iz@dZddlZddlZddlZddlZddlZddlZddlZddlZddl Z ddl Z ddl m Z ddl mZddlZddlmZddlmZmZmZmZejdZeddd d ZGd d eZGddeZGddeZdS)aW Generation and Analysis of X3DNA helicoidal parameter profiles --- :mod:`MDAnalysis.analysis.legacy.x3dna` ========================================================================================================== :Author: Elizabeth Denning :Year: 2013-2014 :Copyright: Lesser GNU Public License v2.1+ .. versionadded:: 0.8 .. versionchanged:: 0.16.0 This module is difficult to test due to restrictions on the X3DNA_ code. It is therefore considered unmaintained and legacy code. It was moved to the :mod:`MDAnalysis.analysis.legacy` package (see `issue 906`_) .. _`issue 906`: https://github.com/MDAnalysis/mdanalysis/issues/906 With the help of this module, X3DNA_ can be run on frames in a trajectory. Data can be combined and analyzed. X3DNA_ :footcite:p:`Lu2003,Lu2008` must be installed separately. .. rubric:: References .. footbibliography:: .. _X3DNA: http://x3dna.org/ Example applications -------------------- Single structure ~~~~~~~~~~~~~~~~ B-DNA structure:: from MDAnalysis.analysis.x3dna import X3DNA, X3DNAtraj from MDAnalysis.tests.datafiles import PDB_X3DNA # set path to your x3dna binary in bashrc file H = X3DNA(PDB_X3DNA, executable="x3dna_ensemble analyze -b 355d.bps -p pdbfile") H.run() H.collect() H.plot() Trajectory ~~~~~~~~~~ Analyzing a trajectory:: u = MDAnalysis.Universe(psf, trajectory) H = X3DNAtraj(u, ...) H.run() H.plot() H.save() The profiles are available as the attribute :attr:`X3DNAtraj.profiles` (``H.profiles`` in the example) and are indexed by frame number but can also be indexed by an arbitrary order parameter as shown in the next example. Analysis classes ---------------- .. autoclass:: X3DNA :members: :inherited-members: .. attribute:: profiles ``x3dna_ensemble analyze -b 355d.bps -p pdbfile attribute``: After running :meth:`X3DNA.collect`, this dict contains all the X3DNA profiles, indexed by the frame number. If only a single frame was analyzed then this will be ``X3DNA.profiles[0]``. Note that the order is random; one needs to sort the keys first. .. autoclass:: X3DNAtraj :members: :inherited-members: .. attribute:: profiles After running :meth:`X3DNA.collect`, this dict contains all the X3DNA profiles, indexed by the frame number. Utilities --------- .. autoexception:: ApplicationError N) OrderedDict)ApplicationError) asiterable deprecaterealpathwhichzMDAnalysis.analysis.x3dna2.7.03.0.0LX3DNA module is deprecated and will be removed inMDAnalysis 3.0.0, see #3788releaseremovemessagectjdt|jdurggggggggggggf \ }}}}}}}}} } } } t t |D][} ||| j||| j ||| j ||| j ||| j | || j ||| j||| j||| j| || j| || j| || j]t)j|t)j|t)j|t)j|t)j|t)j|t)j|t)j|t)j| t)j| t)j| t)j| f \ }}}}}}}}} } } } gg}}t t |dD]}|t)j|dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j| dd|ft)j| dd|fg |t)j|dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j| dd|ft)j| dd|fg nggggggggggggf \}}}} } } t t |D]/} ||| j||| j||| j| || j| || j| || j1t)j|t)j|t)j|t)j|t)j|t)j|t)j|t)j|t)j| t)j| t)j| t)j| f \}}}} } } gg}}t t |dD]}|t)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j| dd|ft)j| dd|fg|t)j|dd|ft)j|dd|ft)j|dd|ft)j| dd|ft)j| dd|ft)j| dd|fgt)j|t)j|}}||fS)a!Get mean and standard deviation of helicoidal parameters from a saved `profile`. The `profile` should have been saved with :meth:`BaseX3DNA.save`. Then load it with :: profile = cPickle.load(open("x3dna.pickle")) h_mean, h_std = mean_std_from_x3dnaPickle(profile) Arguments --------- profile : dict A :attr:`X3DNA.profiles` dict with results from the :class:`X3DNA` analysis. Returns ------- (list, list) The tuple contains two lists with the means and the standard deviations for the helicoidal parameters. The order for both lists is ``[shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist]``. .. deprecated:: 2.7.0 X3DNA will be removed in 3.0.0. zKX3DNA module is deprecated and will be removed in MDAnalysis 3.0, see #3788)categoryFrN)warningswarnDeprecationWarning x3dna_paramrangelenappendvaluesShearStretchStaggerBuckle PropellerOpeningRiseShiftSlideTiltRollTwistnparraymeanstd)profilebp_shear bp_stretch bp_staggerbp_risebp_shiftbp_slide bp_bucklebp_propbp_openbp_tiltbp_rollbp_twistina_avgna_stdjs j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/legacy/x3dna.pymean_std_from_x3dnaPickler<sx D MU#e##2r2r2r2r2r2E *j'8XyRY[bdkmt s7||$$ 7 7A OOGNN,,Q/5 6 6 6   gnn..q19 : : :   gnn..q19 : : :   W^^--a07 8 8 8 NN7>>++A.8 9 9 9 NN7>>++A.6 7 7 7 NN7>>++A.3 4 4 4 OOGNN,,Q/5 6 6 6 OOGNN,,Q/5 6 6 6 NN7>>++A.3 4 4 4 NN7>>++A.3 4 4 4 OOGNN,,Q/5 6 6 6 6x))28J+?+?*AUAUWYW_`gWhWh HX   2 2BHY4G4GRYIZIZ HW  rx00"(72C2CRXhEWEWX *j'8XyRY[bdkmt Rs8A;''((  A MMGHQQQTN++GJqqq!t,--GJqqq!t,--GIaaadO,,GGAAAqDM**GGAAAqDM**GHQQQTN++GHQQQTN++GGAAAqDM**GGAAAqDM**GGAAAqDM**GHQQQTN++     MMF8AAAqD>**F:aaad+,,F:aaad+,,F9QQQT?++F7111a4=))F7111a4=))F8AAAqD>**F8AAAqD>**F7111a4=))F7111a4=))F7111a4=))F8AAAqD>**     # FCEb"bRTVXZ\^`bdfhjlnpBp?8Wgxs7||$$ 7 7A NN7>>++A.3 4 4 4 OOGNN,,Q/5 6 6 6 OOGNN,,Q/5 6 6 6 NN7>>++A.3 4 4 4 NN7>>++A.3 4 4 4 OOGNN,,Q/5 6 6 6 6 HX   HZ HZ HW   HX   HX   HY   HW   HW   HW   HW   HX   C ?8WgxRs8A;''((  A MMGHQQQTN++GHQQQTN++GGAAAqDM**GGAAAqDM**GGAAAqDM**GHQQQTN++     MMF8AAAqD>**F8AAAqD>**F7111a4=))F7111a4=))F7111a4=))F8AAAqD>**     Xf%%rx'7'7FF 6>c<eZdZdZd dZdZdZdZdZdZ e Z d S) BaseX3DNAaiBaseclass for X3DNA_ analysis, providing plotting and utility functions. When methods return helicoidal basepair parameter as lists, then the order is always ====== ============== index parameter ====== ============== 0 shear 1 stretch 2 stagger 3 buckle 4 propeller 5 opening 6 shift 7 slide 8 rise 9 tilt 10 roll 11 twist ====== ============== for each nucleic acid pair. .. deprecated:: 2.7.0 X3DNA will be removed in 3.0.0. .. _X3DNA: http://x3dna.org x3dna.pickleclddl}||jt|d|jdS)zSave :attr:`profiles` as a Python pickle file *filename*. Load profiles dictionary with :: import cPickle profiles = cPickle.load(open(filename)) rNwb)cPickledumpprofilesopenHIGHEST_PROTOCOL)selffilenamerCs r;savezBaseX3DNA.saveBsC  M4$//1I     r=cggggggggggggf \ }}}}}}}}} } } } tt|jD]} ||j| j||j| j||j| j||j| j||j| j | |j| j ||j| j ||j| j ||j| j | |j| j| |j| j| |j| jt#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j| t#j| t#j| t#j| f \ }}}}}}}}} } } } gg}}tt|dD]}|t#j|dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j| dd|ft#j| dd|fg |t#j|dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j| dd|ft#j| dd|fg t#j|t#j|}}||fS)aReturns the mean and standard deviation of base parameters. Returns ------- (list, list) The tuple contains two lists with the means and the standard deviations for the helicoidal parameters. The order for both lists is ``[shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist]``. rN)rrrErrrrrrrrr r!r"r#r$r%r&r'r(r))rHr+r,r-r.r/r0r1r2r3r4r5r6r7r8r9r:s r;mean_stdzBaseX3DNA.mean_stdQs2r2r2r2r2r2E *j'8XyRY[bdkmt s4=))** = =A OODM002215; < < <   dm2244Q7? @ @ @   dm2244Q7? @ @ @   T]1133A6= > > > NN4=//11!4> ? ? ? NN4=//11!4< = = = NN4=//11!49 : : : OODM002215; < < < OODM002215; < < < NN4=//11!49 : : : NN4=//11!49 : : : OODM002215; < < < <x))28J+?+?*AUAUWYW_`gWhWh HX   2 2BHY4G4GRYIZIZ HW  rx00"(72C2CRXhEWEWX *j'8XyRY[bdkmt Rs8A;''((  A MMGHQQQTN++GJqqq!t,--GJqqq!t,--GIaaadO,,GGAAAqDM**GGAAAqDM**GHQQQTN++GHQQQTN++GGAAAqDM**GGAAAqDM**GGAAAqDM**GHQQQTN++     MMF8AAAqD>**F:aaad+,,F:aaad+,,F9QQQT?++F7111a4=))F7111a4=))F8AAAqD>**F8AAAqD>**F7111a4=))F7111a4=))F7111a4=))F8AAAqD>**      &))28F+;+;v~r=c ggggggggggggf \ }}}}}}}}} } } } tt|jD]} ||j| j||j| j||j| j||j| j||j| j | |j| j ||j| j ||j| j ||j| j | |j| j| |j| j| |j| jt#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j| t#j| t#j| t#j| f \ }}}}}}}}} } } } g}tt|dD]r}|t#j|dd|ft#j|dd|ft#j|dd|ft#j|d|t#j|dd|ft#j| dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j| dd|ft#j| dd|fg tt#j|}|S)a5Returns the mean value for the base parameters. Returns ------- list The list contains the means for the helicoidal parameters. The order is ``[shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist]``. rN)rrrErrrrrrrrr r!r"r#r$r%r&r'r()rHr+r,r-r.r/r0r1r2r3r4r5r6r7r8r:s r;r(zBaseX3DNA.means2r2r2r2r2r2E *j'8XyRY[bdkmt s4=))** = =A OODM002215; < < <   dm2244Q7? @ @ @   dm2244Q7? @ @ @   T]1133A6= > > > NN4=//11!4> ? ? ? NN4=//11!4< = = = NN4=//11!49 : : : OODM002215; < < < OODM002215; < < < NN4=//11!49 : : : NN4=//11!49 : : : OODM002215; < < < <x))28J+?+?*AUAUWYW_`gWhWh HX   2 2BHY4G4GRYIZIZ HW  rx00"(72C2CRXhEWEWX *j'8XyRY[bdkmt  s8A;''((  A MMGHQQQTN++GJqqq!t,--GJqqq!t,--GIbqbM**GGAAAqDM**GGAAAqDM**GHQQQTN++GHQQQTN++GGAAAqDM**GGAAAqDM**GGAAAqDM**GHQQQTN++      &!! r=c ggggggggggggf \ }}}}}}}}} } } } tt|jD]} ||j| j||j| j||j| j||j| j||j| j | |j| j ||j| j ||j| j ||j| j | |j| j| |j| j| |j| jt#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j|t#j| t#j| t#j| t#j| f \ }}}}}}}}} } } } g}tt|dD]r}|t#j|dd|ft#j|dd|ft#j|dd|ft#j|d|t#j|dd|ft#j| dd|ft#j|dd|ft#j|dd|ft#j|dd|ft#j| dd|ft#j| dd|ft#j| dd|fg tt#j|}|S)aKReturns the standard deviation for the base parameters. Returns ------- list The list contains the standard deviations for the helicoidal parameters. The order is ``[shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist]``. rN)rrrErrrrrrrrr r!r"r#r$r%r&r'r))rHr+r,r-r.r/r0r1r2r3r4r5r6r7r9r:s r;r)z BaseX3DNA.stds2r2r2r2r2r2E *j'8XyRY[bdkmt s4=))** = =A OODM002215; < < <   dm2244Q7? @ @ @   dm2244Q7? @ @ @   T]1133A6= > > > NN4=//11!4> ? ? ? NN4=//11!4< = = = NN4=//11!49 : : : OODM002215; < < < OODM002215; < < < NN4=//11!49 : : : NN4=//11!49 : : : OODM002215; < < < <x))28J+?+?*AUAUWYW_`gWhWh HX   2 2BHY4G4GRYIZIZ HW  rx00"(72C2CRXhEWEWX *j'8XyRY[bdkmt  s8A;''((  A MMF8AAAqD>**F:aaad+,,F:aaad+,,F9RaR=))F7111a4=))F7111a4=))F8AAAqD>**F8AAAqD>**F7111a4=))F7111a4=))F7111a4=))F8AAAqD>**      &!! r=c |\}}tt|dD]}|dt jd}t tdt|dd|fdz}|||dd|f|dd|fd|dt|dd|fdz| d|j dj j |}|d vr)|d |n(|d ||jd ||jdS) aPlot time-averaged base parameters for each basse pair in a 1D graph. One plot is produced for each parameter. It shows the the mean and standard deviation for each individual base pair. Each plot is saved to PNG file with name ".png". Parameters ---------- ax : matplotlib.pyplot.Axes (optional) Provide `ax` to have all plots plotted in the same axes. raxoNz-o)yerrfmtzNucleic Acid Number)rrrr r!r"z {!s} ($\AA$)z {0!s} (deg)z {0!s}.png)rLrrpoppltsubplotlisterrorbarset_xlim set_xlabelrErdtypenames set_ylabelformatfiguresavefigclf)rHkwargsr8r9krPxparams r;plotzBaseX3DNA.plot ss6!9~~&&  AD#+c"2"233BU1c&A,//!34455A KK6!!!Q$     FFFP666p666p"""H ( ( ($HHHr=r?cReZdZdZeddddZdZdZd Zd S) X3DNAaqRun X3DNA_ on a single frame or a DCD trajectory. Only a subset of all X3DNA control parameters is supported and can be set with keyword arguments. For further details on X3DNA_ see the `X3DNA docs`_. Running X3DNA with the :class:`X3DNA` class is a 3-step process: 1. set up the class with all desired parameters 2. run X3DNA with :meth:`X3DNA.run` 3. collect the data from the output file with :meth:`X3DNA.collect` The class also provides some simple plotting functions of the collected data such as :meth:`X3DNA.plot` or :meth:`X3DNA.plot3D`. When methods return helicoidal basepair parameter as lists, then the order is always ====== ============== index parameter ====== ============== 0 shear 1 stretch 2 stagger 3 buckle 4 propeller 5 opening 6 shift 7 slide 8 rise 9 tilt 10 roll 11 twist ====== ============== .. versionadded:: 0.8 .. deprecated:: 2.7.0 X3DNA will be removed in 3.0.0. .. _`X3DNA docs`: http://forum.x3dna.org/ r r r r c gd|_g|_||_tdt |i|_|dd}|dd|_t||jd<|jdtdj dit }t |t d t ttj|tj|jd}|d d |_|jd urt'jd |_nt'jd|_|jD]=\}}|t|'tdt >t1|_dS)aSet up parameters to run X3DNA_ on PDB *filename*. Parameters ---------- filename : str The `filename` is used as input for X3DNA in the :program:`xdna_ensemble` command. It specifies the name of a PDB coordinate file to be used. This must be in Brookhaven protein databank format or something closely approximating this. executable : str (optional) Path to the :program:`xdna_ensemble` executable directories (e.g. ``/opt/x3dna/2.1 and /opt/x3dna/2.1/bin``) must be set and then added to export in bashrc file. See X3DNA documentation for set-up instructions. x3dna_param : bool (optional) Determines whether base step or base pair parameters will be calculated. If ``True`` (default) then stacked *base step* parameters will be analyzed. If ``False`` then stacked *base pair* parameters will be analyzed. logfile : str (optional) Write output from X3DNA to `logfile` (default: "bp_step.par") See Also -------- :class:`X3DNAtraj` ) z auxiliary.parz bestpairs.pdbz bp_order.datzbp_helical.parzcf_7methods.parzcol_chains.scrzcol_helices.scrzhel_regions.pdbzref_frames.datz hstacking.pdbz stacking.pdbz*Setting up X3DNA analysis for %(filename)r executable xdna_ensemblerTNz*X3DNA binary {x3dna_exe_name!r} not found.zT%(x3dna_exe_name)r must be on the PATH or provided as keyword argument 'executable'.logfilez bp_step.parFz6x3dna_ensemble analyze -b 355d.bps --one %(filename)r z0find_pair -s %(filename)r stdout |analyze stdin z> zz)];;  u $ $$OLDMM%OFDM "X^^--  MGT|uT{{2 RFF $  r=c 2|dd}|d|j}t|}|||d|j}|j|z}|rXt|d5}||dddn #1swxYwYt d|t d|t d|j d t|d5}tj|gd } dddn #1swxYwYt|d 5}|D]2} | d r d| _n3dddn #1swxYwY| jdkr!td| j|t dtdS)zRun X3DNA on the input file.inpfileNoutfilerwz(Wrote X3DNA input file %r for inspectionz4Starting X3DNA on %(filename)r (trajectory: %(dcd)r)z%srvT)shellr)z *** ERROR ***ERRORrz#X3DNA Failure (%d). Check output %rz'X3DNA finished: output file %(outname)r)rUrwr|copyupdaterrrFwriterzdebugr{r} subprocesscallstrip startswith returncode bit_lengthr~) rHrcinpnameoutname x3dnaargsrinpfoutputx3dnalines r;runz X3DNA.runs**Y--**Y 55JJOO%%    jj0@AA mi'  Ngs## q                 LLCW M M M BI     T48O4555 '3   76OSE666E 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 '3   6  ::<<**+EFF'*E$E                 q LL5      =tvvFFFFFs6CCC8EE #E 76F99F=F=c |d|j}|dd}|dtjj}t d|d}d|jvrddl}|j|j}t|}|dkrGt d |jtd |jt d ||jt|_t d |||d}g} t|d 5} d} | D]0} | } |jdur| drBd} t d| } t+d}g} x| rZt| dkr2 | \ }}}}}}}}}}}}}nO#t d|| t d|xYw| t5|t5|t5|t5|t5|t5|t5|t5|t5|t5|t5|t5|g d} | drCd} t d| } t+d}g} /| rt| dkr | \}}}}}}}nO#t d|| t d|xYw| t5|t5|t5|t5|t5|t5|g.d} 2|jdur#t6j| dd}n"t6j| dd}||j|<t d|t||tj|dt?|z}tj dtj!|stj"|tj|d ||}t7j#||t d||dddn #1swxYwYt|j|kr/t dt|jdSt $d t|j|dS)!aParse the output from a X3DNA run into numpy recarrays. Can deal with outputs containing multiple frames. The method saves the result as :attr:`X3DNA.profiles`, a dictionary indexed by the frame number. Each entry is a :class:`np.recarray`. If the keyword `outdir` is supplied (e.g. ".") then each profile is saved to a gzipped data file. Parameters ---------- run : str, int (optional identifier, free form [1] outdir : str (optional) save output data under `outdir`/`run` if set to any other value but ``None`` [``None``] x3dnaoutrrRoutdirz,Collecting X3DNA profiles for run with id %s*rNz'Glob pattern %r did not find any files.z*Glob pattern {0!r} did not find any files.z-Found %d input files based on glob pattern %sz)Run %s: Reading %d X3DNA profiles from %rrFz# ShearTzStarted reading datazRun %d: Problem parsing line %rzCheck input file %r.z # Shiftz#f8,f8,f8,f8,f8,f8,f8,f8,f8,f8,f8,f8zOShear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist)formatsr]zf8,f8,f8,f8,f8,f8z Shift,Slide,Rise,Tilt,Roll,Twistz4Collected X3DNA profile for frame %d (%d datapoints)run_zrm -f tmp*.outzbp_step_{0!s}_{1:04d}.dat.gzz#Finished with frame %d, saved as %rz&Collected X3DNA profiles for %d framesz5Missing data: Found %d X3DNA profiles from %d frames.)%rUrwrrcurdirrzr{rIglobrr ValueErrorr_rrErFrstriprrrsplitintrcritical exceptionrfloatr&rec fromrecordsjoinstrsystemexistsmakedirssavetxtwarning)rHrc x3dna_outputrrlengthr filenamesx3dna_profile_norecordsr read_datarfieldsSequencerrrrrrr!r"r r#r$r%frame_x3dna_outputrundirframe_x3dna_txts r;collectz X3DNA.collects6zz*dl;; jj""Hbgn55 BCHHH $-   KKK! $-00I^^F{{ =t}!@GG  KK?    $   7        , $ $R Ii .i .{{}}#u,,'788!$(  %;<<??? 9$#]R R R R R R R R R R R R R R R h t}   ' ' KK8#dm:L:L      NNGDM""     sGB&W9>"H! W9!A I--EW93OW9A PGW99W=W=c|jD]'} tj|#t$rY$wxYw|jD]}t j|ddS)NT) ignore_errors)rxrunlinkrryshutilrmtree)rHrds r;__del__z X3DNA.__del__sz  A  !      1 1A M!4 0 0 0 0 0 1 1s   --N) rlrmrnrorrrrrrqr=r;rsrs;s((TY * S&S&S&j!G!G!GF^^^@11111r=rscLeZdZdZeddddZdZdZd S) X3DNAtrajaAnalyze all frames in a trajectory. The :class:`X3DNA` class provides a direct interface to X3DNA. X3DNA itself has limited support for analysing trajectories but cannot deal with all the trajectory formats understood by MDAnalysis. This class can take any universe and feed it to X3DNA. By default it sequentially creates a PDB for each frame and runs X3DNA on the frame. .. deprecated:: 2.7.0 X3DNA will be removed in 3.0.0. r r r r c 0||_|dd|_|dd|_|dd|_|dd|_|dd|_||_dS) a Set up the class. Parameters ---------- universe : Universe The input trajectory as part of a :class:`~MDAnalysis.core.universe.Universe`; the trajectory is converted to a sequence of PDB files and X3DNA is run on each individual file. (Use the `start`, `stop`, and `step` keywords to slice the trajectory.) selection : str (optional) MDAnalysis selection string (default: "nucleic") to select the atoms that should be analyzed. start : int (optional) stop : int (optional) step : int (optional) frame indices to slice the trajectory as ``universe.trajectory[start, stop, step]``; by default, the whole trajectory is analyzed. x3dna_param : bool (optional) indicates whether stacked bases or stacked base-pairs will be analyzed. ``True`` is bases and ``False`` is stacked base-pairs [Default is ``True``]. kwargs : keyword arguments (optional) All other keywords are passed on to :class:`X3DNA` (see there for description). See Also -------- :class:`X3DNA` selectionnucleicrTstartNstopstep)universerUrrrrr x3dna_kwargs)rHrrcs r;rzX3DNAtraj.__init__sT! K;;!::mT::ZZ.. JJvt,, JJvt,, "r=c |d|j}|d|j}|d|j}|d|j}|j}||t}|j |j }|j j |||D]} td| jt!jd\} } t%j| || t%jd|  || |j| fi|} t%j| n:#t2$rYn.wxYw# t%j| w#t2$rYwwxYwxYwt5| d krdd t5| | | } t| t;j| | d || j<||_ d S) zRun X3DNA on the whole trajectory and collect profiles. Keyword arguments `start`, `stop`, and `step` can be used to only analyse part of the trajectory. The defaults are the values provided to the class constructor. rrrrzX3DNA analysis frame %4d z.pdb)suffixzfind_pair {0!s} 355d.bpsrRz6Got {0} profiles ({1}) --- should be 1 (time step {2})rN)!rUrrrrrrrrr select_atomsr trajectoryrzr{frametempfilemkstemprcloserrr_ run_x3dnarrrkeysrrrrrE)rHrcrrrrx3dna_kwrErtsfdpdbfilex3dna_profileserr_msgs r;rz X3DNAtraj.runs` 7DJ//zz&$),,zz&$),,jj0@AA $))++==-,,T^<<-*5d?; < > >"*&999KB HRLLL MM' " " " I077@@ A A A  g&&&!/!D!D8!D!DIg&&&&DIg&&&&D>""a''RYY'')<)<)>)> W%%% g&&&!/!6!6!8!8!;HRX    sB)#F2 F"" F/.F/2G4G G G GG Gc |j|d<t|fi|}|||jS)z)Run X3DNA on a single PDB file `pdbfile`.r)rrsrrrE)rHrrcHs r;rzX3DNAtraj.run_x3dna<sF $ 0} ' $ $V $ $  zr=N)rlrmrnrorrrrrqr=r;rrsx  Y * *#*#*#\&!&!&!Pr=r) rorrloggingros.pathrrrrr collectionsrmatplotlib.pyplotpyplotrVnumpyr& MDAnalysisrMDAnalysis.lib.utilrrrr getLoggerrzr<objectr?rsrrqr=r;rs0__@   ######''''''FFFFFFFFFFFF  6 7 7    & JJJZV$V$V$V$V$V$V$V$rR1R1R1R1R1IR1R1R1j rrrrr rrrrrr=