[BioPython] hsexposure.py

[Peter]

On Thu, Feb 12, 2009 at 12:05 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Fri, Feb 6, 2009 at 5:42 PM, Bhima A van der Molen <bav853 at bham.ac.uk> wrote:
>> There is a niffty little script included with the BioPython download in
>> the scripts folder called hsexposure.py which is supposed to calculate
>> the half sphere exposure of each residue in the PDB file.  However, when
>> I run it with the option to calculate HSE (all variations) I get 0
>> stored in the b-factor column of my PDB file instead of the count..
>
> It looks like the hsexposure script may be a tiny it out of date, I'll
> have a quick look at this.

It looks like Thomas must have been trying two naming schemes for the
xtra data dictionary keys, unfortunately the example script got
checked in using EXP_HSEAD, EXP_HSEAU, EXP_HSEBD and EXP_HSEBU but the
Bio.PDB.HSExposure module was checked in using the similar but
different EXP_HSE_A_D, EXP_HSE_A_U, EXP_HSE_B_U and EXP_HSE_B_D.  I
have updated the script in CVS, which you will be able to download
from here in about an hour's time:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Scripts/Structure/hsexpo?cvsroot=biopython

This now seems to work :)

Peter