§ Æ ´i8ãóz—dZddlZddlmZddlmZddlmZm Z m Z ddl m Z ddl mZmZmZGd„de¦«ZdS) a Neighbor Search wrapper for MDAnalysis --- :mod:`MDAnalysis.lib.NeighborSearch` =============================================================================== This module contains classes that allow neighbor searches directly with `AtomGroup` objects from `MDAnalysis`. éN)Úcapped_distance)Ú unique_int_1d)Ú AtomGroupÚ SegmentGroupÚ ResidueGroup)ÚOptionalÚUnionÚListc ó¬—eZdZdZ ddedeejddfd„Z dded e d e dee ee e ffd „Zd eed e de ee e ffd „ZdS)ÚAtomNeighborSearchzåThis class can be used to find all atoms/residues/segments within the radius of a given query position. For the neighbor search, this class is a wrapper around :class:`~MDAnalysis.lib.distances.capped_distance`. NÚ atom_groupÚboxÚreturncó:—||_|j|_||_dS)a” Parameters ---------- atom_list : AtomGroup list of atoms box : array-like or ``None``, optional, default ``None`` Simulation cell dimensions in the form of :attr:`MDAnalysis.trajectory.timestep.Timestep.dimensions` when periodic boundary conditions should be taken into account for the calculation of contacts. N)r ÚuniverseÚ_uÚ_box)Úselfr rs úg/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/lib/NeighborSearch.pyÚ__init__zAtomNeighborSearch.__init__/s €ð%ˆŒØÔ%ˆŒØˆŒ ˆ ˆ óÚAÚatomsÚradiusÚlevelcó<—g} |j}n#t$r |j}YnwxYwt||jj||jd¬¦«}|jdkr7ttj |dd…dftj ¬¦«¦«}|  ||¦«S)a2 Return all atoms/residues/segments that are within *radius* of the atoms in *atoms*. Parameters ---------- atoms : AtomGroup, MDAnalysis.core.groups.AtomGroup AtomGroup object radius : float Radius for search in Angstrom. level : str char (A, R, S). Return atoms(A), residues(R) or segments(S) within *radius* of *atoms*. Returns ------- AtomGroup : :class:`~MDAnalysis.core.groups.AtomGroup` When ``level='A'``, AtomGroup is being returned. ResidueGroup : :class:`~MDAnalysis.core.groups.ResidueGroup` When ``level='R'``, ResidueGroup is being returned. SegmentGroup : :class:`~MDAnalysis.core.groups.SegmentGroup` When ``level='S'``, SegmentGroup is being returned. .. versionchanged:: 2.0.0 Now returns :class:`AtomGroup` (when empty this is now an empty :class:`AtomGroup` instead of an empty list), :class:`ResidueGroup`, or a :class:`SegmentGroup` F)rÚreturn_distancesrNé)Údtype) Ú positionsÚAttributeErrorÚpositionrr rÚsizerÚnpÚasarrayÚintpÚ _index2level)rrrrÚ unique_idxr"Úpairss rÚsearchzAtomNeighborSearch.searchBs·€ð@ˆ ð &à”ˆHˆHøÝð &ð &ð &à”~ˆHˆHˆHð &øøøõ Ø Ø ŒOÔ %Ø Ø” Ø"ð  ñ ô ˆð Œ:˜Š>ˆ>Ý&¥r¤z°%¸¸¸¸1¸´+ÅRÄWÐ'MÑ'MÔ'MÑNÔNˆJØ× Ò  ¨UÑ3Ô3Ð3s „ Œ Ÿ Úindicescó¤—|j|}|dkr|S|dkr|jS|dkr|jStd |¦«¦«‚)aTConvert list of atom_indices in a AtomGroup to either the Atoms or segments/residues containing these atoms. Parameters ---------- indices list of atom indices level : str char (A, R, S). Return atoms(A), residues(R) or segments(S) within *radius* of *atoms*. rÚRÚSz{0}: level not implemented)r ÚresiduesÚsegmentsÚNotImplementedErrorÚformat)rr+rÚ atomgroups rr'zAtomNeighborSearch._index2levelusf€ð”O GÔ,ˆ Ø CŠ<ˆ<ØÐ Ø cŠ\ˆ\ØÔ%Ð %Ø cŠ\ˆ\ØÔ%Ð %å%Ø,×3Ò3°EÑ:Ô:ñôð r)N)r)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrÚnptÚ ArrayLikerÚfloatÚstrr rrr*r Úintr'©rrr r 'sꀀ€€€ðððEIððØ#ðØ*2°3´=Ô*Aðà ððððð(=@ð14ð14Øð14Ø(-ð14Ø69ð14à %˜  <°Ð=Ô>Ô ?ð14ð14ð14ð14ðfؘC”yðØ),ðà ˆy˜,¨ Ð4Ô 5ððððððrr )r7Únumpyr$ÚMDAnalysis.lib.distancesrÚMDAnalysis.lib.utilrÚMDAnalysis.core.groupsrrrÚ numpy.typingÚtypingr8rr r Úobjectr r=rrúrEsÍðð0ððÐÐÐØ4Ð4Ð4Ð4Ð4Ð4Ø-Ð-Ð-Ð-Ð-Ð-ØHÐHÐHÐHÐHÐHÐHÐHÐHÐHØÐÐÐÐÐØ(Ð(Ð(Ð(Ð(Ð(Ð(Ð(Ð(Ð(ðfðfðfðfðf˜ñfôfðfðfðfr