[BioPython] PDBParser & Structure class

[Iddo Friedberg]

Hi Thomas,

Well, I downloaded it today and played around with it some. Still a bit
early for me to give any intelligent analysis. I like the
hierarchichal architecture, which is the best I have seen yet. It also
seems to parse quite fast. En-face it seems like a pretty cool tool. A
structural package is always a good thing.

I have had a problem duplicating the code on page 5 of your document.
Seems like this is a code-documentation discrepancy.


>>> from PyStructure.PDBParser import PDBParser
>>> struct = PDBParser("test","1ati.pdb")
>>> model=struct[0]
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
AttributeError: PDBParser instance has no attribute '__getitem__'


Because, what I actually have to do is:

>>> struct = PDBParser().get("test","1ati.pdb")


Am I right?

Yours,

Iddo



On Thu, 16 May 2002, Thomas Hamelryck wrote:

: Hi,
:
: A couple of weeks ago I promised to send in a PDBParser annex
: Structure class to deal with macromolecular structure (ie. PDB) files.
: I finished this today, and would appreciate some feedback :-).

--

Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/