§ Å ´iÿãó¤—dZgd¢ZddlZddlZddlmZmZm Z ddl m Z m Z ddl mZddlmZddlZddlZejd¦«Zdd „Zdd „Zd „ZdS)a— Distance analysis --- :mod:`MDAnalysis.analysis.distances` ========================================================== This module provides functions to rapidly compute distances between atoms or groups of atoms. :func:`dist` and :func:`between` can take atom groups that do not even have to be from the same :class:`~MDAnalysis.core.universe.Universe`. See Also -------- :mod:`MDAnalysis.lib.distances` )Údistance_arrayÚself_distance_arrayÚcontact_matrixÚdistÚbetweenéN)Úcapped_distancerr)Úcontact_matrix_no_pbcÚcontact_matrix_pbc)ÚAtomNeighborSearch)Ú calc_bondszMDAnalysis.analysis.distancesç.@ÚnumpycóÀ—|dkrltjt|¦«t|¦«fdt¬¦«}t ||||d¬¦«}tj|¦«\}}d|||f<|S|dkret j t|¦«t|¦«fd¬¦«}|t||||¦«nt|||¦«|SdS) aCalculates a matrix of contacts. There is a fast, high-memory-usage version for small systems (*returntype* = 'numpy'), and a slower, low-memory-usage version for larger systems (*returntype* = 'sparse'). If *box* dimensions are passed then periodic boundary conditions are applied. Parameters --------- coord : array Array of coordinates of shape ``(N, 3)`` and dtype float32. cutoff : float, optional, default 15 Particles within `cutoff` are considered to form a contact. returntype : string, optional, default "numpy" Select how the contact matrix is returned. * ``"numpy"``: return as an ``(N. N)`` :class:`numpy.ndarray` * ``"sparse"``: return as a :class:`scipy.sparse.lil_matrix` 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. Returns ------- array or sparse matrix The contact matrix is returned in a format determined by the `returntype` keyword. See Also -------- :mod:`MDAnalysis.analysis.contacts` for native contact analysis .. versionchanged:: 0.11.0 Keyword *suppress_progmet* and *progress_meter_freq* were removed. rF)Údtype)Ú max_cutoffÚboxÚreturn_distancesTÚsparseÚboolN) ÚnpÚfullÚlenrrÚ transposeÚscipyrÚ lil_matrixr r ) ÚcoordÚcutoffÚ returntyperÚadjÚpairsÚidxÚidyÚsparse_contactss úg/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/distances.pyrrGsü€ðRWÒÐÝŒg•s˜5‘z”z¥3 u¡:¤:Ð.°½TÐBÑBÔBˆÝØ 5 V°Àuð ñ ô ˆõ”< Ñ&Ô&‰ˆˆS؈ˆCˆH‰ àˆ Ø xÒ Ð õ œ,×1Ò1Ý ‰ZŒZ˜U™œÐ $¨Fð2ñ ô ˆð ˆ?å ˜u o°s¸FÑ CÔ CÐ CÐ Cõ " %¨¸&Ñ AÔ AÐ AØÐð Ð ócó†—|jj|jjkrtd¦«‚ |\}}n(#ttf$rt |¦«x}}YnwxYwt j|j¦«|z}t j|j¦«|z}t|j |j |¦«}t j|||g¦«S)a¬Return distance between atoms in two atom groups. The distance is calculated atom-wise. The residue ids are also returned because a typical use case is to look at CA distances before and after an alignment. Using the `offset` keyword one can also add a constant offset to the resids which facilitates comparison with PDB numbering. Arguments --------- A, B : AtomGroup :class:`~MDAnalysis.core.groups.AtomGroup` with the same number of atoms offset : integer or tuple, optional, default 0 An integer `offset` is added to *resids_A* and *resids_B* (see below) in order to produce PDB numbers. If `offset` is :class:`tuple` then ``offset[0]`` is added to *resids_A* and ``offset[1]`` to *resids_B*. Note that one can actually supply numpy arrays of the same length as the atom group so that an individual offset is added to each resid. Returns ------- resids_A : array residue ids of the `A` group (possibly changed with `offset`) resids_B : array residue ids of the `B` group (possibly changed with `offset`) distances : array distances between the atoms z7AtomGroups A and B do not have the same number of atoms) ÚatomsÚn_atomsÚ ValueErrorÚ TypeErrorÚintrÚarrayÚresidsr Ú positions) ÚAÚBÚoffsetrÚoff_AÚoff_BÚ residues_AÚ residues_BÚds r$rr‰sÉ€ðB „w„˜!œ'œ/Ò)Ð)ÝØ Eñ ô ð ð$؉ ˆˆuˆuøÝ •zÐ "ð$ð$ð$ݘF™ œ Ð#ˆð$øøø唘!œ(Ñ#Ô# eÑ+€JÝ”˜!œ(Ñ#Ô# eÑ+€Jå1”; ¤ ¨SÑ1Ô1€AÝ Œ8Z ¨QÐ/Ñ 0Ô 0Ð0s«1±"AÁAcó¢—t|¦«}| ||¦«}| ||¦«}| |¦«S)a’Return sub group of `group` that is within `distance` of both `A` and `B` This function is not aware of periodic boundary conditions. Can be used to find bridging waters or molecules in an interface. Similar to "*group* and (AROUND *A* *distance* and AROUND *B* *distance*)". Parameters ---------- group : AtomGroup Find members of `group` that are between `A` and `B` A : AtomGroup B : AtomGroup `A` and `B` are the groups of atoms between which atoms in `group` are searched for. The function works is more efficient if `group` is bigger than either `A` or `B`. distance : float maximum distance for an atom to be counted as in the vicinity of `A` or `B` Returns ------- AtomGroup :class:`~MDAnalysis.core.groups.AtomGroup` of atoms that fulfill the criterion .. versionadded: 0.7.5 )r ÚsearchÚ intersection)Úgroupr/r0ÚdistanceÚns_groupÚresAÚresBs r$rr¹sL€õ@" %Ñ(Ô(€HØ ?Š?˜1˜hÑ 'Ô '€DØ ?Š?˜1˜hÑ 'Ô '€DØ × Ò ˜TÑ "Ô "Ð"r%)r rN)rN)Ú__doc__Ú__all__rrÚ scipy.sparserÚMDAnalysis.lib.distancesrrrÚMDAnalysis.lib.c_distancesr r ÚMDAnalysis.lib.NeighborSearchr r ÚwarningsÚloggingÚ getLoggerÚloggerrrr©r%r$úrJs$ðð4 ð ð ð ð €ðÐÐÐØÐÐÐððððððððððð ðððððððð=Ð<Ð<Ð<Ð<Ð<Ø/Ð/Ð/Ð/Ð/Ð/ð€€€Ø€€€à ˆÔ Ð:Ñ ;Ô ;€ð?ð?ð?ð?ðD-1ð-1ð-1ð-1ð`##ð##ð##ð##ð##r%