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Issue #2925 has been updated by Lenna Peterson.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15375?detail_id=1687">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>Assignee</strong> deleted (<del><i>Biopython Dev Mailing List</i></del>)</li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Can't reproduce.</p>
<pre>
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")
</pre>
<p>output:<br /><pre>
[]
[]
[]
[]
[]
</pre></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2925#change-15375">Bug #2925: false exception in Bio.PDB.NeighborSearch.search</a></h1>
<ul><li>Author: Li Zhenhua</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: </li>
<li>Category: Main Distribution</li>
<li>Target version: 1.52</li>
<li>URL: </li></ul>
<p>Bio.PDB.NeighborSearch.search<br />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.</p>
<hr />
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