i(rdZddlZddlmZddlmZmZddlm Z Gdd e Z Gd d e Z dS) a8Fitting transformations --- :mod:`MDAnalysis.transformations.fit` ================================================================= Translate and/or rotates the coordinates of a given trajectory to align a given AtomGroup to a reference structure. .. autoclass:: fit_translation .. autoclass:: fit_rot_trans N)align)euler_from_matrix euler_matrix)TransformationBasec2eZdZdZ dfd ZdZxZS)fit_translationa Translates a given AtomGroup so that its center of geometry/mass matches the respective center of the given reference. A plane can be given by the user using the option `plane`, and will result in the removal of the translation motions of the AtomGroup over that particular plane. Example ------- Removing the translations of a given AtomGroup `ag` on the XY plane by fitting its center of mass to the center of mass of a reference `ref`: .. code-block:: python ag = u.select_atoms("protein") ref = mda.Universe("reference.pdb") transform = mda.transformations.fit_translation(ag, ref, plane="xy", weights="mass") u.trajectory.add_transformations(transform) Parameters ---------- ag : Universe or AtomGroup structure to translate, a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole :class:`~MDAnalysis.core.universe.Universe` reference : Universe or AtomGroup reference structure, a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole :class:`~MDAnalysis.core.universe.Universe` plane: str, optional used to define the plane on which the translations will be removed. Defined as a string of the plane. Suported planes are yz, xz and xy planes. weights : {"mass", ``None``} or array_like, optional choose weights. With ``"mass"`` uses masses as weights; with ``None`` weigh each atom equally. If a float array of the same length as `ag` is provided, use each element of the `array_like` as a weight for the corresponding atom in `ag`. Returns ------- MDAnalysis.coordinates.timestep.Timestep .. versionchanged:: 2.0.0 The transformation was changed from a function/closure to a class with ``__call__``. .. versionchanged:: 2.0.0 The transformation was changed to inherit from the base class for limiting threads and checking if it can be used in parallel analysis. NTct||||_||_||_||_|jGdddd} ||j|_n-#t tf$rt|jddwxYw |jj j |jj j kr!|jd|jd}t|n0#t$r#|jd |jd }t|dwxYwtj |jj |jj \|_|_tj|jj |j |_|j|j|_dS) N max_threadsparallelizablerrryzxzxy is not a valid plane and z" have mismatchednumber of residues or z is not validUniverse/AtomGroupweights)super__init__ag referenceplaner TypeErrorKeyError ValueErroratoms n_residuesAttributeErrorrget_matching_atomsrefmobile get_weightscenterref_com selfrrrrr raxeserrmsg __class__s h/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/transformations/fit.pyrzfit_translation.__init__^s #N    "  : !1A..D !$*- x(    z888  3w}'4>+?+JJJw**T^*** !((( K 3 3 37&&&&& !((d 2  3 !& 8 N $'-! ! $+(NNN xt|44 A""*B AC-Dctj|jj|jtj}|j|z }|j d||j<|xj |z c_ |S)Nr) npasarrayr%r r'rfloat32r(r positions)r*ts mobile_comvectors r. _transformzfit_translation._transformsfZ K  $ $T\ 2 2BJ   * : !!"F4:    )NNNT__name__ __module__ __qualname____doc__rr8 __classcell__r-s@r.r r +sf00l,5,5,5,5,5,5\       r9r c2eZdZdZ dfd ZdZxZS) fit_rot_transaf Perform a spatial superposition by minimizing the RMSD. Spatially align the group of atoms `ag` to `reference` by doing a RMSD fit. This fit works as a way to remove translations and rotations of a given AtomGroup in a trajectory. A plane can be given using the flag `plane` so that only translations and rotations in that particular plane are removed. This is useful for protein-membrane systems to where the membrane must remain in the same orientation. Note ---- ``max_threads`` is set to 1 for this transformation with which it performs better. Example ------- Removing the translations and rotations of a given AtomGroup `ag` on the XY plane by fitting it to a reference `ref`, using the masses as weights for the RMSD fit: .. code-block:: python ag = u.select_atoms("protein") ref = mda.Universe("reference.pdb") transform = mda.transformations.fit_rot_trans(ag, ref, plane="xy", weights="mass") u.trajectory.add_transformations(transform) Parameters ---------- ag : Universe or AtomGroup structure to translate and rotate, a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole :class:`~MDAnalysis.core.universe.Universe` reference : Universe or AtomGroup reference structure, a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole :class:`~MDAnalysis.core.universe.Universe` plane: str, optional used to define the plane on which the rotations and translations will be removed. Defined as a string of the plane. Supported planes are "yz", "xz" and "xy" planes. weights : {"mass", ``None``} or array_like, optional choose weights. With ``"mass"`` uses masses as weights; with ``None`` weigh each atom equally. If a float array of the same length as `ag` is provided, use each element of the `array_like` as a weight for the corresponding atom in `ag`. Returns ------- MDAnalysis.coordinates.timestep.Timestep .. versionchanged:: 2.0.0 The transformation was changed from a function/closure to a class with ``__call__``. .. versionchanged:: 2.0.0 The transformation was changed to inherit from the base class for limiting threads and checking if it can be used in parallel analysis. NrTcTt||||_||_||_||_|jGdddd} ||j|_n-#t tf$rt|jddwxYw |jj j |jj j kr!|jd|jd}t|n0#t$r#|jd |jd }t|dwxYwtj |jj |jj \|_|_tj|jj |j |_|j|j|_|jj j|jz |_dS) Nr rrrrrrz# have mismatched number of residuesrz is not valid Universe/AtomGroupr)rrrrrrrrrr r!r"rr#r$r%r&r'r(r4ref_coordinatesr)s r.rzfit_rot_trans.__init__s #N    "  : !1A..D !$*- x(    z888  3w}'4>+?+JJJw**T^***!((( K  3 3 37&&&&& !((d 2  3 !& 8 N $'-! ! $+(NNN xt|44 #x~7$,Fr/cr|jj|j}|jjj|z }t j||j|j\}}|j}|j  tj |tj d ddf}tj|tj df}tjt!|dtj}t%d|jD]} | |j kr ||j nd|| < t)|d|d|ddddddf}||j ||j <|j|z |_tj|j|j|_|j|z|_|S) Nrrsxyz)r+rr)r%r r'rr4rrotation_matrixrDr(rr1r_zerosreshapec_r2rr3rangesizerdotT) r*r5r6mobile_coordinatesrotationdumpr7matrix euler_angsis r.r8zfit_rot_trans._transforms[&--dl;; ![.8:E.  4dl   $ : !U8RXa[[%8%8A%>%>>?FU628A;;./F!&v666 J1jo..  ./4:ooJtz**11 $1 z!}jm&qb"1"fH",DJ!7F4: |j0 vblHJ77 |f,  r9)NNrTr:r@s@r.rBrBsl::@,G,G,G,G,G,G\r9rB) r>numpyr1analysisrlib.transformationsrrbaserr rBr9r.r]s.  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