Bio :: PDB :: NeighborSearch :: NeighborSearch :: Class NeighborSearch
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Class NeighborSearch

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object --+
         |
        NeighborSearch

Class 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 Bio.KDTree C++ module, so it's fast.

Instance Methods [hide private]
 
__init__(self, atom_list, bucket_size=10)
Create the object.
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_get_unique_parent_pairs(self, pair_list) source code
 
search(self, center, radius, level="A")
Neighbor search.
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search_all(self, radius, level="A")
All neighbor search.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, atom_list, bucket_size=10)
(Constructor)

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Create 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.
Overrides: object.__init__

search(self, center, radius, level="A")

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Neighbor 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 - Numeric array
  • radius - float
  • level - char (A, R, C, M, S)

search_all(self, radius, level="A")

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All neighbor search.

Search all entities that have atoms pairs within radius.

Arguments:

  • radius - float
  • level - char (A, R, C, M, S)