indZddlZddlmZddlZddlmZejdZ GddeZ dS) a0 Simple atomic distance analysis --- :mod:`MDAnalysis.analysis.atomicdistances` ============================================================================== :Author: Xu Hong Chen :Year: 2023 :Copyright: Lesser GNU Public License v2.1+ This module provides a class to efficiently compute distances between two groups of atoms with an equal number of atoms over a trajectory. Specifically, for two atom groups ``ag1`` and ``ag2``, it will return the distances .. math:: |ag1[i] - ag2[i]| for all :math:`i` from :math:`0` to `n_atoms` :math:`- 1`, where `n_atoms` is the number of atoms in each atom group. By default, this computation is done with periodic boundary conditions, but this can be easily turned off. These distances are grouped by time step in a NumPy array. For more general functions on computing distances between atoms or groups of atoms, please see :class:`MDAnalysis.analysis.distances`. See Also -------- :mod:`MDAnalysis.analysis.distances` :mod:`MDAnalysis.lib.distances` Basic usage ----------- This example uses files from the MDAnalysis test suite (:data:`~MDAnalysis.tests.datafiles.GRO` and :data:`~MDAnalysis.tests.datafiles.XTC`). To get started, execute :: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import GRO, XTC >>> import MDAnalysis.analysis.atomicdistances as ad We will calculate the distances between an atom group of atoms 101-105 and an atom group of atoms 4001-4005 with periodic boundary conditions. To select these atoms: :: >>> u = mda.Universe(GRO, XTC) >>> ag1 = u.atoms[100:105] >>> ag2 = u.atoms[4000:4005] We can run the calculations using any variable of choice such as ``my_dists`` and access our results using ``my_dists.results``: :: >>> my_dists = ad.AtomicDistances(ag1, ag2).run() >>> my_dists.results array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209], [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345], [23.27210749, 30.38714688, 32.48269361, 31.91444505, 31.84583838], [18.40607922, 39.21993135, 39.33468192, 41.0133789 , 39.46885946], [26.26006981, 37.9966713 , 39.14991106, 38.13423586, 38.95451427], [26.83845081, 34.66255735, 35.59335027, 34.8926705 , 34.27175056], [37.51994763, 38.12161091, 37.56481743, 36.8488121 , 35.75278065], [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816], [38.76272761, 41.31816555, 38.81588421, 39.82491432, 38.890219 ], [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]]) To do the computation without periodic boundary conditions, we can enter the keyword argument ``pbc=False`` after ``ag2``. The result is different in this case: :: >>> my_dists_nopbc = ad.AtomicDistances(ag1, ag2, pbc=False).run() >>> my_dists_nopbc.results array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209], [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345], [23.27210749, 30.38714688, 32.482695 , 31.91444505, 31.84583838], [18.40607922, 39.21992825, 39.33468192, 41.0133757 , 39.46885946], [26.26006981, 37.99666906, 39.14990985, 38.13423708, 38.95451311], [26.83845081, 34.66255625, 35.59335027, 34.8926705 , 34.27174827], [51.86981409, 48.10347964, 48.39570072, 49.14423513, 50.44804292], [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816], [56.39657447, 41.31816555, 38.81588421, 39.82491432, 38.890219 ], [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]]) N) calc_bonds) AnalysisBasez#MDAnalysis.analysis.atomicdistancesc0eZdZdZdfd ZdZdZxZS)AtomicDistancesaWClass to calculate atomic distances between two AtomGroups over a trajectory. Parameters ---------- ag1, ag2 : AtomGroup :class:`~MDAnalysis.core.groups.AtomGroup` with the same number of atoms pbc : bool, optional If ``True``, calculates atomic distances with periodic boundary conditions (PBCs). Setting `pbc` to ``False``, calculates atomic distances without considering PBCs. Defaults to ``True``. Attributes ---------- results : :class:`numpy.ndarray` The distances :math:`|ag1[i] - ag2[i]|` for all :math:`i` from :math:`0` to `n_atoms` :math:`- 1` for each frame over the trajectory. n_frames : int Number of frames included in the analysis. n_atoms : int Number of atoms in each atom group. .. versionadded:: 2.5.0 Tc ,|jj|jjkrtd|jj|jjkrtdt t |j|jjfi|||_||_ ||_ dS)Nz/AtomGroups do not have the same number of atomsz+AtomGroups are not from the same trajectory) atomsn_atoms ValueErroruniverse trajectorysuperr__init___ag1_ag2_pbc)selfag1ag2pbckwargs __class__s m/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/atomicdistances.pyrzAtomicDistances.__init__s 9  1 1 1D \ $ (? ? ?MNN N-ot$$- L #  '-      cdtj|j|jjjf|_dSN)npzerosn_framesrr r results)rs r_preparezAtomicDistances._prepares%x 0G HII rc|jr |jjnd}t|jj|jj||j|j<dSr)rr dimensionsr positionsrr _frame_index)rboxs r _single_framezAtomicDistances._single_framesH&*i9di""T*4 I !4c+ +  T&'''r)T)__name__ __module__ __qualname____doc__rr!r' __classcell__)rs@rrrysh8$JJJ       rr) r+numpyrMDAnalysis.lib.distancesrloggingbaser getLoggerloggerrrrr4s4SSj//////  @ A A8 8 8 8 8 l8 8 8 8 8 r