[Biopython] Residue Depth module.

[Bhima Auro van der Molen]

Hi everyone

I have been trying to calculate residue depths in PDB files, using the
hsexpo.py script, which calls and makes use of the "msms" "pdb_to_xyz,"
"pdb_to_xyzn" programs and the ResidueDepth.py module which on my system
is located at:
/var/lib/python-support/python2.6/Bio/PDB/ResidueDepth.py

I opened up the ResidueDepth.py file and when I was debugging it I found
that the:
*from AbstractPropertyMap import AbstractPropertyMap *
returns an error, however when I altered it to:
*from Bio.PDB.AbstractPropertyMap import AbstractPropertyMap
*it seemed to fix that specific problem. 

However the consistent problem I am having each time I try and run the
hsexpo.py script with the option for RD or RDa, is the following error
message:
/Traceback (most recent call last):
  File "hsexpo.py", line 101, in <module>
    d=ResidueDepth(m, pdbfile)
  File "/var/lib/python-support/python2.6/Bio/PDB/ResidueDepth.py", line
134, in __init__
    surface=get_surface(pdb_file)
  File "/var/lib/python-support/python2.6/Bio/PDB/ResidueDepth.py", line
85, in get_surface
    surface=_read_vertex_array(surface_file)
  File "/var/lib/python-support/python2.6/Bio/PDB/ResidueDepth.py", line
53, in _read_vertex_array
    fp=open(filename, "r")
IOError: [Errno 2] No such file or directory: '/tmp/tmpy8yHlH.vert
/
When I look in the /tmp folder I can see a number of tmp* files but not
the one(s) that it is looking for specifically.

To ensure that all the required system files were in the right place,
i.e. a correct installation of msms with pdb_to_xyz etc, I moved the
binaries to /usr/bin and tested the binaries from my home directory..
these worked alright..  I should clarify that even though I am running
Python 2.6, I encountered the same problem in 2.5.2 and 2.5.4 as well.

If anyone can help me figure out why this is not working I'd be grateful..

Thanks
Bhima