[Biopython-dev] [Bug 1772] Bio.PDB's parse_pdb_header never stops parsing if there is no ATOM record

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Apr 25 17:22:50 EDT 2005


dhendrix at compbio.berkeley.edu changed:

           What    |Removed                     |Added
             Status|RESOLVED                    |REOPENED
         Resolution|WORKSFORME                  |

------- Additional Comments From dhendrix at compbio.berkeley.edu  2005-04-25 17:22 -------
Thank you so much for the quick turnaround.  Iddo Friedberg suggested that I use
the top level of the CVS.  I updated python and my biopython (and NumPy, etc...)
and encountered the same behavior, as well as another little bug that I had
fixed a while ago.  Here are my diffs to parse_pdb_header.py, which are small
but vital for me to get parse_pdb_header working for me.
<         f=open(file,'r')
>         f=open(filename,'r')
<         if not re.search("\AATOM",l) and not re.search("\AEND",l):
>         if not re.search("\AATOM",l):

I can send you a little test program that fails on the current version of
parse_pdb_header, if that will help.  Regardless, I think it's a good idea to
stop reading the file when you reach the end of it!

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