[Biopython-dev] [Bug 2666] Bio.PDB.NeighborSearch self test often fails with KDTree MemoryError

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2666


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|Bio.PDB.NeighborSearch self |Bio.PDB.NeighborSearch self
                   |test often fails with       |test often fails with KDTree
                   |MemoryError                 |MemoryError




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-17 06:42 EST -------
I suspect this is failing when there are NO entries found within the specified
radius.  Changing this line:

print "Found ", len(ns.search_all(5.0))

to use a larger search radius seems to "fix" the test, e.g.

print "Found ", len(ns.search_all(10.0))

Similarly, dropping it to radius 2.0 makes it fail almost every time.  I
suspect something is amiss in the KDTree C code from the traceback.


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