[Biopython-dev] [Bug 2658] New: 1.49b version of PDB Neighborsearch still based on Numeric

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2658

           Summary: 1.49b version of PDB Neighborsearch still based on
                    Numeric
           Product: Biopython
           Version: 1.49b
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P3
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: rbickerton at gmail.com


Using python 2.52, running:

python ./lib/python2.5/site-packages/Bio/PDB/NeighborSearch.py

gives:

Traceback (most recent call last):
  File "./lib/python2.5/site-packages/Bio/PDB/NeighborSearch.py", line 138, in
<module>
    ns=NeighborSearch(al)
  File "./lib/python2.5/site-packages/Bio/PDB/NeighborSearch.py", line 41, in
__init__
    assert(self.coords.typecode()=="f")
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exit 1

A bit of google digging suggested that .typecode()=="f" is a Numarray function
that should be updated to its Numpy equivalent.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.