Bio.PDB.NeighborSearch module¶
Fast atom neighbor lookup using a KD tree (implemented in C).
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class
Bio.PDB.NeighborSearch.
NeighborSearch
(atom_list, bucket_size=10)¶ Bases:
object
Class for neighbor searching.
This class can be used for two related purposes:
To find all atoms/residues/chains/models/structures within radius of a given query position.
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.
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__init__
(self, atom_list, bucket_size=10)¶ 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.
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search
(self, center, radius, level='A')¶ 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)
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search_all
(self, radius, level='A')¶ All neighbor search.
Search all entities that have atoms pairs within radius.
- Arguments:
radius - float
level - char (A, R, C, M, S)