i=dZddlZddlZddlZddlZddlmZmZddl m Z ej dZ dZ dZd Zd ZGd d eZGd deZdS)aA Elastic network analysis of MD trajectories --- :mod:`MDAnalysis.analysis.gnm` ============================================================================== :Author: Benjamin Hall :Year: 2011 :Copyright: Lesser GNU Public License v2.1 or later Analyse a trajectory using elastic network models, following the approach of :footcite:p:`Hall2007`. An example is provided in the MDAnalysis Cookbook_, listed as GNMExample_. .. _GNMExample: https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/GNMExample.py .. _Cookbook: https://github.com/MDAnalysis/MDAnalysisCookbook The basic approach is to pass a trajectory to :class:`GNMAnalysis` and then run the analysis: .. code-block:: python u = MDAnalysis.Universe(PSF, DCD) C = MDAnalysis.analysis.gnm.GNMAnalysis(u, ReportVector="output.txt") C.run() output = zip(*C.results) with open("eigenvalues.dat", "w") as outputfile: for item in output[1]: outputfile.write(item + "\n") The results are found in :attr:`GNMAnalysis.results`, which can be used for further processing (see :footcite:p:`Hall2007`). .. rubric:: References .. footbibliography:: Analysis tasks -------------- .. autoclass:: GNMAnalysis :members: .. autoclass:: closeContactGNMAnalysis :members: Utility functions ----------------- The following functions are used internally and are typically not directly needed to perform the analysis. .. autofunction:: generate_grid .. autofunction:: order_list .. versionchanged:: 0.16.0 removed unused function :func:`backup_file` N) AnalysisBase ResultsGroup)ResultszMDAnalysis.analysis.GNMc6||z }tj||SN)npdot)abdiffs a/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/gnm.py_dsqrgs q5D 6$  c tj|}|j\}}}|}| ||}|| fdt t ||z z dzD}t|D]}\}} t | d|z z } t | dz z } t | dz z } || | | |~|S)a|Simple grid search. An alternative to searching the entire list of each atom; divide the structure into `cutoff` sized boxes This way, for each particle you only need to search the neighbouring boxes to find the particles within the `cutoff`. Observed a 6x speed up for a smallish protein with ~300 residues; this should get better with bigger systems. Parameters ---------- positions : array coordinates of the atoms cutoff : float find particles with distance less than `cutoff` from each other; the grid will consist of boxes with sides of at least length `cutoff` c vg|]5}fdttz z dzD6S)c ng|]1}dttz z dzD2S)cg|]}gSr).0is r z7generate_grid....s C C CAR C C Crrrangeint)rjcutoffhigh_zlow_zs rrz,generate_grid...sV    D CsFUNf#<==ABB C C C   rrr)rkrhigh_yrlow_yrs rrz!generate_grid..st           3&899A=>>      rrr) r asarrayTmaxminrr enumerateappend) positionsrxyzhigh_xlow_xgridrposx_posy_posz_posr!rr"rs ` @@@@r generate_gridr5lsd& 9%%IkGAq! UUWWF UUWWF UUWWF EEGGE EEGGE EEGGE         sFUNf4559::    DI&&,,3SVe^v-..SVe^v-..SVe^v-.. U E5!((++++ Krc#fKt||}t|}t|d}t|dd}tjt |t |t |D]\}}}||||} g} d} tj| | | D]\\} } }|| z}|| z}||z}d|cxkr|kr:n%d|cxkr|kr*n5d|cxkr|krnE| ||||z } ]| D] }| D]}||fV dS)a return atom pairs that are in neighboring regions of space from a verlet-grid Parameters ---------- positions : ndarray atom positions cutoff : float size of grid box Yields ------ i_atom, j_atom indices of close atom pairs r)rrN)r5len itertoolsproductr)r*rr0n_xn_yn_zcell_xcell_ycell_zatoms all_atoms nei_cellsr+r,r-gxgygzi_atomj_atoms rneighbour_generatorrIs F + +D d))C d1g,,C d1gaj//C"+"3 c E#JJc ##%%V V$V,   (IyII . .GAq!!B!B!BB}}}}}}}}}b31====S=====T"Xb\"--  % %F# % %fn$$$$ % %%%rct|}t|}|i}tt|D] }|||||<!|S)z]Returns a dictionary showing the order of eigenvalues (which are reported scrambled normally))listsortrr8index)wordered unorderedlist_maprs r order_listrRse1ggGQI LLNNNH 3q66]]22oogaj11 OrcheZdZdZdZedZ dfd Z dd Zd Z d Z d Z d Z xZ S) GNMAnalysisa?Basic tool for GNM analysis. Each frame is treated as a novel structure and the GNM calculated. By default, this stores the dominant eigenvector and its associated eigenvalue; either can be used to monitor conformational change in a simulation. Parameters ---------- universe : Universe Analyze the full trajectory in the universe. select : str (optional) MDAnalysis selection string cutoff : float (optional) Consider selected atoms within the cutoff as neighbors for the Gaussian network model. ReportVector : str (optional) filename to write eigenvectors to, by default no output is written Bonus_groups : tuple This is a tuple of selection strings that identify additional groups (such as ligands). The center of mass of each group will be added as a single point in the ENM (it is a popular way of treating small ligands such as drugs). You need to ensure that none of the atoms in `Bonus_groups` is contained in `selection` as this could lead to double counting. No checks are applied. Attributes ---------- results.times : numpy.ndarray simulation times used in analysis results.eigenvalues : numpy.ndarray calculated eigenvalues results.eigenvectors : numpy.ndarray calculated eigenvectors See Also -------- :class:`closeContactGNMAnalysis` .. versionchanged:: 0.16.0 Made :meth:`generate_output` a private method :meth:`_generate_output`. .. versionchanged:: 1.0.0 Changed `selection` keyword to `select` .. versionchanged:: 2.0.0 Use :class:`~MDAnalysis.analysis.AnalysisBase` as parent class and store results as attributes ``times``, ``eigenvalues`` and ``eigenvectors`` of the ``results`` attribute. .. versionchanged:: 2.8.0 Enabled **parallel execution** with the ``multiprocessing`` and ``dask`` backends; use the new method :meth:`get_supported_backends` to see all supported backends. TcdS)N)serialmultiprocessingdaskr)clss rget_supported_backendsz"GNMAnalysis.get_supported_backendss44rprotein and name CA@Ncvtt|j|_|_|_t_gj_ gj_ d_ |_ |rfd|Dng_ jj_dS)NcDg|]}j|Sr)u select_atoms)ritemselfs rrz(GNMAnalysis.__init__..s) @ @ @4TV  & & @ @ @r)superrT__init__ trajectoryr_selectrrresults eigenvalues eigenvectors _timesteps ReportVector Bonus_groupsr`ca)rbuniverserfrrkrl __class__s` rrdzGNMAnalysis.__init__ s k4  ))(*=>>>  yy #%  $& !(  @ @ @ @< @ @ @ @  &%%dk22rrc t|}|rwt|d5}t||dD]2}td||ddz||d|d|3 dddn #1swxYwY|j||d|j||ddS)aOAppends time, eigenvalues and eigenvectors to results. This generates the output by adding eigenvalue and eigenvector data to an appendable object and optionally printing some of the results to file. This is the function to replace if you want to generate a more complex set of outputs r rr)fileN)rRopenr(printrhr)ri) rbrNv outputobjectrkcounterrQoupras r_generate_outputzGNMAnalysis._generate_output"s%a==  lC(( C%a n55DQ! (1+Q                  ''(1+777!((8A;88888sAA>>BBc |jj}|jD]*}tj||f}+t |}tj||ftj}|j dz}t||j D]u\}}||krjt|||||krJd|||<d|||<|||dz|||<|||dz|||<v|S)a,Generate the Kirchhoff matrix of contacts. This generates the neighbour matrix by generating a grid of near-neighbours and then calculating which are are within the cutoff. Returns ------- array the resulting Kirchhoff matrix r#gr) rmr*rlr vstackcenter_of_massr8zerosfloat64rrIr)rbr*ranatomsmatrixcutoffsqrGrHs rgenerate_kirchoffzGNMAnalysis.generate_kirchoff=sG% % F FD 9d.A.A.C.C"DEEIIY66*BJ77;>1)T[II D DNFF6*If,=>>II)-vv&)-vv&)/)?!)Cvv&)/)?!)Cvv& rc|} tj|\}}}ng#tjj$rPd|jd}|d|jjdz }tj |t |YdSwxYw| |||j |j|jjdS)NzSVD with cutoff z failed to converge. zSkip frame at .)rkrw)rr linalgsvd LinAlgErrorr_tstimewarningswarnloggerwarningryrgrkframe)rbr_rNrumsgs r _single_framezGNMAnalysis._single_frameas'')) immF++GAq!!y$   GT[GGGC 4DHM444 4C M#    NN3    FF    L*HN      s#:A BBc|j|j_tj|jj|j_tj|jj|j_dSr)timesrgr r$rhrirbs r _concludezGNMAnalysis._concludetsF!Z #%:dl.F#G#G  $&Jt|/H$I$I !!!rcfttjtjtjdS)N)rirhr)lookup)rndarray_hstackrs r_get_aggregatorzGNMAnalysis._get_aggregatorys5 , ;+:%4    r)r[r\NN)Nr)__name__ __module__ __qualname____doc__%_analysis_algorithm_is_parallelizable classmethodrZrdryrrrr __classcell__ros@rrTrTs77r-1)55[5 % 3333332>?99996"""H   &JJJ        rrTc2eZdZdZ dfd ZdZxZS) closeContactGNMAnalysisaPGNMAnalysis only using close contacts. This is a version of the GNM where the Kirchoff matrix is constructed from the close contacts between individual atoms in different residues. Parameters ---------- universe : Universe Analyze the full trajectory in the universe. select : str (optional) MDAnalysis selection string cutoff : float (optional) Consider selected atoms within the cutoff as neighbors for the Gaussian network model. ReportVector : str (optional) filename to write eigenvectors to, by default no output is written weights : {"size", None} (optional) If set to "size" (the default) then weight the contact by :math:`1/\sqrt{N_i N_j}` where :math:`N_i` and :math:`N_j` are the number of atoms in the residues :math:`i` and :math:`j` that contain the atoms that form a contact. Attributes ---------- results.times : numpy.ndarray simulation times used in analysis results.eigenvalues : numpy.ndarray calculated eigenvalues results.eigenvectors : numpy.ndarray calculated eigenvectors Notes ----- The `MassWeight` option has now been removed. See Also -------- :class:`GNMAnalysis` .. versionchanged:: 0.16.0 Made :meth:`generate_output` a private method :meth:`_generate_output`. .. deprecated:: 0.16.0 Instead of ``MassWeight=True`` use ``weights="size"``. .. versionchanged:: 1.0.0 MassWeight option (see above deprecation entry). Changed `selection` keyword to `select` .. versionchanged:: 2.0.0 Use :class:`~MDAnalysis.analysis.AnalysisBase` as parent class and store results as attributes ``times``, ``eigenvalues`` and ``eigenvectors`` of the `results` attribute. protein@Nsizecltt|||||||_dSr)rcrrdweights)rbrnrfrrkrros rrdz closeContactGNMAnalysis.__init__s> %t,,55 ffl    rc|jj}|jj}|jj}t j||ft j}|jdz}t j t|jj }|j dkr+dt j d|jj Dz }t||jD]\}}||krt|||||kry||} ||} || || z} || | xx| zcc<|| | xx| zcc<|| | xx| z cc<|| | xx| z cc<|S)N)dtyper#rrc&g|]}|jjSr)rAn_atoms)rrs rrz=closeContactGNMAnalysis.generate_kirchoff..s;;;Q;;;r)rm n_residuesr* resindicescopyr r}r~ronesr8residuesrsqrtrIr) rb nresiduesr*residue_index_maprrinv_sqrt_res_sizesrGrHiresiduejresiduecontacts rrz)closeContactGNMAnalysis.generate_kirchoffsG& G%  G.33559i0 CCC;> WS)9%:%:;; <6 ! !!"RW;;$'*:;;;&&" 2)T[II 6 6NFF6*If,=>>II,V4,V4&x03Eh3OOx ***g5***x ***g5***x ***g5***x ***g5*** r)rrNr)rrrrrdrrrs@rrrse77x      rr)rr9loggingrnumpyr baserrMDAnalysis.analysis.baser getLoggerrrr5rIrRrTrrrrrs*6==|,,,,,,,,-,,,,,  4 5 5 )))X$%$%$%Nv v v v v ,v v v rdddddkdddddr