[Biopython-dev] [Bug 3166] Bio.PDB.DSSP fails to work on PDBs with HETATM

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jan 19 04:02:26 UTC 2011


------- Comment #9 from eric.talevich at gmail.com  2011-01-18 23:02 EST -------
Created an attachment (id=1564)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1564&action=view)
Patch based on Hongbo Zhu's attachment

I adapted the previous code to the current Biopython head.

Of note:
- the pseudo-doctest in the DSSP class docstring wasn't runnable. I fixed that.
- Instead of mkstemp I used NamedTemporary file -- this way Python will delete
the tempfile automatically when the handle is closed
- Some code compression, but I kept most of Hongbo Zhu's comments intact -- I
found them useful
- I tweaked the test script at the end of the file

Tested this with PDB 1MOT, 3KIC, 1VSY, 3LLT, 3NR9 and checked with pylint.
Seems OK to me.

Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list