[BioPython] some files missing in sources of 1.40b and weird non-error

[Kristina Rogale Plazonic]

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