ó TS!Ic@s÷ddlZddlTddlmZddlmZmZmZmZdZ ddd„ƒYZ e dkródd l m Z d dd „ƒYZx`ed d ƒD]LZgedƒD]Zeƒ^q³Ze eƒZdGeejdƒƒGHq WndS(iÿÿÿÿN(t*(t PDBException(tunfold_entitiestget_unique_parentst entity_levelst uniqueifys?Fast atom neighbor lookup using a KD tree (implemented in C++).tNeighborSearchcBs;eZdZdd„Zd„Zdd„Zdd„ZRS(s^ 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 Bio.KDTree C++ module, so it's fast. i cCs||_td„|ƒ}tj|ƒjdƒ|_|dksHt‚|jjddksdt‚td|ƒ|_ |j j |jƒdS(s o atom_list - list of atoms. This list is used in the queries. It can contain atoms from different structures. o bucket_size - bucket size of KD tree. You can play around with this to optimize speed if you feel like it. cSs |jƒS(N(t get_coord(ta((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyt$stfiiN( t atom_listtmaptnumpytarraytastypetcoordstAssertionErrortshapetKDTreetkdtt set_coords(tselfR t bucket_sizet coord_list((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyt__init__s cCs†g}xs|D]k\}}|jƒ}|jƒ}||krCq q ||kre|j||fƒq |j||fƒq Wt|ƒS(N(t get_parenttappendR(Rt pair_listtparent_pair_listte1te2tp1tp2((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyt_get_unique_parent_pairs.s    tAc Cs™|tkrtd|ƒ‚n|jj||ƒ|jjƒ}g}|j}x%|D]}||}|j|ƒqWW|dkrˆ|St||ƒSdS(s–Neighbor search. Return all atoms/residues/chains/models/structures that have at least one atom within radius of center. What entitity level is returned (e.g. atoms or residues) is determined by level (A=atoms, R=residues, C=chains, M=models, S=structures). o center - Numeric array o radius - float o level - char (A, R, C, M, S) s%s: Unknown levelR#N(RRRtsearcht get_indicesR RR( Rtcentertradiustleveltindicest n_atom_listR tiR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyR$Bs     c Csá|tkrtd|ƒ‚n|jj|ƒ|jjƒ}|j}g}x;|D]3\}}||}||} |j|| fƒqTW|dkr›|S|} x9ddddgD]%} |j| ƒ} || kr´| Sq´WdS(s©All neighbor search. Search all entities that have atoms pairs within radius. o radius - float o level - char (A, R, C, M, S) s%s: Unknown levelR#tRtCtMtSN(RRRt all_searchtall_get_indicesR RR"( RR'R(R)R tatom_pair_listti1ti2ta1ta2tnext_level_pair_listtl((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyt search_all]s"      (t__name__t __module__t__doc__RR"R$R9(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyRs     t__main__(trandomtAtomcBseZd„Zd„ZRS(cCsdtdƒ|_dS(Nidi(R>tcoord(R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyR~scCs|jS(N(R@(R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyRs(R:R;RR(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyR?}s iiidsFound g@(((R t Bio.KDTreet PDBExceptionsRt SelectionRRRRR<RR:t numpy.randomR>R?trangeR+tjtaltnstlenR9(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/NeighborSearch.pyts  "j "