idZddlZddlZddlZddlZddlZddlm Z ddl Z ddl m Z ddl mZddlmZdd lmZejd Z ddlZn"#e$rdZed YnwxYwGd d ejZGddejZGddejZGddejjZdS)uAMBER trajectories --- :mod:`MDAnalysis.coordinates.TRJ` ======================================================== AMBER_ can write :ref:`ASCII trajectories` ("traj") and :ref:`binary trajectories` ("netcdf"). MDAnalysis supports reading of both formats and writing for the binary trajectories. Note ---- Support for AMBER is still somewhat *experimental* and feedback and contributions are highly appreciated. Use the `Issue Tracker`_ or get in touch on the `GitHub Discussions`_. .. rubric:: Units AMBER trajectories are assumed to be in the following units: * lengths in Angstrom (Å) * time in ps (but see below) .. _netcdf-trajectories: Binary NetCDF trajectories -------------------------- The `AMBER netcdf`_ format make use of NetCDF_ (Network Common Data Form) format. Such binary trajectories are recognized in MDAnalysis by the '.ncdf' suffix and read by the :class:`NCDFReader`. Binary trajectories can also contain velocities and forces, and can record the exact time step. In principle, the trajectories can be in different units than the AMBER defaults of ångström and picoseconds but at the moment MDAnalysis only supports those and will raise a :exc:`NotImplementedError` if anything else is detected. .. autoclass:: NCDFReader :members: .. autoclass:: NCDFWriter :members: .. autoclass:: NCDFPicklable :members: .. _ascii-trajectories: ASCII TRAJ trajectories ----------------------- ASCII AMBER_ TRJ coordinate files (as defined in `AMBER TRJ format`_) are handled by the :class:`TRJReader`. It is also possible to directly read *bzip2* or *gzip* compressed files. AMBER ASCII trajectories are recognised by the suffix '.trj', '.mdcrd' or '.crdbox (possibly with an additional '.gz' or '.bz2'). .. Note:: In the AMBER community, these trajectories are often saved with the suffix '.crd' but this extension conflicts with the CHARMM CRD format and MDAnalysis *will not correctly autodetect AMBER ".crd" trajectories*. Instead, explicitly provide the ``format="TRJ"`` argument to :class:`~MDAnalysis.core.universe.Universe`:: u = MDAnalysis.Universe("top.prmtop", "traj.crd", format="TRJ") In this way, the AMBER :class:`TRJReader` is used. .. rubric:: Limitations * Periodic boxes are only stored as box lengths A, B, C in an AMBER trajectory; the reader always assumes that these are orthorhombic boxes. * The trajectory does not contain time information so we simply set the time step to 1 ps (or the user could provide it as kwarg *dt*) * Trajectories with fewer than 4 atoms probably fail to be read (BUG). * If the trajectory contains exactly *one* atom then it is always assumed to be non-periodic (for technical reasons). * Velocities are currently *not supported* as ASCII trajectories. .. autoclass:: TRJReader :members: .. Links .. _AMBER: http://ambermd.org .. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory .. The formats page was archived as .. http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fformats.html&date=2018-02-11 .. Use the archived version if the original (https://ambermd.org/FileFormats.php#trajectory) disappears. [orbeckst] .. _AMBER netcdf format: http://ambermd.org/netcdf/nctraj.xhtml .. The formats page was archived as .. http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fnetcdf%2Fnctraj.xhtml&date=2018-02-11 .. Use the archived version if the original disappears. [orbeckst] .. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml .. _NetCDF: http://www.unidata.ucar.edu/software/netcdf .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues .. _GitHub Discussions: https://github.com/MDAnalysis/mdanalysis/discussions N)isclose)Timestep)base)util)store_init_argumentszMDAnalysis.coordinates.AMBERz@netCDF4 is not available. Writing AMBER ncdf files will be slow.ceZdZdZgdZdddZeZedfd Z dZ d Z d Z e d Zd Ze d ZdZdZdZxZS) TRJReaderaCAMBER trajectory reader. Reads the ASCII formatted `AMBER TRJ format`_. Periodic box information is auto-detected. The number of atoms in a timestep *must* be provided in the `n_atoms` keyword because it is not stored in the trajectory header and cannot be reliably autodetected. The constructor raises a :exc:`ValueError` if `n_atoms` is left at its default value of ``None``. The length of a timestep is not stored in the trajectory itself but can be set by passing the `dt` keyword argument to the constructor; it is assumed to be in ps. The default value is 1 ps. .. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based. kwarg `delta` renamed to `dt`, for uniformity with other Readers )TRJMDCRDCRDBOXpsAngstrom)timelengthNc tt|j|fi||td||_d|_d|_|j|jfi|j |_ tj d|_ ttjd|jzt#|j z |_d|jzt#|j z}tj d||_tj d|_||dS)Nz-AMBER TRJ reader REQUIRES the n_atoms keywordz10F8.3g@z {0:d}F8.3z3F8.3)superr __init__ ValueError_n_atoms _n_framestrjfile _Timestepn_atoms _ts_kwargstsr FORTRANReaderdefault_line_parserintnpceillenlines_per_frameformatlast_line_parserbox_line_parser_detect_amber_box_read_next_timestep)selffilenamerkwargs last_per_line __class__s d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/TRJ.pyrzTRJReader.__init__sR'i';;F;;; ?LMM M   $.AAAA$(#5h#?#? "273+=  $A&A&,&$'$' ( ( DL(3t/G+H+HH $ 2;3E3E 44!! $1'::       """""c|j||j|j||dz |j_|SNr)ropen_trajectoryseek_offsetsrframer*)r+r7s r0 _read_framezTRJReader._read_framesX <   " " " $-.///  '')))r1c|j}|j|g}t|jD]\}} ||j|n=#t$r0||j|YnwxYw||j dz krn|gkrt|j r:t|j}|j |}|gdz|_tj||jd|jdd<|xjdz c_|S)NrV@r;r;r)rrr4 enumerateextendr readrr'r%EOFErrorperiodicnextr( dimensionsr"arrayreshaper_posr7)r+r_coordsnumberlineboxs r0r*zTRJReader._read_next_timestepsl W <   " " "%dl33  LFD At7<rBclose)r+wmsgrrHnentriess r0r)zTRJReader._detect_amber_boxs. <1  !DMOD M$   5     """ WDL!!+==dCC q== DM 055d;;oooMBMM!DM }r1c|j|jS ||j|_|jS#t$rYdSwxYw)z>Number of frames (obtained from reading the whole trajectory).Nr)r_read_trj_n_framesr,IOErrorr+s r0n_frameszTRJReader.n_frames*s^ > %> ! "!44T]CCDN> !   11 s6 AAc|j}|jr|dz }gx|_}d}tj|j5}|}|rK||zdkr'|||}|dz }|Kdddn #1swxYwY| t|S)Nrr) r%r@r6ropenanyr,readlineappendtellpopr$)r+r,lpfoffsetscounterfrHs r0rSzTRJReader._read_trj_n_frames6s " =  1HC"$$  \$- ( ( A::<***!!!F+++Z " "X ""X   r1r ceZdZdZddgZdZdZdddd d ZeZ e dfd Z e d Z e dZdZdZdZddZdZdZdZxZS) NCDFReadera Reader for `AMBER NETCDF format`_ (version 1.0). AMBER binary trajectories are automatically recognised by the file extension ".ncdf". The number of atoms (`n_atoms`) does not have to be provided as it can be read from the trajectory. The trajectory reader can randomly access frames and therefore supports direct indexing (with 0-based frame indices) and full-feature trajectory iteration, including slicing. Velocities are autodetected and read into the :attr:`Timestep._velocities` attribute. Forces are autodetected and read into the :attr:`Timestep._forces` attribute. Periodic unit cell information is detected and used to populate the :attr:`Timestep.dimensions` attribute. (If no unit cell is available in the trajectory, then :attr:`Timestep.dimensions` will return ``[0,0,0,0,0,0]``). Current limitations: * only trajectories with time in ps and lengths in Angstroem are processed The NCDF reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` must be installed. It supports the *mmap* keyword argument (when reading): ``mmap=True`` is memory efficient and directly maps the trajectory on disk to memory (using the :class:`~mmap.mmap`); ``mmap=False`` may consume large amounts of memory because it loads the whole trajectory into memory but it might be faster. The default is ``mmap=None`` and then default behavior of :class:`scipy.io.netcdf_file` prevails, i.e. ``True`` when *filename* is a file name, ``False`` when *filename* is a file-like object. .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml See Also -------- :class:`NCDFWriter` .. versionadded: 0.7.6 .. versionchanged:: 0.10.0 Added ability to read Forces .. versionchanged:: 0.11.0 Frame labels now 0-based instead of 1-based. kwarg `delta` renamed to `dt`, for uniformity with other Readers. .. versionchanged:: 0.17.0 Uses :mod:`scipy.io.netcdf` and supports the *mmap* kwarg. .. versionchanged:: 0.20.0 Now reads scale_factors for all expected AMBER convention variables. Timestep variables now adhere standard MDAnalysis units, with lengths of angstrom, time of ps, velocity of angstrom/ps and force of kJ/(mol*Angstrom). It is noted that with 0.19.2 and earlier versions, velocities would have often been reported in values of angstrom/AKMA time units instead (Issue #2323). .. versionchanged:: 1.0.0 Support for reading `degrees` units for `cell_angles` has now been removed (Issue #2327) .. versionchanged:: 2.0.0 Now use a picklable :class:`scipy.io.netcdf_file`-- :class:`NCDFPicklable`. Reading of `dt` now defaults to 1.0 ps if `dt` cannot be extracted from the first two frames of the trajectory. :meth:`Writer` now also sets `convert_units`, `velocities`, `forces` and `scale_factor` information for the :class:`NCDFWriter`. NCDFNCT1.0rr Angstrom/pskcal/(mol*Angstrom)rrvelocityforceNc ||_tt|j|fi|t |j|jd|_ |jj}d|d dvsld|d vsCd |j}t |t|nR#t$rEd |j}t |t|dwxYw |jjd}||jksId ||j}t%j|t|n8#t$r+d |j}t|dwxYw|jjd ksCd |j}t |t| |jjd d ksd}t|n #t.$rd}t|dwxYwt1|jdrt1|jdsHd |j}t%j|t| |jjd|_|5||jkr*d ||j}t|n8#t.$r+d |j}t|dwxYw |jjd|_|j"|jjdjd|_n)#t.$rd|jd}t|dwxYw |jj|_n#t$r d|_YnwxYw ||jjdj dd|_!nG#t.$r:d|_!d}t%j|t|YnwxYw||jjdj d ddddddd!|_"|jjD]} t1|jj| d"r| |j"vrU|jj| j#} tI| tJtLj'fst| d#| |j"| <d$ | }tQ|d%|jjv|_)|j)r+||jjd%j d&d'|jjv|_*|j*r+||jjd'j d(d)|jjv|_+|j+rX||jjd)j d |jjd*j } || d+d|_,|j-|jf|j)|j*|d,|j.|_/|0ddS)-NF)mmap maskandscaleAMBERutf-8,zNCDF trajectory {0} does not conform to AMBER specifications, http://ambermd.org/netcdf/nctraj.xhtml ('AMBER' must be one of the token in attribute Conventions)z*NCDF trajectory {0} is missing ConventionszFNCDF trajectory format is {0!s} but the reader implements format {1!s}z0NCDF trajectory {0} is missing ConventionVersionrzNCDF trajectory {0} does not conform to AMBER specifications, as detailed in https://ambermd.org/netcdf/nctraj.xhtml (NetCDF file does not use 64 bit offsets [version_byte = 2])spatialrz0Incorrect spatial value for NCDF trajectory filez2NCDF trajectory does not contain spatial dimensionprogramprogramVersionz~NCDF trajectory {0} may not fully adhere to AMBER standards as either the `program` or `programVersion` attributes are missingatomzkSupplied n_atoms ({0}) != natom from ncdf ({1}). Note: n_atoms can be None and then the ncdf value is used!z5NCDF trajectory {0} does not contain atom informationr7 coordinatesrzNCDF trajectory z# does not contain frame informationr picosecondTz^NCDF trajectory does not contain `time` information; `time` will be set as an increasing indexangstromr cell_lengths cell_anglesr velocitiesforces scale_factor is not a floatz2scale_factors for variable {0} are not implementedrangstrom/picosecondrkilocalorie/mole/angstromrrdegree)rrreader)1_mmaprrwr NCDFPicklabler,r Conventionsdecodesplitr&loggerfatal TypeErrorAttributeErrorrConventionVersionversionrKrLwarning version_byterBKeyErrorhasattrrrV variablesshapetitleremarks _verify_unitsrrhas_time scale_factorsr isinstancefloatr"floatingNotImplementedErrorhas_velocities has_forcesr@_current_framerrrr8) r+r,rrr- conventionserrmsgrrPvariablercell_angle_unitsr/s r0rzNCDFReader.__init__sX (j$(<)>   V$$$''' / / /AHHm%%F LL V$$$ .  / / $ > E Eg N N $ 44228&*DL3:3: d###t$$$ / / /GNNm%%FV$$$ . / |(A--,-3F4=,A,A  LL F## # /<*95::K'''; / / /IFV$$$ . /  i00 ! &677 !--3VDM-B-B  M$    NN4  /<26:DL"w$,'>'>%%+VGT\%B%B!((( / / /$$*F4=$9$9 V$$$ . / / L3GA3F665G+'I**J=AM 5NAO&O,0PPP2Q ARRc|d|kr8d|d|}t|dS)Nrz]NETCDFReader currently assumes that the trajectory was written in units of {0} instead of {1})rr&r) eval_unitexpected_unitsrs r0rzNCDFReader._verify_unitscsd   G $ $ 6 6CCI6 ''00.DBDB &f-- - 7 6r1c tj|d5}|jd}dddn #1swxYwY|S)N)rr)scipyio netcdf_filerB)r,r-r`rs r0 parse_n_atomszNCDFReader.parse_n_atomsks X ! !( ! 6 6 +!l6*G + + + + + + + + + + + + + + +s<AAc|j|}|t|dr|jj||S|jj|||zS)zHelper function to get variable at given frame from NETCDF file and scale if necessary. Note ---- If scale_factor is 1.0 within numerical precision then we don't apply the scaling. Nr)rrrr)r+rr7rs r0_get_var_and_scalezNCDFReader._get_var_and_scaleqsU)(3  7<#;#; <)(3E: :<)(3E:\I Ir1c|j}|jtdtjt |tjt krtd||jks|dkr'td |j| d||j dd<|j r| d||_|jr | d||jdd<|jr | d||jdd<|jrQtjd }| d ||dd <| d ||d d<||_|jr||j ||j|jr||jd |jr||jd |jr"||jdd ||_||_|S)NzTrajectory is closedz(frame must be a positive integer or zerorz$frame index must be 0 <= frame < {0}rrrrrrrTinplace)rrrTr"dtypetyper!rrV IndexErrorr&rrErrr _velocitiesr_forcesr@zerosrB convert_unitsconvert_pos_from_nativeconvert_time_from_nativeconvert_velocities_from_nativeconvert_forces_from_nativer7r)r+r7runitcells r0r8zNCDFReader._read_framesW W < 011 1 8DKK BHSMM 1 1FGG G DM ! !UQYYCJJ    ,,]EBB = =--fe<5IIHRaRL22=%HHHQRRL$BM   @  ( ( 1 1 1  ) )   " B33BN<@4BBB J// D/III} @,,R]2A2->???# r1cd|_dS)Nrf)rrUs r0rMzNCDFReader._reopens r1c|||j} ||jdzS#t$r tdwxYwr3)rr8rrrTrks r0r*zNCDFReader._read_next_timestepsR :B $##D$7!$;<< < $ $ $t # $s(;c |jjdd}|jjdd}n#ttf$rtwxYw||z S)zGets dt based on the time difference between the first and second frame. If missing (i.e. an IndexError is triggered), raises an AttributeError which triggers the default 1 ps return of dt(). rrr)rrrrr)r+t1t0s r0_get_dtzNCDFReader._get_dts`  !'/2B'/2BBH% ! ! !  !Bws 03A cX|j"|jd|_dSdS)a^Close trajectory; any further access will raise an :exc:`IOError`. .. Note:: The underlying :mod:`scipy.io.netcdf` module may open netcdf files with :class:`~mmap.mmap` if ``mmap=True`` was set. Hence *any* reference to an array *must* be removed before the file can be closed. NrmrUs r0rOzNCDFReader.closes3 < # L   DLLL $ #r1c |d|j}|d|j|d|j|d|j|d|j|jD]&}|d||j|'t||fi|S)aReturns a NCDFWriter for `filename` with the same parameters as this NCDF. All values can be changed through keyword arguments. Parameters ---------- filename : str filename of the output NCDF trajectory n_atoms : int (optional) number of atoms remarks : str (optional) string that is stored in the title field convert_units : bool (optional) ``True``: units are converted to the AMBER base format velocities : bool (optional) Write velocities into the trajectory forces : bool (optional) Write forces into the trajectory scale_time : float (optional) Scale factor for time units scale_cell_lengths : float (optional) Scale factor for cell lengths scale_cell_angles : float (optional) Scale factor for cell angles scale_coordinates : float (optional) Scale factor for coordinates scale_velocities : float (optional) Scale factor for velocities scale_forces : float (optional) Scale factor for forces Returns ------- :class:`NCDFWriter` rrrrrscale_) r\r setdefaultrrrrr NCDFWriter)r+r,r-rkeys r0WriterzNCDFReader.WritersH**Y 55)T\222/4+=>>>,(;<<<(DO444% G GC   nsnnd.@.E F F F F(G66v666r1)NNrb)rnrorprqr& multiframerrrrrr r staticmethodrrrr8rMr*rrOrrtrus@r0rwrwfs8CCJd^FJG!&+ - -E IjjjjjjX..\.\ J J J&&&P!!!$$$$       +7+7+7+7+7+7+7r1rwcheZdZdZddgZdZdZdddd d Z dd ZddZ dZ dZ dZ dZ dZd S)ruWriter for `AMBER NETCDF format`_ (version 1.0). AMBER binary trajectories are automatically recognised by the file extension ".ncdf" or ".nc". Velocities are written out if they are detected in the input :class:`Timestep`. The trajectories are always written with ångström for the lengths and picoseconds for the time (and hence Å/ps for velocities and kilocalorie/mole/Å for forces). Scale factor variables for time, velocities, cell lengths, cell angles, coordinates, velocities, or forces can be passed into the writer. If so, they will be written to the NetCDF file. In this case, the trajectory data will be written to the NetCDF file divided by the scale factor value. By default, scale factor variables are not written. The only exception is for velocities, where it is set to 20.455, replicating the default behaviour of AMBER. Unit cell information is written if available. .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml Parameters ---------- filename : str name of output file n_atoms : int number of atoms in trajectory file convert_units : bool (optional) ``True``: units are converted to the AMBER base format; [``True``] velocities : bool (optional) Write velocities into the trajectory [``False``] forces : bool (optional) Write forces into the trajectory [``False``] scale_time : float (optional) Scale factor for time units [`None`] scale_cell_lengths : float (optional) Scale factor for cell lengths [``None``] scale_cell_angles : float (optional) Scale factor for cell angles [``None``] scale_coordinates : float (optional) Scale factor for coordinates [``None``] scale_velocities : float (optional) Scale factor for velocities [20.455] scale_forces : float (optional) Scale factor for forces [``None``] Note ---- MDAnalysis uses :mod:`scipy.io.netcdf` to access AMBER files, which are in netcdf 3 format. Although :mod:`scipy.io.netcdf` is very fast at reading these files, it is *very* slow when writing, and it becomes slower the longer the files are. On the other hand, the netCDF4_ package (which requires the compiled netcdf library to be installed) is fast at writing but slow at reading. Therefore, we try to use :mod:`netCDF4` for writing if available but otherwise fall back to the slower :mod:`scipy.io.netcdf`. **AMBER users** might have a hard time getting netCDF4 to work with a conda-based installation (as discussed in `Issue #506`_) because of the way that AMBER itself handles netcdf: When the AMBER environment is loaded, the following can happen when trying to import netCDF4:: >>> import netCDF4 Traceback (most recent call last): File "", line 1, in File "/scratch2/miniconda/envs/py35/lib/python3.5/site-packages/netCDF4/__init__.py", line 3, in from ._netCDF4 import * ImportError: /scratch2/miniconda/envs/py35/lib/python3.5/site-packages/netCDF4/_netCDF4.cpython-35m-x86_64-linux-gnu.so: undefined symbol: nc_inq_var_fletcher32 The reason for this (figured out via :program:`ldd`) is that AMBER builds its own NetCDF library that it now inserts into :envvar:`LD_LIBRARY_PATH` *without the NetCDF4 API and HDF5 bindings*. Since the conda version of :mod:`netCDF4` was built against the full NetCDF package, the one :program:`ld` tries to link to at runtime (because AMBER requires :envvar:`LD_LIBRARY_PATH`) is missing some symbols. Removing AMBER from the environment fixes the import but is not really a convenient solution for users of AMBER. At the moment there is no obvious solution if one wants to use :mod:`netCDF4` and AMBER in the same shell session. If you need the fast writing capabilities of :mod:`netCDF4` then you need to unload your AMBER environment before importing MDAnalysis. .. _netCDF4: https://unidata.github.io/netcdf4-python/ .. _`Issue #506`: https://github.com/MDAnalysis/mdanalysis/issues/506#issuecomment-225081416 Raises ------ FutureWarning When writing. The :class:`NCDFWriter` currently does not write any `scale_factor` values for the data variables. Whilst not in breach of the AMBER NetCDF standard, this behaviour differs from that of most AMBER writers, especially for velocities which usually have a `scale_factor` of 20.455. In MDAnalysis 2.0, the :class:`NCDFWriter` will enforce `scale_factor` writing to either match user inputs (either manually defined or via the :class:`NCDFReader`) or those as written by AmberTools's :program:`sander` under default operation. See Also -------- :class:`NCDFReader` .. versionadded: 0.7.6 .. versionchanged:: 0.10.0 Added ability to write velocities and forces .. versionchanged:: 0.11.0 kwarg `delta` renamed to `dt`, for uniformity with other Readers .. versionchanged:: 0.17.0 Use fast :mod:`netCDF4` for writing but fall back to slow :mod:`scipy.io.netcdf` if :mod:`netCDF4` is not available. .. versionchanged:: 0.20.1 Changes the `cell_angles` unit to the AMBER NetCDF convention standard of `degree` instead of the `degrees` written in previous version of MDAnalysis (Issue #2327). .. versionchanged:: 2.0.0 ``dt``, ``start``, and ``step`` keywords were unused and are no longer set. Writing of ``scale_factor`` values has now been implemented. By default only velocities write a scale_factor of 20.455 (echoing the behaviour seen from AMBER). ryrxTrzrrr{r|r}NFc  ||_|dkrtd||_||_|pd|_d|_d|_d|_||_||_ ||| | | | d|_ |j D]:}|6t|ttjfsd|d}t!|;d|_dS)Nrz)NCDFWriter: no atoms in output trajectoryz;AMBER NetCDF format (MDAnalysis.coordinates.trj.NCDFWriter)Trz scale_factor r)r,rrrr _first_framerr@rrrvaluesrrr"rr curr_frame)r+r,rrrrr scale_timescale_cell_lengthsscale_cell_anglesscale_coordinatesscale_velocities scale_forcesr-valuers r0rzNCDFWriter.__init__s ! a<<HII I *_"_    ( # 200.& (('..00 ( (E!"55"+*>??"????'''r1c|js2ttjd|jt rt j|jdd}nXtj |jddd}d}t |tj|t|d d t|d t jt|d d t|ddt|dd|dd|d|j|dd|dd|dd|dd|ddd}t|dd|jdr|jd|_|dd d!}t/jt3d"|dd<|d#dd$}t|dd%|jd#r|jd#|_||_|jr%|d&d'd(}t|dd|jd&r|jd&|_|dd d)}t/jt3d*|dd<|d+d'd,} t| dd-|jd+r|jd+| _|dd d.} t/jt3d/t3d0t3d1g| dd<|jrG|d2dd} t| dd3|jd2r|jd2| _|jrG|d4dd} t| dd5|jd4r|jd4| _t r|d|d|_||_dS)6aInitialize netcdf AMBER 1.0 trajectory. The trajectory is opened when the first frame is written because that is the earliest time that we can detect if the output should contain periodicity information (i.e. the unit cell dimensions). Based on Joshua Adelman's `netcdf4storage.py`_ in `Issue 109`_ and uses Jason Swail's hack from `ParmEd/ParmEd#722`_ to switch between :mod:`scipy.io.netcdf` and :mod:`netCDF4`. .. _`Issue 109`: https://github.com/MDAnalysis/mdanalysis/issues/109 .. _`netcdf4storage.py`: https://storage.googleapis.com/google-code-attachments/mdanalysis/issue-109/comment-2/netcdf4storage.py .. _`ParmEd/ParmEd#722`: https://github.com/ParmEd/ParmEd/pull/722 z#Attempt to write to closed file {0}w NETCDF3_64BIT)r&rF)moderrzfCould not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing.rz%MDAnalysis.coordinates.TRJ.NCDFWriterrrrrrz application MDAnalysisr7Nrrr cell_spatial cell_angularlabelrf4)r7rrrrrc)rxyzr)r7rrf8)r7r)rabcr)r7rr)rralphazbeta gammarrrr) rrTerrnoEIOr&r,netCDF4DatasetrrrrrrKrLsetattrr __version__createDimensionrcreateVariablerrr"asarraylistr@rrset_auto_maskandscalesyncr) r+r@ncfilerPcoordsrrrrrrvelocsrs r0 _init_netcdfzNCDFWriter._init_netcdfs&  M 5<>FID NN4 M$     #JKKK(**@AAA w///+U333 |444 w# % % %v#| - - -y!,,,~q111~q111w***&&}d'CEE,,,  m , D"&"4]"CF '' 3 FFZU ,, $$VT:>>g|,,,  f % ; $ 26 :D   = !001JLLL L': 6 6 6!.1 O,0,>~,N )!001CEEL je55LO // t0IKKK K( 3 3 3!-0 M+/+=m+L (!001JLLL j$w--gII*LO   G**<+GIIF FG%: ; ; ;!,/ G&*&8&F# ? C**8T+GIIF FG%@ A A A!(+ C&*&8&B#  0  ( ( / / / ! r1c|jduS)a^Test if timestep ``ts`` contains a periodic box. Parameters ---------- ts : :class:`Timestep` :class:`Timestep` instance containing coordinates to be written to trajectory file Returns ------- bool Return ``True`` if `ts` contains a valid simulation box N)rBrks r0 is_periodiczNCDFWriter.is_periodics}D((r1cX |j}n>#t$r1 |jj}n #t$rd}t|dwxYwYnwxYw|j|jkrt d|j)|||| |S)aWrite information associated with ``ag`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe .. versionchanged:: 1.0.0 Added ability to use either AtomGroup or Universe. Renamed from `write_next_timestep` to `_write_next_frame`. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. z-Input obj is neither an AtomGroup or UniverseNz>NCDFWriter: Timestep does not have the correct number of atoms)r@) rr trajectoryrrrTrrr_write_next_timestep)r+agrrs r0_write_next_framezNCDFWriter._write_next_frame)s 2BB 2 2 2 2]%! 2 2 2H''T1 2 2 : % %PRR R <    t'7'7';';  < < <((,,,s! A "A?AAc|j|}|t|dr||jj||j<dS||z |jj||j<dS)zHelper function to set variables and scale them if necessary. Note ---- If scale_factor is numerically close to 1.0, the variable data is not scaled. Nr)rrrrr)r+varnamedatasfactors r0_set_frame_var_and_scalez#NCDFWriter._set_frame_var_and_scaleMs`$W- ?ggq11??CDL "7 +DO < < >H %%mS999 %%fd333 = G  ) ).(2A2, G G G  ) )-!"" F F F   DJ! /!>>?//   ) ), C C C ? <ZF! +66E7++  ) )(F ; ; ;  1r1cX|j"|jd|_dSdSrbrmrUs r0rOzNCDFWriter.closes1 < # L   DLLL $ #r1) NTFFNNNNNN)T)rnrorprqr&rrrrrrrrrrrOr1r0rrs~~@F^FJG!&+ - -E GK<@<@:>" """"Hppppd))) "-"-"-H N N NBBBH     r1rceZdZdZdZdZdS)raNetCDF file object (read-only) that can be pickled. This class provides a file-like object (as returned by :class:`scipy.io.netcdf_file`) that, unlike standard Python file objects, can be pickled. Only read mode is supported. When the file is pickled, filename and mmap of the open file handle in the file are saved. On unpickling, the file is opened by filename, and the mmap file is loaded. This means that for a successful unpickle, the original file still has to be accessible with its filename. .. note:: This class subclasses :class:`scipy.io.netcdf_file`, please see the `scipy netcdf API documentation`_ for more information on the parameters and how the class behaviour. Parameters ---------- filename : str or file-like a filename given a text or byte string. mmap : None or bool, optional Whether to mmap `filename` when reading. True when `filename` is a file name, False when `filename` is a file-like object. version : {1, 2}, optional Sets the netcdf file version to read / write. 1 is classic, 2 is 64-bit offset format. Default is 1 (but note AMBER ncdf *requires* 2). maskandscale : bool, optional Whether to automatically scale and mask data. Default is False. Example ------- :: f = NCDFPicklable(NCDF) print(f.variables['coordinates'].data) f.close() can also be used as context manager:: with NCDFPicklable(NCDF) as f: print(f.variables['coordinates'].data) See Also --------- :class:`MDAnalysis.lib.picklable_file_io.FileIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.BufferIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.TextIOPicklable` :class:`MDAnalysis.lib.picklable_file_io.GzipPicklable` :class:`MDAnalysis.lib.picklable_file_io.BZ2Picklable` .. versionadded:: 2.0.0 .. _`scipy netcdf API documentation`: https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.netcdf_file.html c6|j|j|j|jfSrb)r,use_mmaprrrUs r0 __getstate__zNCDFPicklable.__getstate__s  t}d.?!# #r1ch||d|d|d|ddS)Nrrrr)rrr)r)r+argss r0 __setstate__zNCDFPicklable.__setstate__s@ d1gDGT!W#'7  , , , , ,r1N)rnrorprqr(r+r$r1r0rrs=;;x###,,,,,r1r) rqscipy.io.netcdfrnumpyr"rKrloggingmathrrtimesteprrrlibrlib.utilr getLoggerrr ImportErrorr ReaderBaser rw WriterBaserrrrr$r1r0r7s.llZ ++++++  9 : :WNNNNWWWG NNUVVVVVW IIIIIIIIXQ7Q7Q7Q7Q7Q7Q7Q7h h h h h h h h h V C,C,C,C,C,EH(C,C,C,C,C,s AA.-A.