[Biopython-dev] [Biopython (old issues only) - Bug #2925] (Resolved) false exception in Bio.PDB.NeighborSearch.search

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Sat Nov 12 22:23:26 UTC 2016

Issue #2925 has been updated by Lenna Peterson.

Description updated
Status changed from New to Resolved
Assignee deleted (Biopython Dev Mailing List)
% Done changed from 0 to 100

Can't reproduce.

import numpy as np
from Bio import PDB

infile = "1bfg.pdb"

p = PDB.PDBParser()

s = p.get_structure("test", infile)

atom_list = PDB.Selection.unfold_entities(s, "A")

ns = PDB.NeighborSearch(atom_list)

empty_place = np.array([999, 999, 999])
for level in ["A", "R", "C", "M", "S"]:
    neighbors2 = ns.search(empty_place, 5.0, level=level)
    print PDB.Selection.unfold_entities(neighbors2, "R")


Bug #2925: false exception in Bio.PDB.NeighborSearch.search

* Author: Li Zhenhua
* Status: Resolved
* Priority: Normal
* Assignee: 
* Category: Main Distribution
* Target version: 1.52
* URL: 
if there is no atom nearby(within a distance smaller than radius) and the level is not "A",  an exception will be thrown. it would be better to return an empty list.

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