iWdZddlmZmZmZmZddlZddlZddl Z ddl m Z ddl mZmZddlmZmZeeeefZ Gdd eZGd d eZGd d eZGddeZdS)a Updated nucleic acid analysis --- :mod:`MDAnalysis.analysis.nucleicacids` ========================================================================= :Author: Alia Lescoulie :Year: 2022-2023 :copyright: LGPLv2.1 The module provides classes for analyzing nucleic acids structures. This is an updated, higher performance version of previous nucleic acid tools. For applications see :footcite:p:`Denning2011,Denning2012`. .. rubric:: References .. footbibliography:: Distances --------- .. autoclass:: NucPairDist :members: :inherited-members: .. autoclass:: WatsonCrickDist :members: :exclude-members: select_strand_atoms :inherited-members: .. autoclass:: MinorPairDist :members: :exclude-members: select_strand_atoms :inherited-members: .. autoclass:: MajorPairDist :members: :exclude-members: select_strand_atoms :inherited-members: .. versionadded 2.2.0 )ListDictTupleUnionN) calc_bonds) AnalysisBase ResultsGroup)Residue ResidueGroupcPeZdZUdZdZedZeje d<eje d<e e d<de ejde ejd d ffd Z e ddededededededededed ee eje ejffdZd dZd dZd dZdZxZS)! NucPairDista Atom pair distance calculation base class. Takes two lists of :class:`~MDAnalysis.core.groups.AtomGroup` and computes the distances between them over a trajectory. Used as a superclass for the other nucleic acid distances classes. The distance will be measured between atoms sharing an index in the two lists of :class:`~MDAnalysis.core.groups.AtomGroup`. Parameters ---------- selection1: List[AtomGroup] List of :class:`~MDAnalysis.core.groups.AtomGroup` containing an atom of each nucleic acid being analyzed. selection2: List[AtomGroup] List of :class:`~MDAnalysis.core.groups.AtomGroup` containing an atom of each nucleic acid being analyzed. kwargs: dict Arguments for :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- results.pair_distances: numpy.ndarray 2D array of pair distances. First dimension is simulation time, second dimension contains the pair distances for each each entry pair in selection1 and selection2. .. versionadded:: 2.4.0 .. note:: `results.pair_distances` is slated for deprecation in version 3.0.0, use `results.distances` instead. .. deprecated:: 2.7.0 `results.pair_distances` will be removed in version 3.0.0, use :attr:`results.distances` instead. results.distances: numpy.ndarray stored in a 2d numpy array with first index selecting the Residue pair, and the second index selecting the frame number Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair. .. versionadded:: 2.7.0 times: numpy.ndarray Simulation times for analysis. Raises ------ ValueError If the selections given are not the same length ValueError An :class:`~MDAnalysis.core.groups.AtomGroup` in one of the strands not a valid nucleic acid ValueError If a given residue pair from the provided strands returns an empty :class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom pairs used in the distance calculations *Version Info* .. versionchanged:: 2.5.0 The ability to access by passing selection indices to :attr:`results` is now removed as of MDAnalysis version 2.5.0. Please use :attr:`results.pair_distances` instead. The :attr:`results.times` was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute :attr:`times` instead. .. versionchanged:: 2.7.0 Added static method :attr:`select_strand_atoms` as a helper for selecting atom pairs for distance analysis. .. versionchanged:: 2.9.0 Enabled **parallel execution** with the ``multiprocessing`` and ``dask`` backends; use the new method :meth:`get_supported_backends` to see all supported backends. TcdS)N)serialmultiprocessingdask)clss j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/nucleicacids.pyget_supported_backendsz"NucPairDist.get_supported_backendss44_s1_s2_n_sel selection1 selection2returnNc tt|j|djjfi|t |t |krt dt ||_|d|_|d|_ td|jD].}|xj||z c_|xj ||z c_ /dS)NrzSelections must be same lengthr) superr__init__universe trajectorylen ValueErrorrrrrange)selfrrkwargsi __class__s rr zNucPairDist.__init__s *k4  ) qM " -  17    z??c*oo - -=>> >z?? a=a=q$+&& & &A HH 1 %HH HH 1 %HHH & &rGAUTCstrand1strand2a1_namea2_nameg_namea_nameu_namet_namec_namec |||g} ||g} g} g} t|j|jD]} | djd| vr||}}n-| djd| vr||}}ntd| d| djd|}| djd|}t d||fDs?t|dkr | d|fn | d|f}t|dd| || || | fS)ar A helper method for nucleic acid pair distance analyses. Used for selecting specific atoms from two strands of nucleic acids. Parameters ---------- strand1: List[Residue] The first nucleic acid strand strand2: List[Residue] The second nucleic acid strand a1_name: str The selection for the purine base of the strand pair a2_name: str the selection for the pyrimidine base of the strand pair g_name: str (optional) Name of Guanine in topology, by default assigned to G a_name: str (optional) Name of Adenine in topology, by default assigned to A u_name: str (optional) Name of Uracil in topology, by default assigned to U t_name: str (optional) Name of Thymine in topology, by default assigned to T c_name: str (optional) Name of Cytosine in topology, by default assigned to C Returns ------- Tuple[List[AtomGroup], List[AtomGroup]] returns a tuple containing two lists of :class:`~MDAnalysis.core.groups.AtomGroup`\s corresponding to the provided selections from each strand. Raises ------ ValueError: An :class:`~MDAnalysis.core.groups.AtomGroup` in one of the strands not a valid nucleic acid ValueError: An :class:`~MDAnalysis.core.groups.Residue` returns an empty :class:`~MDAnalysis.core.groups.AtomGroup` with the provided selection .. versionadded:: 2.7.0 rz AtomGroup in z is not a valid nucleic acidzname rc3<K|]}t|dkVdS)rN)r#).0ags r z2NucPairDist.select_strand_atoms..s,88rs2ww{888888rz< returns an empty AtomGroupwith selection string "name {a2}") zipresiduesresnamer$atoms select_atomsallr#append)r/r0r1r2r3r4r5r6r7 pyrimidinespurinessel1sel2paira1a2ag1ag2err_infos rselect_strand_atomszNucPairDist.select_strand_atomsst#)&&!9 $f-$&$&('*:;;  DAwq![00 'Ba#w.. 'B FDFFFq'-,,\R\\::Cq'-,,\R\\::C88c3Z88888 %(XX]]T!WbMMa" !#A;<<< KK    KK    d|rcZtj|j|jg|j_dSN)npzerosn_framesrresults distancesr&s r_preparezNucPairDist._prepare's*-/X ]DK (. .  rc~t|jj|jj}||jj|jddf<dSrP)rr positionsrrTrU _frame_index)r&dists r _single_framezNucPairDist._single_frame,s<%dh&8$(:LMM7; t0!!!3444rc0|jd|jd<dS)NrUpair_distances)rTrVs r _concludezNucPairDist._conclude1s)-k)B %&&&rc:tdtjiS)NrU)lookup)r ndarray_vstackrVs r_get_aggregatorzNucPairDist._get_aggregator5s&\8    r)r*r+r,r-r.)rN)__name__ __module__ __qualname____doc__%_analysis_algorithm_is_parallelizable classmethodrmda AtomGroup__annotations__intrr staticmethodr strrrNrWr\r_rc __classcell__r)s@rrrVsPPd-1)55[5   KKK&'&'&  &&&&&&, [[[[[ [  [  [[[[ tCM"D$77 8[[[\[z    <<<< CCCC       rrc\eZdZdZ dd ed ed ed ed edededededdffd ZxZS)WatsonCrickDista Watson-Crick base pair distance for selected residues over a trajectory. Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects or two lists of :class:`~MDAnalysis.core.groups.Residue` and calculates the distance between the nitrogen atoms in the Watson-Crick hydrogen bond over the trajectory. Bases are matched either by their index in the two :class:`~MDAnalysis.core.groups.ResidueGroup` provided as arguments, or based on the indices of the provided lists of :class:`~MDAnalysis.core.groups.Residue` objects depending on which is provided. .. note:: Support for :class:`~MDAnalysis.core.groups.Residue` is slated for deprecation and will raise a warning when used. It still works but :class:`~MDAnalysis.core.groups.ResidueGroup` is preferred. Parameters ---------- strand1: ResidueClass First list of bases .. deprecated:: 2.7.0 Using a list of :class:`~MDAnalysis.core.groups.Residue` will be removed in 3.0.0. Use a :class:`~MDAnalysis.core.groups.ResidueGroup`. strand2: ResidueClass Second list of bases .. deprecated:: 2.7.0 Using a list of :class:`~MDAnalysis.core.groups.Residue` will be removed in 3.0.0. Use a :class:`~MDAnalysis.core.groups.ResidueGroup`. n1_name: str (optional) Name of Nitrogen 1 of nucleic acids, by default assigned to "N1" n3_name: str (optional) Name of Nitrogen 3 of nucleic acids, by default assigned to "N3" g_name: str (optional) Name of Guanine in topology, by default assigned to "G" a_name: str (optional) Name of Adenine in topology, by default assigned to "A" u_name: str (optional) Name of Uracil in topology, by default assigned to "U" t_name: str (optional) Name of Thymine in topology, by default assigned to "T" c_name: str (optional) Name of Cytosine in topology, by default assigned to C **kwargs: dict Key word arguments for :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- results.distances: numpy.ndarray Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair. .. versionadded:: 2.7.0 results.pair_distances: numpy.ndarray 2D array of pair distances. First dimension is simulation time, second dimension contains the pair distances for each each entry pair in selection1 and selection2. .. versionadded:: 2.4.0 .. deprecated:: 2.7.0 `results.pair_distances` will be removed in version 3.0.0, use :attr:`results.distances` instead. times: numpy.ndarray Simulation times for analysis. Raises ------ TypeError If the provided list of :class:`~MDAnalysis.core.Residue` contains non-Residue elements .. deprecated:: 2.7.0 Starting with version 3.0.0, this exception will no longer be raised because only :class:`~MDAnalysis.core.groups.ResidueGroup` will be allowed. ValueError If `strand1` and `strand2` are not the same length ValueError: An :class:`~MDAnalysis.core.groups.AtomGroup` in one of the strands not a valid nucleic acid ValueError If a given residue pair from the provided strands returns an empty :class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom pairs used in the distance calculations *Version Info* .. versionchanged:: 2.5.0 Accessing results by passing strand indices to :attr:`results` was deprecated and is now removed as of MDAnalysis version 2.5.0. Please use :attr:`results.pair_distances` instead. The :attr:`results.times` was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute :attr:`times` instead. .. versionchanged:: 2.7.0 `strand1` and `strand2` now also accept a :class:`~MDAnalysis.core.groups.ResidueGroup` as input. The previous input type, ``List[Residue]`` is still supported, but it is **deprecated** and will be removed in release 3.0.0. N1N3r*r+r,r-r.r/r0n1_namen3_namer3r4r5r6r7rNc dtdtfd} | |}| |}||||||||||  } tt|j| d| dfi| dS)Nstrandrct|tr_td|Dst|dt jt d|dt|}|S)Nc3@K|]}t|tVdSrP) isinstancer )r:resids rr<zBWatsonCrickDist.__init__..verify_strand..s,JJ%:eW55JJJJJJrz contains non-Residue elementsz ResidueGroup should be used for z insteadof giving a Residue list)r|listrB TypeErrorwarningswarnDeprecationWarningr )rys r verify_strandz/WatsonCrickDist.__init__..verify_strands&$'' <JJ6JJJJJO#v$M$M$MNNN &7v777(4F';';Mrr3r4r6r5r7rr) ResidueClassr rNrrsr )r&r/r0rvrwr3r4r5r6r7r'rstrand_atomgroupsr)s rr zWatsonCrickDist.__init__s , <    *!. g 6 6 - g 6 6  $ $ %    .ot$$- a "3A"6  :@     r)rtrur*r+r,r-r.)rdrerfrgrror rprqs@rrsrs=sttt6 6 6 6  6  6  6 6 6 6 6  6 6 6 6 6 6 6 6 6 6 rrsc\eZdZdZ dd ed ed ed ed edededededdffd ZxZS) MinorPairDistaMinor-Pair basepair distance for selected residues over a trajectory. Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects and calculates the Minor-groove hydrogen bond length between the nitrogen and oxygen atoms over the trajectory. Bases are matched by their index in the two :class:`~MDAnalysis.core.groups.ResidueGroup` provided as arguments. Parameters ---------- strand1: List[Residue] First list of bases strand2: List[Residue] Second list of bases o2_name: str (optional) Name of Oxygen 2 of nucleic acids; by default assigned to "O2"; c2_name: str (optional) Name of Carbon 2 of nucleic acids; by default assigned to "C2"; g_name: str (optional) Name of Guanine in topology; by default assigned to "G"; a_name: str (optional) Name of Adenine in topology by default assigned to "A"; u_name: str (optional) Name of Uracil in topology; by default assigned to "U"; t_name: str (optional) Name of Thymine in topology; by default assigned to "T"; c_name: str (optional) Name of Cytosine in topology; by default assigned to "C"; **kwargs: keyword arguments for :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- results.distances: numpy.ndarray stored in a 2d numpy array with first index selecting the Residue pair, and the second index selecting the frame number times: numpy.ndarray Simulation times for analysis. Raises ------ ValueError If the selections given are not the same length A :class:`~MDAnalysis.core.Residue` in one of the strands not a valid nucleic acid ValueError If a given residue pair from the provided strands returns an empty :class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom pairs used in the distance calculations .. versionadded:: 2.7.0 O2C2r*r+r,r-r.r/r0o2_namec2_namer3r4r5r6r7rNc ||||||||||  } tt|j| d| dfi| dSNrrr)rNrrr ) r&r/r0rrr3r4r5r6r7r' selectionsr)s rr zMinorPairDist.__init__,  $ $ %    ,mT""+ qM:a=  ,2     r)rrr*r+r,r-r.rdrerfrgr ror rprqs@rrrs<<D                         rrc\eZdZdZ dd ed ed ed ed edededededdffd ZxZS) MajorPairDista$Minor-Pair base pair distance for selected residues over a trajectory. Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects and calculates the Major-groove hydrogen bond length between the nitrogen and oxygen atoms over the trajectory. Bases are matched by their index in the two :class:`~MDAnalysis.core.groups.ResidueGroup` provided as arguments. Parameters ---------- strand1: List[Residue] First list of bases strand2: List[Residue] Second list of bases o6_name: str (optional) Name of Oxygen 6 of nucleic acids; by default assigned to "O6" n4_name: str (optional) Name of Nitrogen 4 of nucleic acids; by default assigned to "N4" g_name: str (optional) Name of Guanine in topology; by default assigned to "G" a_name: str (optional) Name of Adenine in topology; by default assigned to "A" u_name: str (optional) Name of Uracil in topology; by default assigned to "U" t_name: str (optional) Name of Thymine in topology; by default assigned to "T" c_name: str (optional) Name of Cytosine in topology; by default assigned to "C" **kwargs: arguments for :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- results.distances: numpy.ndarray Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair. times: numpy.ndarray Simulation times for analysis. Raises ------ ValueError A :class:`~MDAnalysis.core.Residue` in one of the strands not a valid nucleic acid ValueError If a given residue pair from the provided strands returns an empty :class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom pairs used in the distance calculations ValueError if the selections given are not the same length .. versionadded:: 2.7.0 N4O6r*r+r,r-r.r/r0n4_nameo6_namer3r4r5r6r7rNc ||||||||||  } tt|j| d| dfi| dSr)rNrrr ) r&r/r0rrr3r4r5r6r7r'rr)s rr zMajorPairDist.__init__rr)rrr*r+r,r-r.rrqs@rrrMs>>H                         rr)rgtypingrrrrrnumpyrQ MDAnalysisrjrUrbaser r MDAnalysis.core.groupsr r rrrsrrrrrrs0((T,+++++++++++!!!!!!,,,,,,,,88888888 T']L01  d d d d d ,d d d Nm m m m m km m m `] ] ] ] ] K] ] ] @_ _ _ _ _ K_ _ _ _ _ r