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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.
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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. |
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) |
All neighbor search. Search all entities that have atoms pairs within radius. o radius - float o level - char (A, R, C, M, S) |
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