[BioPython] some files missing in sources of 1.40b and weird
non-error
Kristina Rogale Plazonic
kris at Math.Princeton.EDU
Thu May 12 11:31:23 EDT 2005
Hi!
Both the tar.gz and zip archive of 1.40b offered on the download page of
the website seem to be incomplete - in particular these files are missing
KDTree/__init__.py,
KDTree/KDTree.py
and maybe others. (source was downloaded yesterday.)
As a result PDB module's NeighborSearch.py doesn't work anymore with a
strange error:
>>> ns = Bio.PDB.NeighborSearch(atlist) Traceback (most recent call last):
File "<stdin>", line 1, in ?
TypeError: 'module' object is not callable
- as you see, python doesn't report missing KDTree module called from
NeighborSearch at all!!! (Sample scripts do report missing KDTree module.)
Indeed, it seems that NeighborSearch is then a module with no classes at
all; i.e. all that is contained in NeighborSearch.py after the second line
from Bio.KDTree import *
is ignored, with no error reported.
I'm utterly confused. Does this happen because of some setting in
biopython?
Thanks,
Kristina
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