i>dZddlZddlZddlZddlZddlZddlmZddl m Z Gdde j Z Gd d e j ZdS) ab PDBQT structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.PDBQT` =========================================================================== MDAnalysis reads coordinates from PDBQT_ files and additional optional data such as B-factors, partial charge and AutoDock_ atom types. It is also possible to substitute a PDBQT file for a PSF file in order to define the list of atoms (but no connectivity information will be available in this case). .. _PDBQT: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf .. _AutoDock: http://autodock.scripps.edu/ N)util)basec,eZdZdZdZdddZdZdZdS) PDBQTReaderaPDBQTReader that reads a PDBQT-formatted file, no frills. Records read: - CRYST1 for unitcell A,B,C, alpha,beta,gamm - ATOM. HETATM for x,y,z Original `PDB format documentation`_ with `AutoDOCK extensions`_ .. _PDB format documentation: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html .. _AutoDOCK extensions: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file ============= ============ =========== ============================================= COLUMNS DATA TYPE FIELD DEFINITION ============= ============ =========== ============================================= 1 - 6 Record name "CRYST1" 7 - 15 Real(9.3) a a (Angstroms). 16 - 24 Real(9.3) b b (Angstroms). 25 - 33 Real(9.3) c c (Angstroms). 34 - 40 Real(7.2) alpha alpha (degrees). 41 - 47 Real(7.2) beta beta (degrees). 48 - 54 Real(7.2) gamma gamma (degrees). 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. IGNORED 18 - 21 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. IGNORED 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 67 - 70 LString(4) footnote Usually blank. IGNORED. 71 - 76 Real(6.4) partialChrg Gasteiger PEOE partial charge *q*. 79 - 80 LString(2) atomType AutoDOCK atom type *t*. ============= ============ =========== ============================================= We ignore torsion notation and just pull the partial charge and atom type columns:: COMPND NSC7810 REMARK 3 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: A7_7 and C22_23 REMARK 2 A between atoms: A9_9 and A11_11 REMARK 3 A between atoms: A17_17 and C21_21 ROOT 123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference) ATOM 1 A1 INH I 1.054 3.021 1.101 0.00 0.00 0.002 A ATOM 2 A2 INH I 1.150 1.704 0.764 0.00 0.00 0.012 A ATOM 3 A3 INH I -0.006 0.975 0.431 0.00 0.00 -0.024 A ATOM 4 A4 INH I 0.070 -0.385 0.081 0.00 0.00 0.012 A ATOM 5 A5 INH I -1.062 -1.073 -0.238 0.00 0.00 0.002 A ATOM 6 A6 INH I -2.306 -0.456 -0.226 0.00 0.00 0.019 A ATOM 7 A7 INH I -2.426 0.885 0.114 0.00 0.00 0.052 A ATOM 8 A8 INH I -1.265 1.621 0.449 0.00 0.00 0.002 A ATOM 9 A9 INH I -1.339 2.986 0.801 0.00 0.00 -0.013 A ATOM 10 A10 INH I -0.176 3.667 1.128 0.00 0.00 0.013 A ENDROOT BRANCH 9 11 ATOM 11 A11 INH I -2.644 3.682 0.827 0.00 0.00 -0.013 A ATOM 12 A16 INH I -3.007 4.557 -0.220 0.00 0.00 0.002 A ATOM 13 A12 INH I -3.522 3.485 1.882 0.00 0.00 0.013 A ATOM 14 A15 INH I -4.262 5.209 -0.177 0.00 0.00 -0.024 A ATOM 15 A17 INH I -2.144 4.784 -1.319 0.00 0.00 0.052 A ATOM 16 A14 INH I -5.122 4.981 0.910 0.00 0.00 0.012 A ATOM 17 A20 INH I -4.627 6.077 -1.222 0.00 0.00 0.012 A ATOM 18 A13 INH I -4.749 4.135 1.912 0.00 0.00 0.002 A ATOM 19 A19 INH I -3.777 6.285 -2.267 0.00 0.00 0.002 A ATOM 20 A18 INH I -2.543 5.650 -2.328 0.00 0.00 0.019 A BRANCH 15 21 ATOM 21 C21 INH I -0.834 4.113 -1.388 0.00 0.00 0.210 C ATOM 22 O1 INH I -0.774 2.915 -1.581 0.00 0.00 -0.644 OA ATOM 23 O3 INH I 0.298 4.828 -1.237 0.00 0.00 -0.644 OA ENDBRANCH 15 21 ENDBRANCH 9 11 BRANCH 7 24 ATOM 24 C22 INH I -3.749 1.535 0.125 0.00 0.00 0.210 C ATOM 25 O2 INH I -4.019 2.378 -0.708 0.00 0.00 -0.644 OA ATOM 26 O4 INH I -4.659 1.196 1.059 0.00 0.00 -0.644 OA ENDBRANCH 7 24 TORSDOF 3 123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference) .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based PDBQTNAngstromtimelengthc g}tjdtj}tj|j5}|D]}|drn|drstj|dd|dd|ddf\}}}tj|dd|dd |d d f\}} } ||||| | f|dd<|d r0||d d |d d|dd gdddn #1swxYwYt||_ |j j |fi|j |_ ||j _d|j _|jrT||j j|j j+||j jdddSdSdS)N)dtypezEND CRYST1!(/6)ATOMHETATM&.r)npzerosfloat32ropenanyfilename startswithappendlenn_atoms _Timestepfrom_coordinates _ts_kwargsts dimensionsframe convert_unitsconvert_pos_from_native_pos) selfcoordsunitcellpdbfilelinexyzABGs f/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/PDBQT.py_read_first_framezPDBQTReader._read_first_framesV8ARZ000 \$- ( ( KG K K??7++E??8,, 3 jadT"R%[$r"u+>GAq!!jbed2b5k42;?GAq!#$Q1a"2HQQQK??#566KMM42;RU T"R%["IJJJ' K K K K K K K K K K K K K K K(6{{ 1$.1&LLDOLL%   E  ( ( 6 6 6w!-,,TW-?-CDDDDD  E E.-sC*D22D69D6c t|fi|S)zReturns a permissive (simple) PDBQTWriter for *filename*. Parameters ---------- filename : str filename of the output PDBQT file Returns ------- :class:`PDBQTWriter` ) PDBQTWriterr0r"kwargss r;WriterzPDBQTReader.Writers8..v...)__name__ __module__ __qualname____doc__formatunitsr<rArBr;rr3sW[[zFZ 0 0EEEEB / / / / /rBrcLeZdZdZdddddZdZdd d Zd d d ZdZdZ ddZ dS)r>aPDBQT writer that implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec. .. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html .. _PDBQT: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf .. versionchanged:: 2.6.0 Files are now written in `wt` mode, and keep extensions, allowing for files to be written under compressed formats zATOM {serial:5d} {name:<4.4s} {resName:<4.4s}{chainID:1.1s}{resSeq:4d}{iCode:1.1s} {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}{tempFactor:6.2f} {charge:< 1.3f} {element:<2.2s} zREMARK {0} zTITLE {0} zrCRYST1{box[0]:9.3f}{box[1]:9.3f}{box[2]:9.3f}{ang[0]:7.2f}{ang[1]:7.2f}{ang[2]:7.2f} {spacegroup:<11s}{zvalue:4d} )rREMARKTITLErr Nr r g"?g-@)minmaxc |tj|dd|_tj|jd|_dS)NpdbqtT)extkeepwt)rr"anyopenpdbr?s r;__init__zPDBQTWriter.__init__s3 hG$GGG < t44rBc8|jdSN)rUclose)r0s r;rYzPDBQTWriter.closes rBc8 |j}n #t$rd}t|dwxYw||j|n% |jjj}n#t$rd}YnwxYw|j}|j}i}g}dD]V\} } t|| || <#t$r0tj | f|| <| | YSwxYw |j |d<nX#t$rK |j |d<n<#t$r/tj d|d<| dYnwxYwYnwxYw|r;tjdd| ||j|s| t+j|jn-#t0$r } | jt2jkr Yd} ~ nd} ~ wwxYwt7d |jd |jd d t9|zdzt9|jjz} |j|jd| | |jj} |j|jd| dd| ddddtCtE||d|d|d|d|d|d|d|d|d dD]\}\ }}}}}}}}}}tGj$|d}tGj$|d}|dd}tK|dkrd |z}|&d!d}|j|jd"|||||||||||# |dS)$a5Write selection at current trajectory frame to file. Parameters ---------- selection : AtomGroup The selection to be written frame : int (optional) optionally move to frame index `frame` before writing; the default is to write the current trajectory frame Note ---- The last letter of the :attr:`~MDAnalysis.core.groups.Atom.segid` is used as the PDB chainID. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based z-Input obj is neither an AtomGroup or UniverseNr) )altLocs )charges)icodesr\)namesX) occupanciesg?)residsr)resnamesUNK) tempfactorsr^)typesz chainids)r\zlSupplied AtomGroup was missing the following attributes: {miss}. These will be written with default values. z, )misszaPDB files must have coordinate values between {0:.3f} and {1:.3f} Angstroem: No file was written.rMrNzFRAME z FROM rLrrzP 1r)boxang spacegroupzvaluer`rdrcr_rbrfr]rg)startr\r) serialnameresNamechainIDresSeqiCodepos occupancy tempFactorchargeelement)'universeAttributeError TypeError trajectoryr*r,atoms positionsgetattr itertoolscycler$rhsegidswarningswarnrGjoinhas_valid_coordinatespdb_coor_limitsrYosremover"OSErrorerrnoENOENT ValueErrorstrrUwritefmtconvert_dimensions_to_unitcell enumeratezipr ltruncate_intr%strip)r0 selectionr,uerrmsgrcoorattrsmissing_topologyattrdflterrr4rjrrrxrsresnamechainidresidicodery tempfactorr{r|s r;rzPDBQTWriter.writes, ."AA . . .DFF## - .   L     -!     O    . .JD$ .%eT22d ! . . .'otg66d  ''----- . 4 %E*   4 4 4 4$)Lj!!! 4 4 4$-OF$;$;j! '' 33333 4 4   M6tyy)9::6;;   ))$*>EE  JJLLL  $-((((   9 ,, 6(/1Ee1L #e**$x/#al6K2L2LL tx(//5566611!,/BB  HX  % %GQRRU1 &     & gj!j!hhm$m$i g     / /  F            '22F&ua00E8D4yy1}}Tzmmoobcc*G HNN ''!## ')!#(       sy 'A AA9B  7CC C D+! C,+D+,6D%"D+$D%%D+*D+F55 G?GGrX) rCrDrErFrrGrHrrVrYrrIrBr;r>r>s E %" -  CFZ 0 0E' ::O555^^^^^^rBr>)rFrrrnumpyrrlibrrSingleFrameReaderBaser WriterBaser>rIrBr;rs2  O/O/O/O/O/$,O/O/O/dCCCCC$/CCCCCrB