[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
Fri Jan 14 10:06:00 UTC 2011


macrozhu+biopy at gmail.com changed:

           What    |Removed                     |Added
Attachment #1556 is|0                           |1
           obsolete|                            |
Attachment #1557 is|0                           |1
           obsolete|                            |

------- Comment #5 from macrozhu+biopy at gmail.com  2011-01-14 05:05 EST -------
Created an attachment (id=1561)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1561&action=view)
fix DSSP crash when reading PDB with DisorderedResidue

The current version of DSSP.py does not handle DisorderedResidue well. 

Case 1, Point mutations, e.g. 1h9h chain E resi 22
BioPython uses the last residue as default (resi SER in this case). But DSSP
takes the first one (alternative location is blank,A or 1, CYS in this case).
>python DSSP.py 1h9h.pdb

Case 2, one of the disordered residues is HET. e.g. 3piu chain A Residue 273
>python DSSP.py 3piu.pdb

In the first case, the DisorderedResidue.is_disordered() returns 2, and in the
2nd case, the DisorderedResidue.is_disordered() returns 1. These values are
used to cope with DisorderedResidue in DSSP.py.


tempfile.mktemp() should be replaced by tempfile.mkstemp()

(see http://docs.python.org/library/tempfile.html#tempfile.mktemp 
"Deprecated since version 2.3: Use mkstemp() instead.")

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