[BioPython] PDBParser & Structure class

[Thomas Hamelryck]

Hi Iddo,

> 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.

Thanks for the feedback. I was wondering if there is any interest to make the 
package part of Biopython (after it has matured of course)? Is a GNU lesser 
public license acceptable for Biopython?

> 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?

Yes, you are right. I've corrected the documentation. Thanks!

Friendly regards,

---
Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
Intitute for Molecular Biology            ULTR Department
Paardenstraat 65    1640 Sint-Gensius-Rode, Belgium
                http://ultr.vub.ac.be/~thomas