o Rŀg@sNdZddlZddlmZddlmZddlmZddlmZGdddZ dS) z=Fast atom neighbor lookup using a KD tree (implemented in C).N) PDBException) entity_levels)unfold_entities) uniqueifyc@s6eZdZdZd ddZddZddd Zdd d Zd S)NeighborSearchaClass for neighbor searching. This class can be used for two related purposes: 1. To find all atoms/residues/chains/models/structures within radius of a given query position. 2. To find all atoms/residues/chains/models/structures that are within a fixed radius of each other. NeighborSearch makes use of the KDTree class implemented in C for speed. cCsbddlm}||_dd|D}tj|dd|_|dksJ|jjddks(J||j||_d S) a4Create the object. Arguments: - atom_list - list of atoms. This list is used in the queries. It can contain atoms from different structures. - bucket_size - bucket size of KD tree. You can play around with this to optimize speed if you feel like it. r)KDTreecSsg|]}|qS) get_coord).0ar r J/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/NeighborSearch.py .sz+NeighborSearch.__init__..d)dtypeN)Bio.PDB.kdtreesr atom_listnparraycoordsshapekdt)selfr bucket_sizer coord_listr r r __init__ s  zNeighborSearch.__init__cCsZg}|D]$\}}|}|}||krq||kr!|||fq|||fqt|S)N) get_parentappendr)r pair_listparent_pair_liste1e2p1p2r r r _get_unique_parent_pairs7s z'NeighborSearch._get_unique_parent_pairsAcsn|tvr t|dtj|ddd}|jdkrtdj||}fdd|D}|d kr2|St||S) aNeighbor search. Return all atoms/residues/chains/models/structures that have at least one atom within radius of center. What entity level is returned (e.g. atoms or residues) is determined by level (A=atoms, R=residues, C=chains, M=models, S=structures). Arguments: - center - NumPy array - radius - float - level - char (A, R, C, M, S) : Unknown levelrC)r requirements)rz$Expected a 3-dimensional NumPy arraycsg|]}j|jqSr )rindex)r pointrr r r`sz)NeighborSearch.search..r') rrrrequirer Exceptionrsearchr)rcenterradiuslevelpointsrr r-r r0Ks  zNeighborSearch.searchc Cs|tvr t|d|j|}|j}g}|D]}|j}|j}||} ||} || | fq|dkr6|S|} dD]} || } || krI| Sq:dS)zAll neighbor search. Search all entities that have atoms pairs within radius. Arguments: - radius - float - level - char (A, R, C, M, S) r(r')Rr)MSN) rrrneighbor_searchrindex1index2rr&) rr2r3 neighborsratom_pair_listneighbori1i2a1a2next_level_pair_list next_levelr r r search_allfs(   zNeighborSearch.search_allN)r)r')__name__ __module__ __qualname____doc__rr&r0rDr r r r rs   r) rHnumpyrBio.PDB.PDBExceptionsrBio.PDB.Selectionrrrrr r r r s