RiTdZddlZddlmZddlmZddlmZddlmZGddZ y) z=Fast atom neighbor lookup using a KD tree (implemented in C).N) PDBException) entity_levels)unfold_entities) uniqueifyc.eZdZdZddZdZddZddZy) 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. cddlm}||_|Dcgc]}|j}}t j |d|_|dkDsJ|j jddk(sJ||j ||_ycc}w)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)KDTreed)dtypeN) Bio.PDB.kdtreesr atom_list get_coordnparraycoordsshapekdt)selfr bucket_sizer a coord_lists N/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/NeighborSearch.py__init__zNeighborSearch.__init__ sy +"-67akkm7 7hhz5 Q{{  #q((($++{3 8sBcg}|D]W\}}|j}|j}||k(r,||kr|j||fE|j||fYt|S)N) get_parentappendr)r pair_listparent_pair_liste1e2p1p2s r_get_unique_parent_pairsz'NeighborSearch._get_unique_parent_pairs7sv  2FBBBRxb ''R1 ''R1 2)**cF|tvrt|dtj|dd}|jdk7r t d|j j||}|Dcgc]}|j|j}}|dk(r|St||Scc}w)aNeighbor search. Return all atoms/residues/chains/models/structures that have at least one atom within radius of center. What entity level is returned (e.g. atoms or residues) is determined by level (A=atoms, R=residues, C=chains, M=models, S=structures). Arguments: - center - NumPy array - radius - float - level - char (A, R, C, M, S) : Unknown levelr C)r requirements)rz$Expected a 3-dimensional NumPy arrayA) rrrrequirer Exceptionrsearchrindexr)rcenterradiuslevelpointspointrs rr/zNeighborSearch.searchKs  %%89 9F#C@ <<4 BC C0>DEUT^^EKK0E E C< "9e4 4 Fs) BcN|tvrt|d|jj|}|j}g}|D]7}|j }|j }||} ||} |j| | f9|dk(r|S|} dD]} |j| } || k(s| cSy)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_levels r search_allzNeighborSearch.search_allfs  %%89 9HH,,V4 NN ! ,HBB2B2B  ! !2r( +  , C<! !-. ,J#'#@#@AU#V  "++ ,r'N) )r,)__name__ __module__ __qualname____doc__rr&r/rFr'rrrs 4.+(56,r'r) rKnumpyrBio.PDB.PDBExceptionsrBio.PDB.SelectionrrrrrLr'rrPs&D.+-'p,p,r'