd|_dS)aSet up a PQRWriter with full whitespace separation. Parameters ---------- filename : str output filename convert_units: bool (optional) units are converted to the MDAnalysis base format; [``True``] remarks : str (optional) remark lines (list of strings) or single string to be added to the top of the PQR file pqrT)extkeepremarkszPQR file written by MDAnalysisN)rrr'poprE)r*rr'r6s r2__init__zPQRWriter.__init__sC hEEEE  zz)-MNN r8cd |j}n #t$rd}t|dwxYw||j|n% |jjj}n#t$rd}YnwxYw|j}|j}|jr| |i}g}dtj dfdtj dfdtj d fd tj d fd tj d ffD]C\} } t|| || <#t$r| || <| | Y@wxYw |j|d<n,#t$r |j|d<n#t$rYnwxYwYnwxYwd|vst!|ddkrtj d|d<d |vrd} n|} |r;t%jdd|t-j|jd5} t-j|jD]0} | |j| d1| |jd||jjd| |jd| dt;t=||d|d|d|d|d |d dD]\\}\}}}}}}}t?|dkrd|zn|}| |j ||||||||] ddddS#1swxYwYdS)aWrite selection at current trajectory frame to file. Parameters ---------- selection : AtomGroup or Universe MDAnalysis AtomGroup or Universe frame : int (optional) optionally move to frame index `frame`; by default, write the current frame .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based z-Input obj is neither an AtomGroup or UniverseNrnames)Xresnames)UNKresids)rcharges)radii)g?chainidsSYSTEM) rOzlSupplied AtomGroup was missing the following attributes: {miss}. These will be written with default values. z, )misswtrzInput: frame {0} of {1}ztotal charge: {0:+8.4f} e)startrS)serialnameresnamechainidresidposchargeradius)!universeAttributeError TypeError trajectoryr%r&atoms positionsr'convert_pos_to_native itertoolscyclegetattrrrQsegidsall total_chargewarningswarnr=joinrrr asiterablerEwrite fmt_remark enumeratezipr fmt_ATOM)r* selectionr&uerrmsgrf coordinatesattrsmissing_topologyattrdfltrnr-rem atom_indexr_r[r\r]r^r`ras r2rszPQRWriter.writes" ."AA . . .DFF## - .   L     -!     O      & &    iof-- . 22 3 yt,, -  // 0 iof-- .  . .JD$ .%eT22d ! . . ."d  ''----- .  %E*      $)Lj!!!      U""c% *;x*G&H&H" ) 7 7E*  ( ( (LL --//L   M6tyy)9::6;;    \$- . .7 't|44 > > do44S!<<==== MM&&-44q|4     MM&&/66|DDa   'N*%*%(O)$'N   " "  &)YY]]sTzz M(()! ' '#%%)      /" +7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 st 'A AA>D$D98D9= E E1 EE1 E+(E1*E++E10E1E=N%%N),N))T)N) r9r:r;r<r=r>rwrtrGrsr?r8r2r5r5su*FZ 0 0E 9 &JOOOO&QQQQQQr8r5) r<rinumpynprolibrrSingleFrameReaderBaser WriterBaser5r?r8r2rs2RRf8-8-8-8-8-*8-8-8-vEEEEEEEEEEr8