iOdZddlZddlZddlZddlZddlZddlZddlm Z ddlm Z m Z ddl mZddlmZdd lmZGd d e jZGd d e jZdS)aDCD trajectory I/O --- :mod:`MDAnalysis.coordinates.DCD` ============================================================ Classes to read and write DCD binary trajectories, the format used by CHARMM, NAMD, and also LAMMPS. Trajectories can be read regardless of system-endianness as this is auto-detected. Generally, DCD trajectories produced by any code can be read (with the :class:`DCDReader`) although there can be issues with the unitcell (simulation box) representation (see :attr:`DCDReader.dimensions`). DCDs can also be written but the :class:`DCDWriter` follows recent NAMD/VMD convention for the unitcell while still writing AKMA time. Reading and writing these trajectories within MDAnalysis will work seamlessly but if you process those trajectories with other tools you might need to watch out that time and unitcell dimensions are correctly interpreted. See Also -------- :mod:`MDAnalysis.coordinates.LAMMPS` module provides a more flexible DCD reader/writer. .. _Issue 187: https://github.com/MDAnalysis/mdanalysis/issues/187 Classes ------- .. autoclass:: DCDReader :inherited-members: .. autoclass:: DCDWriter :inherited-members: N)units)basecore)DCDFile) triclinic_box)store_init_argumentsceZdZdZdZdZdddZedfd Ze d Z d Z e d Z d ZdZddZddZdZe dZe dZ ddZxZS) DCDReaderu Reader for the DCD format. DCD is used by NAMD, CHARMM and LAMMPS as the default trajectory format. The DCD file format is not well defined. In particular, NAMD and CHARMM use it differently. Currently, MDAnalysis tries to guess the correct **format for the unitcell representation** but it can be wrong. **Check the unitcell dimensions**, especially for triclinic unitcells (see `Issue 187`_). DCD trajectories produced by CHARMM and NAMD( >2.5) record time in AKMA units. If other units have been recorded (e.g., ps) then employ the configurable :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` and set the time unit as a optional argument. You can find a list of units used in the DCD formats on the MDAnalysis `wiki`_. MDAnalysis always uses (*A*, *B*, *C*, α, β, γ) to represent the unit cell. Lengths *A*, *B*, *C* are in the MDAnalysis length unit (Å), and angles α, β, γ are in degrees. The ordering of the angles in the unitcell is the same as in recent versions of VMD's DCDplugin_ (2013), namely the `X-PLOR DCD format`_: The original unitcell is read as ``[A, gamma, B, beta, alpha, C]`` from the DCD file. If any of these values are < 0 or if any of the angles are > 180º then it is assumed it is a new-style CHARMM unitcell (possibly ≥22, at least since c36b2) in which symmetric box vectors were recorded. If all angles are numbers between -1 and +1, then they are treated as cosines of the angle (following the modern NAMD > 2.5/VMD convention). Ultimately, all unitcell representations are converted to the MDAnalysis standard unit cell representation in :attr:`DCDReader.dimensions`. .. deprecated:: 2.4.0 DCDReader currently makes independent timesteps by copying the :class:`Timestep` associated with the reader. Other readers update the :class:`Timestep` inplace meaning all references to the :class:`Timestep` contain the same data. The unique independent :class:`Timestep` behaviour of the DCDReader is deprecated will be changed in 3.0 to be the same as other readers .. warning:: The DCD format is not well defined. Check your unit cell dimensions carefully, especially when using triclinic boxes. Different software packages implement different conventions and MDAnalysis is currently implementing the newer NAMD/VMD convention and tries to guess the new CHARMM one. Old CHARMM trajectories might give wrong unitcell values. For more details see `Issue 187`_. .. _`X-PLOR DCD format`: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html .. _Issue 187: https://github.com/MDAnalysis/mdanalysis/issues/187 .. _DCDplugin: http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c-source.html#l00947 .. _wiki: https://github.com/MDAnalysis/mdanalysis/wiki/FileFormats#dcd DCDCHARMMAKMAAngstromtimelengthTNc tt|j|fd|i|t|j|_|jjd|_tj |jjd|j dd}|||jjdz}|jjd|_ ||j d<|j |jfi|j |_|j}|jjd kr|jd n|jd d |_|||j|_||j_t+jd t. dS) a Parameters ---------- filename : str trajectory filename convert_units : bool (optional) convert units to MDAnalysis units dt : float (optional) overwrite time delta stored in DCD **kwargs : dict General reader arguments. .. versionchanged:: 0.17.0 Changed to use libdcd.pyx library and removed the correl function convert_unitsnatomsdeltarpsNnsavcdtrra,DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.category)superr __init__rfilename_fileheadern_atomsmdaunitsconvertr skip_timestep _ts_kwargs _Timesteptsreadn_framesseek_frame _frame_to_tsrwarningswarnDeprecationWarning)selfrrrkwargsrframe __class__s d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/DCD.pyrzDCDReader.__init__s$ (i'  = =$1 =5; = = =T]++ z(2  !27!;!%F!3T;; :*733B!Z.w7 " $.AAAA !! :  " " JOOA     JOOA    ##E4733  O !3  4 4 4 4 4 4c nt|5}|jd}dddn #1swxYwY|S)Nr)rr!)rr2fr"s r5 parse_n_atomszDCDReader.parse_n_atomsss X   )!hx(G ) ) ) ) ) ) ) ) ) ) ) ) ) ) )s *..c8|jdS)z close readerNr closer1s r5r<zDCDReader.close r6c*t|jS)znumber of frames in trajectory)lenr r=s r5r*zDCDReader.n_framess4:r6cd|j_d|_|j|jddS)zreopen trajectoryrrN)r(r3r,r r<openr=s r5_reopenzDCDReader._reopens@    r6cr|dz |_|j||S)z read frame ir)r,r r+_read_next_timestep)r1is r5 _read_framezDCDReader._read_frames3!e  '')))r6c |j|jdz krtd||j}|j}|xjdz c_|||||_|S)zcopy next frame into timesteprz"trying to go over trajectory limit)r,r*IOErrorr(copyr r)r-)r1r(r3s r5rGzDCDReader._read_next_timesteps| ;$-!+ + +>?? ? :B !! q  %$$$ r6c T||j}t|f||jj|jd|S)z#Return writer for trajectory formatN)r"rr)r" DCDWriterr(rr)r1rr"r2s r5WriterzDCDReader.WritersG ?lG wz,    r6c`|j|_|j|jjd|jjdz z|jjz|_|j|jd<gd}tj |j |}tj dz }d|dcxkrdkrnnd|d cxkrdkrnnd|d cxkrdkrvnnsd tj |dd z|z z |d<d tj |d d z|z z |d <d tj |d d z|z z |d <ntj|d ks tj|dd dkrI|j }|gd|gd|gd} }}t!||| }n ||_|j|_|jrC|j"||jd d||j|S)z*convert a dcd-frame to a :class:`TimeStep`istartrstep)rrrrgrUg?rTrSV@gNgf@)rrrU)rrrT)rUrTrS)r,r3r r!r(rrtelldatanptakeunitcellpiarcsinanyrLr dimensionsxyz positionsrconvert_pos_from_native) r1r3r( _ts_orderucpi_2He1e2e3s r5r-zDCDReader._frame_to_tssE;8dj/9$*:KG:TTTX\X_Xbb*//++'&& WU^Y / /uqy BqE S tr!u';';';';';';';';';1$$$$$$$$$29RU++d2T99BqE29RU++d2T99BqE29RU++d2T99BqEE VBG__ r!""v} 5 5 ##%%A999q|Qyyy\BBr2r**BB  y   7}(,,R]2A2->???  ( ( 6 6 6 r6c|jjS)zFunitcell dimensions (*A*, *B*, *C*, *alpha*, *beta*, *gamma*) )r(r_r=s r5r_zDCDReader.dimensionssw!!r6c|jjS)ztimestep between frames)r(rr=s r5rz DCDReader.dtswzr6afcc|.tjdt|rtd|}||||\}}}|7t |dkrtdt |j}n!t t|j }|j |||||}|j S)aReturn a subset of coordinate data for an AtomGroup Parameters ---------- asel : :class:`~MDAnalysis.core.groups.AtomGroup` The :class:`~MDAnalysis.core.groups.AtomGroup` to read the coordinates from. Defaults to None, in which case the full set of coordinate data is returned. .. deprecated:: 2.7.0 asel argument will be renamed to atomgroup in 3.0.0 atomgroup: AtomGroup (optional) Same as `asel`, will replace `asel` in 3.0.0 start : int (optional) Begin reading the trajectory at frame index `start` (where 0 is the index of the first frame in the trajectory); the default ``None`` starts at the beginning. stop : int (optional) End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded. The trajectory is read to the end with the default ``None``. step : int (optional) Step size for reading; the default ``None`` is equivalent to 1 and means to read every frame. order : str (optional) the order/shape of the return data array, corresponding to (a)tom, (f)rame, (c)oordinates all six combinations of 'a', 'f', 'c' are allowed ie "fac" - return array where the shape is (frame, number of atoms, coordinates) .. versionchanged:: 1.0.0 `skip` and `format` keywords have been removed. .. versionchanged:: 2.4.0 ValueError now raised instead of NoDataError for empty input AtomGroup NzKasel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911rz-Cannot provide both asel and atomgroup kwargsrz0Timeseries requires at least one atom to analyze)orderindices) r.r/r0 ValueErrorcheck_slice_indicesr@listroranger"r readframesr`) r1asel atomgroupstartstoprRrn atom_numbersframess r5 timeserieszDCDReader.timeseriess\   M0+ - - - - R !PQQQI 44UD$GGtT  9~~"" FHHH 122LLdl 3 344L&& 4UL'BBzr6)TNN)NNNNNrl)__name__ __module__ __qualname____doc__formatflavorrr r staticmethodr9r<propertyr*rErIrGrOr-r_rr{ __classcell__)r4s@r5r r Isn33hF Fz 2 2E.4.4.4.4.4.4`\ X***        )))V""X" X ! CCCCCCCCr6r cNeZdZdZdZdZdZdddZ dd Zd Z d Z dZ dS)rNuDCD Writer class The writer follows recent NAMD/VMD convention for the unitcell (box lengths in Å and angle-cosines, ``[A, cos(gamma), B, cos(beta), cos(alpha), C]``) and writes positions in Å and time in AKMA time units. .. warning:: Multiple conventions exist for how unit cells are written to DCD files. Until 2.10.0 MDAnalysis followed the old X-PLOR/CHARMM/NAMD (≤2.5) convention of storing ``[A, gamma, B, beta, alpha, C]`` while wrongly stating that the new NAMD/VMD convention would be followed. In 2.10.0, MDAnalysis switched to following the documented behavior and now stores the box with angle cosines, as described above. The MDAnalysis :class:`DCDReader` can correctly read either format but *if you have code that relies on a specific format for the box information in the raw DCD file, please check your results.* Furthermore, modern versions of CHARMM store box vectors and not box length/angles. When reading MDAnalysis-generated DCD files *in CHARMM*, carefully check your results. .. note:: When writing out timesteps without ``dimensions`` (i.e. set ``None``) the :class:`DCDWriter` will write out a zeroed unitcell (i.e. ``[0, 0, 0, 0, 0, 0]``). As this behaviour is poorly defined, it may not match the expectations of other software. .. versionchanged:: 2.10.0 Up to 2.10.0 the :class:`DCDWriter` wrote a unit cell following old NAMD (≤2.5) convention, even though the docs stated that the new NAMD convention was being used. Now the modern NAMD > 2.5 format is written. See `Issue #5069`_ for details. .. _`Issue #5069`: https://github.com/MDAnalysis/mdanalysis/issues/5069 r TNAMDrrrrrc  ^||_||_|td||_t |jd|_||_||_tj |d|j d}t||z } ||n|}|j ||j|| d|dS)aParameters ---------- filename : str filename of trajectory n_atoms : int number of atoms to be written convert_units : bool (optional) convert from MDAnalysis units to format specific units step : int (optional) number of steps between frames to be written dt : float (optional) time between two frames. If ``None`` guess from first written :class:`TimeStep` remarks : str (optional) remarks to be stored in DCD. Shouldn't be more then 240 characters nsavc : int (optional) DCD files can also store the number of integrator time steps that correspond to the interval between two frames as nsavc (i.e., every how many MD steps is a frame saved to the DCD). By default, this number is just set to one and this should be sufficient for almost all cases but if required, `nsavc` can be changed. istart : int (optional) starting frame number in integrator timesteps. CHARMM defaults to `nsavc`, i.e., start at frame number 1 = `istart` / `nsavc`. The value ``None`` will set `istart` to `nsavc` (the CHARMM default). The MDAnalysis default is 0 so that the frame number and time of the first frame is 0. **kwargs : dict General writer arguments Nzn_atoms argument is requiredwrrr)remarksrrr is_periodicrQ) r_convert_unitsrpr"rr rRrr#r$rfloat write_header) r1rr"rrRrrrrQr2rs r5rzDCDWriter.__init__sR! + ?;<< < T]C00    b$ 6(: ; ;b E!!-5 <      r6c |j}n>#t$r1 |jj}n #t$rd}t|dwxYwYnwxYw|j} |j}n:#t$r-d}tj|tj d}YnwxYw|j r.| |d}| |d}gd}tj||}tjtjd|gd z |gd <|j|| dS) aDWrite information associated with ``obj`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe See Also -------- :meth:`DCDWriter.write` takes a more general input .. versionchanged:: 1.0.0 Added ability to pass AtomGroup or Universe. Renamed from `write_next_timestep` to `_write_next_frame`. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. z-Input obj is neither an AtomGroup or UniverseNzDNo dimensions set for current frame, zeroed unitcell will be writtenT)inplace)rrSrrTrUrrV)rrUrT)r`box)r(AttributeError trajectory TypeErrorrarLr_r.r/rYzerosrconvert_pos_to_nativeconvert_dimensions_to_unitcellrZsindeg2radr write) r1agr(errmsgr`r_wmsgrcrs r5_write_next_framezDCDWriter._write_next_frames& 2BB 2 2 2 2]%! 2 2 2H''T1 2 2l!! %++--JJ % % %&D M$   !JJJ  %   O,,S$,??C<r6c.|dSr|)r<r=s r5__del__zDCDWriter.__del__s r6N)Trrrrr) r}r~rrr multiframerrrrr<rr6r5rNrNcs%%LFJ Fz 2 2E $::::x2+2+2+hr6rN)roserrnonumpyrYstructtypesr.rrr#rrlib.formats.libdcdr lib.mdamathr lib.utilr ReaderBaser WriterBaserNrr6r5rs .##H   ((((((''''''++++++WWWWWWWWtaaaaaaaaaar6