imJdZddlZddlZddlZddlZddlmZddlm Z m Z ddl m Z ddl mZdd lmZ gd Zgd Zgd Zd ZGddejZGddejZdS)a GRO file format --- :mod:`MDAnalysis.coordinates.GRO` ====================================================== Classes to read and write Gromacs_ GRO_ coordinate files; see the notes on the `GRO format`_ which includes a conversion routine for the box. Writing GRO files ----------------- By default any written GRO files will renumber the atom ids to move sequentially from 1. This can be disabled, and instead the original atom ids kept, by using the `reindex=False` keyword argument. This is useful when writing a subsection of a larger Universe while wanting to preserve the original identities of atoms. For example:: >>> u = mda.Universe()` >>> u.atoms.write('out.gro', reindex=False) # OR >>> with mda.Writer('out.gro', reindex=False) as w: ... w.write(u.atoms) Classes ------- .. autoclass:: GROReader :members: .. autoclass:: GROWriter :members: Developer notes: ``GROWriter`` format strings --------------------------------------------- The :class:`GROWriter` class has a :attr:`GROWriter.fmt` attribute, which is a dictionary of different strings for writing lines in ``.gro`` files. These are as follows: ``n_atoms`` For the first line of the gro file, supply the number of atoms in the system. E.g.:: fmt['n_atoms'].format(42) ``xyz`` An atom line without velocities. Requires that the 'resid', 'resname', 'name', 'index' and 'pos' keys be supplied. E.g.:: fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2, pos=(0.0, 1.0, 2.0)) ``xyz_v`` As above, but with velocities. Needs an additional keyword 'vel'. ``box_orthorhombic`` The final line of the gro file which gives box dimensions. Requires the box keyword to be given, which should be the three cartesian dimensions. E.g.:: fmt['box_orthorhombic'].format(box=(10.0, 10.0, 10.0)) ``box_triclinic`` As above, but for a non orthorhombic box. Requires the box keyword, but this time as a length 9 vector. This is a flattened version of the (3,3) triclinic vector representation of the unit cell. The rearrangement into the odd gromacs order is done automatically. .. _Gromacs: http://www.gromacs.org .. _GRO: https://manual.gromacs.org/current/reference-manual/file-formats.html#gro .. _GRO format: http://chembytes.wikidot.com/g-grofile N)base) triclinic_boxtriclinic_vectors) NoDataError)util)Timestep)r)r)rcr|t}|t}|t}t|||SN) _TS_ORDER_X _TS_ORDER_Y _TS_ORDER_Zr)boxxyzs d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/GRO.py_gmx_to_dimensionsrs2 KA KA KA Aq ! !!c4eZdZdZdZddddZeZdZd dZ dS) GROReaderaReader for the Gromacs GRO structure format. .. note:: This Reader will only read the first frame present in a file. .. note:: GRO files with zeroed 3 entry unit cells (i.e. ``0.0 0.0 0.0``) are read as missing unit cell information. In these cases ``dimensions`` will be set to ``None``. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 2.0.0 Reader now only parses boxes defined with 3 or 9 fields. Reader now reads a 3 entry zero unit cell (i.e. ``[0, 0, 0]``) as a being without dimension information (i.e. will the timestep dimension to ``None``). GRONnmnm/pstimelengthvelocityc  tj|jd5}|t |x|_}|j|fi|jx|_}tj |dftj }d}| dd ddz fdtdD|jd < fd tdd D|d <n#t$rd }YnwxYwt!|d D]\} ||kra tj }n7#t$r*tj t%jd }YnwxYwnX fdtdD|j|< fdtdd D||<#t$rd }YwxYwdddn #1swxYwYtj|r||_|rt-jdd |j_t3|dkr[tj|gdr#d}t-j|d|j_n_tj|gdf|j_n>t3|dkrt;||j_nd} t| |jr||jj|jj'||jjdd|jj r#|!|jj"dSdSdS)Nrtr )dtypeF.rcBg|]}d|zzd|dzzzSr.0icsfirst_atomlines r z/GROReader._read_first_frame..sHrBF{R"A,->>?rrcBg|]}d|zzd|dzzzSr,r.r/s rr4z/GROReader._read_first_frame..sH!!!#2Q;bAEl1B#BC!!!rrT)startz (\d+\.\d{5})cBg|]}d|zzd|dzzzSr,r.r0r1r2lines rr4z/GROReader._read_first_frame..sE   >?Db1frB!a%L'889   rcBg|]}d|zzd|dzzzSr,r.r8s rr4z/GROReader._read_first_frame..sH'''R"q&[2a!e +<<='''rz?Not all velocities were present. Unset velocities set to zero.)r;r;zWEmpty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`.V@r=r= z)GRO unitcell has neither 3 nor 9 entries.)#r openanyfilenamereadlineintn_atoms _Timestep _ts_kwargstsnpzerosfloat32findrange_pos ValueError enumeratesplitrefindallany velocitieswarningswarnframelenallclose dimensionsr_r convert_unitsconvert_pos_from_nativehas_velocitiesconvert_velocities_from_native _velocities) selfgrofilerCrFrS missed_velposunitcellwmsgerrmsgr2r3r9s @@@r_read_first_framezGROReader._read_first_framesu \$- . .1 &'      %()9)9););%<%< 'EET_EE EDGb7A,bjAAAJJ%--//N$))#..2BqBGAJ "!!!!!"1a[[!!! 1  " " "!  " 'wa888 & & T'>>#%:djjll#;#;%#%:J==$$ E     CH88    &'''''!&q!'''JsOO"&&&!%JJJ&_1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &1 &f 6*   &BM  4  x==A  {8___55 I; d###%)""%'U85G5G5G+G%H"" ]]a  !3H!=!=DG  @FV$$ $   I  ( ( 6 6 6w!-,,G&rr*w% I33DG4GHHHHH I I  I Is~CH2 DH D"H!D""H&E)(H)1FHF)H G('H( G74H6G77HH  H c 2||j}t|fd|i|S)zReturns a CRDWriter for *filename*. Parameters ---------- filename: str filename of the output GRO file Returns ------- :class:`GROWriter` NrC)rC GROWriter)r`r@rCkwargss rWriterzGROReader.Writer s+ ?lG==7=f===rr) __name__ __module__ __qualname____doc__formatunitsr rDrgrkr.rrrrsc(FTw ? ?EIYIYIYIv>>>>>>rrcteZdZdZdZddddZddd Zd d d d dZeddddzed<ddZdZ dS)ria/GRO Writer that conforms to the Trajectory API. Will attempt to write the following information from the topology: - atom name (defaults to 'X') - resnames (defaults to 'UNK') - resids (defaults to '1') .. note:: The precision is hard coded to three decimal places. .. note:: When dimensions are missing (i.e. set to `None`), a zero width unit cell box will be written (i.e. [0.0, 0.0, 0.0]). .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 0.13.0 Now strictly writes positions with 3dp precision. and velocities with 4dp. Removed the `convert_dimensions_to_unitcell` method, use `Timestep.triclinic_dimensions` instead. Now now writes velocities where possible. .. versionchanged:: 0.18.0 Added `reindex` keyword argument to allow original atom ids to be kept. .. versionchanged:: 2.0.0 Raises a warning when writing timestep with missing dimension information (i.e. set to ``None``). rNr r!r"g"?g-@)minmaxz{0:5d} zY{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f} z+{box[0]:10.5f} {box[1]:9.5f} {box[2]:9.5f} z{box[0]:10.5f} {box[4]:9.5f} {box[8]:9.5f} {box[1]:9.5f} {box[2]:9.5f} {box[3]:9.5f} {box[5]:9.5f} {box[6]:9.5f} {box[7]:9.5f} )rCxyzbox_orthorhombic box_triclinicruz({vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f} xyz_vTc tj|dd|_||_|dd|_||_dS)aSet up a GROWriter with a precision of 3 decimal places. Parameters ----------- filename : str output filename n_atoms : int (optional) number of atoms convert_units : bool (optional) units are converted to the MDAnalysis base format; [``True``] reindex : bool (optional) By default, all the atoms were reindexed to have a atom id starting from 1. [``True``] However, this behaviour can be turned off by specifying `reindex` ``=False``. Note ---- To use the reindex keyword, user can follow the two examples given below.:: u = mda.Universe() Usage 1:: u.atoms.write('out.gro', reindex=False) Usage 2:: with mda.Writer('out.gro', reindex=False) as w: w.write(u.atoms) groT)extkeepreindexN)r r@rCpopr~r[)r`r@r[rCrjs r__init__zGROWriter.__init__OsLB hEEEE  zz)T22   rc  |j}n #t$rd}t|dwxYw |j}d}n#t$rd}YnwxYwg} |j}n@#ttf$r,t jd}|dYnwxYw |j }n@#ttf$r,t jd}|dYnwxYw |j } n@#ttf$r,t jd } |d YnwxYw|j sM |j } n\#ttf$r0td |jd z} |d YnwxYwtd |jd z} |r;tjd d||j} |jr0|| d} |r||d}||j| s9t3d|jd|jdt5j|jd5} | d| |jd|jt?t|j| ||D]\} }}}t5j | | d}t5j |d}|rF| |jd||||| | || | |jd||||| | |j!$tEj#|j!ddgdr|j!+d}tj|tEj$d}n$||j!ddd}| |jd| n |j%j&j'}n#t$r |j'}YnwxYw||(d}| |jd!| ddddS#1swxYwYdS)"aWrite selection at current trajectory frame to file. Parameters ----------- obj : AtomGroup or Universe Note ---- The GRO format only allows 5 digits for *resid* and *atom number*. If these numbers become larger than 99,999 then this routine will chop off the leading digits. .. versionchanged:: 0.7.6 *resName* and *atomName* are truncated to a maximum of 5 characters .. versionchanged:: 0.16.0 `frame` kwarg has been removed .. versionchanged:: 2.0.0 Deprecated support for calling with Timestep has nwo been removed. Use AtomGroup or Universe as an input instead. z-Input obj is neither an AtomGroup or UniverseNTF)Xnames)UNKresnames)rresidsridszSupplied AtomGroup was missing the following attributes: {miss}. These will be written with default values. Alternatively these can be supplied as keyword arguments.z, )miss)inplacezZGRO files must have coordinate values between {0:.3f} and {1:.3f} nm: No file was written.rsrtwtzWritten by MDAnalysis rCr ry)residresnameindexnamercvelru)rrrrrcr r<z@missing dimension - setting unit cell to zeroed box [0., 0., 0.]rv)rrw))atomsAttributeError TypeErrorrSrr itertoolscycleappendrrr~rrKrCrTrUrpjoin positionsr[convert_pos_to_nativeconvert_velocities_to_nativehas_valid_coordinatesgro_coor_limitsrMr r?r@writefmtzip ltruncate_intrYrGrXrHuniversecoordtriclinic_dimensionsflatten)r`objagrfrSr]missing_topologyrrr atom_indicesr output_gro atom_indexrrrtruncated_atom_indextruncated_residrertri_dimss rrzGROWriter.writexs70 .BB . . .DFF## - . "J"NN # # #"NNN #  -HEE , - - -OF++E  # #G , , , , , - 0{HH , 0 0 0 x00H  # #J / / / / / 0 .YFF , . . ._T**F  # #H - - - - - .| 4 /!v "K0 / / /$Q Q77  ''..... /!BJN33L   M6tyy)9::6;;    L   229e2LLI !>>? ))$*> JJ 6(/1Ee1L \$- . .? L*   6 7 7 7   TXi077 CC D D D 58bj!!68U55  0 E7D(,'9 ,a(($#'"4UA">">!$$)00"1$+"6!% )* 5 *: 6 1    $$.."1$+"6!% )* 5 /}$  abb!#5#5#5))$=(+M$'''(1++CC44 bqb)55C  *E54E59G&S3 Q21S32RS3RA S33S7:S7)TN) rlrmrnrorprqrrrrr.rrririsBFTw ? ?E' ::O kJ\   C E 3B3EEL' ' ' ' R_L_L_L_L_Lrri)rorPrrTnumpyrGrcorerr exceptionsrlibr timestepr rrrrSingleFrameReaderBaser WriterBaserir.rrrsO0NN^ 22222222$$$$$$(ii ii ii """C>C>C>C>C>*C>C>C>L|L|L|L|L|L|L|L|L|L|Lr