i(ZdZddlZddlZddlZGddeZGddeZdS)a; :mod:`gOpenMol` --- the gOpenMol plt format =========================================== .. _gOpenMol: http://www.csc.fi/english/pages/g0penMol The module provides a simple implementation of a reader for gOpenMol_ *plt* files. Plt files are binary files. The :class:`Plt` reader tries to guess the endianess of the file, but this can fail (with a :exc:`TypeError`); you are on your own in this case. Only the reader is implemented. If you want to write gridded data use a format that is more standard, such as OpenDX (see :mod:`OpenDX`). Background ---------- gOpenMol http://www.csc.fi/english/pages/g0penMol plt format. Used to be documented at http://www.csc.fi/gopenmol/developers/plt_format.phtml but currently this is only accessible through the internet archive at http://web.archive.org/web/20061011125817/http://www.csc.fi/gopenmol/developers/plt_format.phtml Grid data plt file format ------------------------- Copyright CSC, 2005. Last modified: September 23, 2003 09:18:50 Plot file (plt) format The plot files are regular 3D grid files for plotting of molecular orbitals, electron densities or other molecular properties. The plot files are produced by several programs. It is also possible to format/unformat plot files using the pltfile program in the utility directory. It is also possible to produce plot files with external (own) programs. Produce first a formatted text file and use then the pltfile program to unformat the file for gOpenMol. The format for the plot files are very simple and a description of the format can be found elsewhere in this manual. gOpenMol can read binary plot files from different hardware platforms independent of the system type (little or big endian machines). Format of the binary ``*.plt`` file ................................... The ``*.plt`` file binary and formatted file formats are very simple but please observe that unformatted files written with a FORTRAN program are not pure binary files because there are file records between the values while pure binary files do not have any records between the values. gOpenMol should be able to figure out if the file is pure binary or FORTRAN unformatted but it is not very well tested. Binary ``*.plt`` (grid) file format ................................... Record number and meaning:: #1: Integer, rank value must always be = 3 #2: Integer, possible values are 1 ... 50. This value is not used but it can be used to define the type of surface! Values used (you can use your own value between 1... 50): 1: VSS surface 2: Orbital/density surface 3: Probe surface 200: Gaussian 94/98 201: Jaguar 202: Gamess 203: AutoDock 204: Delphi/Insight 205: Grid Value 100 is reserved for grid data coming from OpenMol! #3: Integer, number of points in z direction #4: Integer, number of points in y direction #5: Integer, number of points in x direction #6: Float, zmin value #7: Float, zmax value #8: Float, ymin value #9: Float, ymax value #10: Float, xmin value #11: Float, xmax value #12 ... Float, grid data values running (x is inner loop, then y and last z): 1. Loop in the z direction 2. Loop in the y direction 3. Loop in the x direction Example:: nx=2 ny=1 nz=3 0,0,0 1,0,0 y=0, z=0 0,0,1 1,0,0 y=0, z=1 0,0,2 1,0,2 y=0, z=2 The formatted (the first few lines) file can look like:: 3 2 65 65 65 -3.300000e+001 3.200000e+001 -3.300000e+001 3.200000e+001 -3.300000e+001 3.200000e+001 -1.625609e+001 -1.644741e+001 -1.663923e+001 -1.683115e+001 -1.702274e+001 -1.721340e+001 -1.740280e+001 -1.759018e+001 -1.777478e+001 -1.795639e+001 -1.813387e+001 -1.830635e+001 ... Formatted ``*.plt`` (grid) file format ...................................... Line numbers and variables on the line:: line #1: Integer, Integer. Rank and type of surface (rank is always = 3) line #2: Integer, Integer, Integer. Zdim, Ydim, Xdim (number of points in the z,y,x directions) line #3: Float, Float, Float, Float, Float, Float. Zmin, Zmax, Ymin, Ymax, Xmin,Xmax (min and max values) line #4: ... Float. Grid data values running (x is inner loop, then y and last z) with one or several values per line: 1. Loop in the z direction 2. Loop in the y direction 3. Loop in the x direction Classes ------- .. autoclass:: Plt :members: Nc(eZdZddZdZdZdZdS)RecordNc0||_||_||_dSN)keybintypevalues)selfrrr s [/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/gridData/gOpenMol.py__init__zRecord.__init__s  c&|jdS||jvS)NT)r )r values r is_legalzRecord.is_legals ; 4 ##r cB|||jSr)rr)r ds r is_legal_dictzRecord.is_legal_dicts}}Qtx[)))r c&dt|zS)NzRecord(%(key)r,%(bintype)r,...))varsr s r __repr__zRecord.__repr__s04::==r r)__name__ __module__ __qualname__r rrrr r rrsU$$$***>>>>>r rcxeZdZdZeddddieddddd d d d d ddddd eddeddeddeddeddeddeddeddeddf ZdZd%dZdZe d Z e d!Z d"Z d#Z d$ZdS)&PltaTA class to represent a gOpenMol_ plt file. Only reading is implemented; either supply a filename to the constructor >>> G = Plt(filename) or load the file with the read method >>> G = Plt() >>> G.read(filename) The data is held in :attr:`GOpenMol.array` and all header information is in the dict :attr:`GOpenMol.header`. :attr:`Plt.shape` D-tuplet describing size in each dimension :attr:`Plt.origin` coordinates of the centre of the grid cell with index 0,0,...,0 :attr:`Plt.delta` DxD array describing the deltas rankI dimensionsurfacez VSS surfacezOrbital/density surfacez Probe surface gridcountOpenMolzGaussian 94/98JaguarGamessAutoDockzDelphi/InsightGrid) r *dnznynxzminfzmaxyminymaxxminxmaxNc ^t||_d|jDd}|jt dt ddDdd|jD|_|| |dSdS)Nc(g|]}|jdk |S)r"r.0rs r z Plt.__init__..s$III!aey6H6HA6H6H6Hr rc3*K|]}|dk|dfVdS)r+z user-definedNr)rAks r zPlt.__init__..s,#W#W1qTVwwQ~$6wwww#W#Wr 3cg|] }|j Sr)rr@s r rCz Plt.__init__..s"J"J"J19"J"J"Jr ) strfilename_header_structr updatedictrangejoin _headerfmtread)r rLrec_surfs r r z Plt.__init__sH  IIt2III!Lt#W#Wa #W#W#WWWXXX''"J"Jd6I"J"J"JKK IIh      r c <ddlm}m}|t||_t |jd5}||x}|_|d|dz|dz}|dt|z|jz}tj ||| ||}dddn #1swxYwY|j|jd <| |d|d|d |_ ||_tj |d |d |d gd tj|jzz|_|d|_dS)z3Populate the instance from the plt file *filename*.r)calcsizeunpackNrbr5r4r3bsaflagrLr;r9r6?r)structrVrWrKrLopen _read_headerheader _data_bintypenumpyarrayrSreshape transpose_deltadeltadiagonaloriginr) r rLrVrWplthnentriesdatafmtas r rSzPlt.reads++++++++MMDM $- & & J#"//44 4A w4(1T72H l3x==01CCG FF7CHHXXg5F5F,G,GHHIIA  J J J J J J J J J J J J J J J #'- JYYqw$499CCEE [[]] k1V9ai6"CDDs5>Z^ZdKeKeGee fI sBCCCc|jjSr)rashapers r rnz Plt.shapes zr cDfdtjDS)z}Edges of the grid cells, origin at centre of 0,0,..,0 grid cell. Only works for regular, orthonormal grids. cg|]U}j||ftjj|dzzj|zdj||fzz VS)r)rZ)rer`arangernrg)rArr s r rCzPlt.edges..stEEE./ 1Q3%,tz!}Q"?"??$+a.Pdj1o%&EEEr )rPrrs`r edgesz Plt.edgess@ EEEE383C3CEEE Er c|j}tj|d|d|dg}tj|d|d|dg}tj||z |jz }tj|S)Nr;r9r6r<r:r8)r^r`raabsrndiag)r riqminqmaxres r rdz Plt._deltasw K{AfIai& :;;{AfIai& :;; $+&&3z%   r ctjj}djD||d fd }dD]}||}|ddkrnd}|t djD]A}||s*tjd |j d ||j B|S) zGRead header bytes, try all possibilities for byte order/size/alignment.cg|] }|j Srr?r@s r rCz$Plt._read_header..s4441444r @c tttj|jz}||d<|S)NrY)rOzipr[rWrR)rYri binheadernamesr s r decode_headerz'Plt._read_header..decode_headers;S gdo.Ey Q QRRSSA"AiLHr z@=<>rr Nz3Cannot decode header --- corrupted or wrong format?zKey z: Illegal value )rz) r[rVrRrMrS TypeErrorrwarningswarnr) r pltfilenheaderrflagr^recr}r~s ` @@r r]zPlt._read_headers /$/2244 3444LL))           D"]4((Ff~""FF >QRR R& W WC$$V,, W CGGGVCG__UVVV r c|j|jfS)z=Return array data as (edges,grid), i.e. a numpy nD histogram.)rarrrs r histogramddzPlt.histogramdd s DJ''r r)rrr__doc__rrMr_r rSpropertyrnrrrdr]rrr r rrs(vfa _==vi1J1@2=3<3C3;3;3=3C39 .0 .0 1 1vd,,vd,,vd,,vf,,vf,,vf,,vf,,vf,,vf,,+.N,M     "  X EEXE!!!,(((((r r)rrr[r`objectrrrr r rs}}|  > > > > >V > > >u(u(u(u(u(&u(u(u(u(u(r