isdZddlZddlZddlZddlZddlmZmZmZddl m Z ddl Z ddl Z ddlmZmZddlmZdd lmZdd lmZGd d eZGd deZGddeZGddeZdS)aS Auxiliary Readers --- :mod:`MDAnalysis.auxiliary.base` ====================================================== Base classes for deriving all auxiliary data readers. See the API in :mod:`MDAnalysis.auxiliary.__init__`. .. autoclass:: AuxStep :members: .. autoclass:: AuxReader :members: .. autoclass:: AuxFileReader :members: N)UnionOptionalDict) defaultdict) asiterableanyopen)units) _AUXREADERS) auxreaderceZdZdZdS)_AuxReaderMetactt||| t|d}|D] }|t|< dS#t$rYdSwxYw)Nformat)type__init__rr KeyError)clsnamebases classdictfmtfs c/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/auxiliary/base.pyrz_AuxReaderMeta.__init__=s{ dD%333 %Yx011C % %!$ A % %    DD sA AAN)__name__ __module__ __qualname__rrrr;s#%%%%%r rceZdZdZ ddZedZedZed Zej d Zed Z e j d Z d Z dS)AuxStepaBase class for auxiliary timesteps. Stores the auxiliary data for the current auxiliary step. On creation, ``step`` is set to -1. .. versionchanged:: 2.4.0 Added memory_limit parameter to control raising memory usage warnings. Parameters ---------- dt : float, optional Change in time between auxiliary steps (in ps). If not specified, will attempt to determine from auxiliary data; otherwise defaults to 1 ps. Ignored if ``constant_dt`` is False. initial_time : float, optional Time of first auxiliary step (in ps). If not specified, will attempt to determine from auxiliary data; otherwise defaults to 0 ps. Ignored if ``constant_dt`` is False. time_selector: optional Key to select 'time' value from the full set of data read for each step, if time selection is enabled; type will vary depending on the auxiliary data format (see individual AuxReader documentation). If ``None`` (default value), time is instead calculated as: ``time = step * dt + initial_time`` data_selector: optional Key(s) to select auxiliary data values of interest from the full set of data read for each step, if data selection is enabled by the reader; type will vary depending on the auxiliary data format (see individual AuxReader documentation). If ``None`` (default value), the full set of data is returned. constant_dt : bool, optional (Default: True) Set to False if ``dt`` is not constant throughout the auxiliary data set, in which case a valid ``time_selector`` must be provided. memory_limit : float, optional Sets the threshold of memory usage by auxiliary data (in GB) at which to issue a warning. Default: 1 GB. Attributes ---------- step : int Number of the current auxiliary step (0-based). r rNTcZd|_||_||_||_||_||_dS)N)step _initial_time_dt _constant_dt_time_selector__data_selector_)selfdt initial_time time_selector data_selector constant_dt memory_limits rrzAuxStep.__init__us: )' -,r c|j||jS|jr|j|jz|jzSt d)aTime in ps of current auxiliary step (as float). Read from the set of auxiliary data read each step if time selection is enabled and a valid ``time_selector`` is specified; otherwise calculated as ``step * dt + initial_time``. Nz6If dt is not constant, must have a valid time selector)_time_selector _select_timer(r%r'r& ValueErrorr+s rtimez AuxStep.times[   *$$T%899 9   9tx'$*<< <K r cR|j||jS|jS)aAuxiliary values of interest for the current step (as ndarray). Read from the full set of data read for each step if data selection is enabled and a valid ``data_selector`` is specified; otherwise defaults to the full set of data. )_data_selector _select_data_datar6s rdataz AuxStep.datas,   *$$T%899 9zr c |jnB#t$r5tjd|jjYdSwxYw|jS)a'Key' to select time from the full set of data read in each step. Will be passed to ``_select_time()``, defined separately for each auxiliary format, when returning the time of the current step. Format will depend on the auxiliary format. e.g. for the XVGReader, this is an index and ``_select_time()`` returns the value in that column of the current step data. Defaults to 'None' if time selection is not enabled. z8{} does not support time selection. Reverting to defaultN)r4AttributeErrorwarningswarnr __class__rr)r6s rr3zAuxStep._time_selectorsm         M &!899   44   ## ;A A c |j}||||_dS#t$r5tjd|jjYdSwxYw)Nz"{} does not support time selection)r4r)r>r?r@rrArr+newselects rr3zAuxStep._time_selector '&F F3KKK#&D     M4;;N+       ;AAc |jnB#t$r5tjd|jjYdSwxYw|jS)al'Key' to select values of interest from full set of auxiliary data. These are the values that will be stored in ``data`` (and ``frame_data`` and ``frame_rep``). Will be passed to ``_select_data()``, defined separately for each auxiliary format, when returning the data of interest for the current step (``data``). Format will depend on the auxiliary format; e.g. for the XVGReader, this is a list of indices and `_select_data()` returns the value(s) in those columns of the current step data. Defaults to 'None' if data selection is not enabled. z8{} does not support data selection. Reverting to defaultN)r:r>r?r@rrArr*r6s rr9zAuxStep._data_selectorsm         M &!899   44   ##rBc |j}||||_dS#t$r5tjd|jjYdSwxYw)Nz"{} does not support data selection)r:r*r>r?r@rrArrDs rr9zAuxStep._data_selectorrGrHcbtj|jtjtjS)aCreate an 'empty' ``data``-like placeholder. Returns an ndarray in the format of ``data`` with all values set to np.nan; to use at the 'representative value' when no auxiliary steps are assigned to a trajectory timestep/within the cutoff. Default behaviour here works when ``data`` is a ndarray of floats. May need to overwrite in individual format's AuxSteps. .. versionchanged:: 2.4.0 dtype changed to np.float64 from np.float_ )dtype)np full_liker<nanfloat64r6s r _empty_datazAuxStep._empty_datas!|DIrvRZ@@@@r )r rNNTN) rrr__doc__rpropertyr7r<r3setterr9rQrr rr"r"Hs**\ ----&X"  X $$X$*''' $$X$.''' A A A A Ar r"cxeZdZdZeZddgZgdZ d6dZdZ dZ d Z d Z d Z d Zd ZdZdZdZ d7deeeeeeffdeeddfdZdZd8dZdZdZdZdZdZdZdZ dZ!d Z"d!Z#d"Z$d#Z%d$Z&e'd%Z(d&Z)e'd'Z*e*j+d(Z*d)Z,d*Z-d+Z.e'd,Z/e'd-Z0e'd.Z1e'd/Z2e'd0Z3e3j+d1Z3e'd2Z4e4j+d3Z4e'd4Z5e5j+d5Z5dS)9 AuxReaderaBase class for auxiliary readers. Allows iteration over a set of data from a trajectory, additional ('auxiliary') to the regular positions/velocities/etc. This auxiliary data may be stored in e.g. an array or a separate file. See the :ref:`Auxiliary API` for more on use. .. versionchanged:: 2.4.0 Behaviour of ``cutoff`` changed, default parameter which specifies not cutoff is set is now None, not -1. .. versionchanged:: 2.4.0 :class:`AuxReader` instances now have a :meth:`copy` method which creates a deep copy of the instance. Parameters ---------- auxname : str, optional Name for auxiliary data. When added to a trajectory, the representative auxiliary value(s) for the timestep may be accessed as ``ts.aux.auxname`` or ``ts.aux['auxname']``. represent_ts_as : str Method to use to calculate representative value of auxiliary data for a trajectory timestep. See :func:`calc_representative` for valid options. cutoff : float, optional Auxiliary steps further from the trajectory timestep than *cutoff* (in ps) will be ignored when calculating representative values. If None (default), all auxiliary steps assigned to that timestep will be used. **kwargs Options to be passed to :class:`~AuxStep` Attributes ---------- auxstep : :class:`~AuxStep` object containing data for current step. frame_data : dict Dictionary containing ``data`` from each auxiliary step assigned to the current trajectory timestep, indexed by the difference in time between the step and trajectory timestep (i.e. ``auxstep.time - ts.time``; in ps) frame_rep : ndarray Representative value(s) of auxiliary data for current trajectory timestep. Note ---- Auxiliary data are assumed to be time ordered and contain no duplicates. closestaverage) represent_ts_ascutoffr,r-r.r/r0auxnamer_auxdataNc t||_||_||dkr|nd|_d|_d|_|jdi||_||j[|j rV|j |j_ ||j |j z |j_ |dSdSdS)Nrr)r[rYrZ frame_data frame_rep_Auxstepauxstep_read_next_stepr.r0r7r&r-r'rewind)r+rYr[rZkwargss rrzAuxReader.__init__Ls  .!' 2v{{ff $t}..v..     )d.> ))-DL &  " " "#y4+<
z.AuxReader.attach_auxiliary..s:::td:::r zAuxiliary data with name z already exists zAuxiliary name 'zW' contains a space. Only dictionary style accession, not attribute style accession of 'z ' will work.rr1geAz9AuxReader: memory usage warning! Auxiliary data takes up z GB of memory (Warning limit: z GB).r)terms isinstancestraux_listr5r?r@get_descriptionr r[r/_auxsrrgetvalues _memory_usage) r+ coord_parentrrrdr[ descriptiondescription_kwargsraux_memory_usager1readerconvs rattach_auxiliaryzAuxReader.attach_auxiliarysR    y)40HH  ::tz:::HH # & & ( !$'H = =G,/// KKKKg~~ AwAA+2AAA ..00K!:K!:6!: 11011C!CK (%-W$5!*-L w '!mmLO<"%G H H    * % be(;;JJ233I ) )r c|jrhttj|j|jdz z |jz |jz }tt||j dz d}n?t|j dzD]"}| ||j krn#|dz }|dkr| dS||dS)a0Position auxiliary reader just before trajectory timestep *ts*. Calling ``next()`` should read the first auxiliary step 'assigned' to the trajectory timestep *ts* or, if no auxiliary steps are assigned to that timestep (as in the case of less frequent auxiliary data), the first auxiliary step after *ts*. Parameters ---------- ts : :class:`~MDAnalysis.coordinates.timestep.Timestep` object The trajectory timestep before which the auxiliary reader is to be positioned. rr r$N)r0rrrr7r,r-maxminrmrangerrru _go_to_step)r+rr%is rrzAuxReader.move_to_tss    BGbeai/$2CCtwNOODs4!122B77DD4z)AuxReader.__getitem__..s'#D#D#DQD$5$5a$8$8#D#D#Dr Nrr zStep must be positive integerz$Stop frame is lower than start framez0Index must be integer, list of integers or slice)rnumbersIntegralrrlistrMndarray _list_iterslicestartstoprmr%r5 IndexError _slice_iter TypeError)r+rrrr%s` r __getitem__zAuxReader.__getitem__s~( a) * * P!!!$$A##A&& & D"*- . . P??#D#D#D#D!#D#D#DEE E 5 ! ! P23'2ED%%ag...1E 6T\))v)%%af--- 6;QDdG$455 B !@AAAt|| !GHHH##E%t$<$<== =NOO Or ct|tjstd|dkr ||jz}|dks ||jkr(t d||j|S)NzStep indices must be integersrz/{} is out of range of auxiliary (num. steps {}))rrrrrmrrr+rs rrzAuxReader._check_indexs!W-.. =;<< < q55DL A q55A%%fQ -- r c#BK|D]}||VdSN)rr+rjs rrzAuxReader._list_iter s< & &A""1%% % % % % & &r c#~Kt|j|j|jD]}||VdSr)rrrr%rrs rrzAuxReader._slice_itersNqw// & &A""1%% % % % % & &r c td)z%Move to and read i-th auxiliary step.z0BUG: Override _go_to_step() in auxiliary reader!r{rs rrzAuxReader._go_to_steps" >   r ci|_dSr)r^r6s rrzAuxReader._reset_frame_datas r cB|j|z }|jj|j|<dS)aUpdate ``frame_data`` with values for the current step. Parameters ---------- ts_time : float the time of the timestep the current step is being 'added to'. Used to calculate difference in time between current step and timestep. N)r7rar<r^)r+ts_timers rrz!AuxReader._add_step_to_frame_datas'I' %)\%6 """r cjj}n%fdjD}t|dkrj}njdkr.Ds<Cs88t{**S***r rrWc,g|]}t|Sr)r)rrs rrz1AuxReader.calc_representative..Os888qCFF888r rXcg|]}|Srr)rrs rrz1AuxReader.calc_representative..YsBBBccBBBr )axis)rZr^itemslenrarQrYrrrMmeanarrayrrrfloatr)r+ cutoff_datavaluemin_diffdatasetrs` rrzAuxReader.calc_representative)s0 ; /KK $ 5 5 7 7K {  q L,,..EE  !Y . .88K88899H .#XI. . . .#H- .  !Y . . AHBB[-?-?-A-ABBBCC! A A A$E***BBG $ BBd {7';D'AA B!AAD"'+K0@0@"@E$KKAA A s& BB('B(7AC<_count_n_stepsr6s rrmzAuxReader.n_stepsrsK !=  ! ! ! //11DM=  !s  *66c"||jkr(td||j|jr||jz|jzS |j|S#t$r)||_|j|cYSwxYw)aReturn time of auxiliary step *i*. Calculated using ``dt`` and ``initial_time`` if ``constant_dt`` is True; otherwise from the list of times as read from the auxiliary data for each step. Parameters ---------- i : int Index (0-based) of step to return time for Returns ------- time : float Time (in ps) of step *i* Raises ------ ValueError When *i* not in valid range z<{0} is not a valid step index (total number of steps is {1})) rmr5rr0r,r-_timesr>read_all_timesrs rrzAuxReader.step_to_time{s,    &q$, 7 7    &tw;!22 2 &{1~%! & & &"1133 {1~%%% &s A0B Bc|jS)zgMethod by which 'representative' timestep values of auxiliary data will be calculated. )_represent_ts_asr6s rrYzAuxReader.represent_ts_ass $$r cv||jvr(td||j||_dS)Nz[{0} is not a valid option for calculating representative value(s). Enabled options are: {1})represent_optionsr5rrr+rEs rrYzAuxReader.represent_ts_assI d, , ,fS$"899  !$r c.|dSrrr6s r__del__zAuxReader.__del__s r c.fdjD}|S)aGet the values of the parameters necessary for replicating the AuxReader. An AuxReader can be duplicated using :func:`~MDAnalysis.auxiliary.core.auxreader`:: description = original_aux.get_description() new_aux = MDAnalysis.auxiliary.auxreader(**description) The resulting dictionary may also be passed directly to :meth:`~MDAnalysis.coordinates.base.ProtoReader.add_auxiliary` to reload an auxiliary into a trajectory:: trajectory.add_auxiliary(**description) Returns ------- dict Key-word arguments and values that can be used to replicate the AuxReader. cXi|]&}|dt|'S)_)stripgetattr)rattrr+s rrz-AuxReader.get_description..s?    JJsOOWT400   r )required_attrs)r+rs` rrzAuxReader.get_descriptions6,    +   r cd|jD]'}t||t||krdS(dS)NFT)rr)r+otherrs r__eq__zAuxReader.__eq__sD'  DtT""geT&:&:::uu;tr c|jjS)zQNumber of the current auxiliary step (as stored in ``auxstep``; 0-based).rxr6s rr%zAuxReader.steps|  r c|jjS)z@Time of current auxiliary step (as stored in ``auxstep``; in ps))rar7r6s rr7zAuxReader.times|  r c|jjS)zPChange in time between auxiliary steps (as stored in ``auxstep``; in ps))rar'r6s rr,z AuxReader.dts|r c|jjS)z>Time of first auxiliary step (as stored in ``auxstep``; in ps))rar&r6s rr-zAuxReader.initial_times|))r c|jjS)aKey to select 'time' value from the full set of data read for each step. As stored in ``austep``. Type differs between auxiliary formats, depending how the data for each step is read in and stored; e.g. data from .xvg files is read in as a list and `time_selector` must be a valid index. If time selection is not enabled by the reader, ``time_selector`` will default to ``None``. See each individual auxiliary reader. )rar3r6s rr.zAuxReader.time_selectors|**r cn|jj}||j_||kr |`dS#t$rYdSwxYwdSr)rar3rr>)r+rEolds rr.zAuxReader.time_selectorsVl)&) # #:: KKK!     :s $ 22c|jjS)a Key(s) to select auxiliary data values of interest from the full set of data read for each step (as stored in ``auxstep``). Type differs between auxiliary formats, depending how the data for each step is read in and stored - e.g. data from .xvg files is read in as a list and `data_selector` must be a list of valid indicies. If data selection is not enabled by the reader, ``data_selector`` will default to ``None``. See each individual auxiliary reader. rar9r6s rr/zAuxReader.data_selectors|**r c||j_dSrrrs rr/zAuxReader.data_selectors&) ###r c|jjS)zVTrue if ``dt`` is constant throughout the auxiliary (as stored in ``auxstep``)rar(r6s rr0zAuxReader.constant_dts|((r c||j_dSrrrs rr0zAuxReader.constant_dts$' !!!r )rWNN)NN)F)6rrrrRr"r`rrrrkrnrqrsrvrurcrbrr~rrrrrrrrrrrrrrrrrrrrrSrmrrYrTrrrr%r7r,r-r.r/r0rr rrVrVs00dH"I.   N?C0 &&&  &&&   %%%N/4/4/4h:> $ ``5d38n!456` `  ````D   2*2*2*2*h # # #D$$$L1P1P1Pf   &&&&&&    7 7 7<<<|   !!X!"&"&"&H%%X% $$$8 !!X! !!X!  X **X* + +X +    + +X +***))X) (((((r rV) metaclassc:eZdZdZfdZdZdZdZdZxZ S) AuxFileReaderaBase class for auxiliary readers that read from file. Extends AuxReader with attributes and methods particular to reading auxiliary data from an open file, for use when auxiliary files may be too large to read in at once. Parameters ---------- filename : str Location of the file containing the auxiliary data. **kwargs Other AuxReader options. See also -------- :class:`AuxReader` Attributes ---------- auxfile File object for the auxiliary file. c t||_tj||_t t|jdi|dS)Nr) r auxfileospathabspathr\superrr)r+filenamerdrAs rrzAuxFileReader.__init__<sPx(( 11 +mT""+55f55555r cX|jdS|jd|_dS)zClose *auxfile*.N)rrr6s rrzAuxFileReader.closeAs. <  F  r cR|jdd|j_dS)z%Reposition to just before first step.rr$N)rseekrar%r6s rruzAuxFileReader._restartHs( ! r c|j|jt|j|_d|j_dS)z Close and then reopen *auxfile*.Nr$)rropenr\rar%r6s r_reopenzAuxFileReader._reopenMs? < # L   DM**  r c||jkr(td||j|}|j|kr|}|j|k|S)aMove to and read i-th auxiliary step. Parameters ---------- i : int Step number (0-indexed) to move to Raises ------ ValueError If step index not in valid range. Note ---- Works by reading through all steps consecutively until correct step is reached. Overwrite if this can be done more efficiently. z:Step index {0} is not valid for auxiliary (num. steps {1}!)rmr5rrcr%rq)r+rrs rrzAuxFileReader._go_to_stepTsr&   ##)6!T\#:#:  i1nnIIKKEi1nn r ) rrrrRrrrur#r __classcell__)rAs@rrr#s~066666  r r)rRrrrr?typingrrr collectionsrrfnumpyrMlib.utilrr r r corer rrobjectr"rVrrr rr-s2"  ((((((((((###### ******** % % % % %T % % %|A|A|A|A|Af|A|A|A~Y (Y (Y (Y (Y (.Y (Y (Y (Y (xLLLLLILLLLLr