[Biopython-dev] Module reorganization for upcoming Bio.PDB enhancements
João Rodrigues
anaryin at gmail.com
Thu Jun 10 23:45:02 UTC 2010
Hello all,
I'm having some issues dealing with this :x
I created a module Bio.Struct that has the following contents:
__init__.py
Protein.py
WWW/
The __init__.py file has a read() method that calls PDBParser and returns a
Structure object. So far so good I think. Then I added a method to
Bio.PDB.Structure more or less like this:
def as_protein(self):
from Bio.Struct.Protein import Protein
prot = Protein(self)
return prot
so when you call it you get a new object. Protein is a class that inherits
from Structure and that has the search_ss_bonds function.
I can make the new object get all the methods from Structure AND from
Protein, but when I try to execute search_ss_bonds, it fails because
child_list, a Structure method, comes empty.. In fact, the whole SMCRA
object comes empty..
How do I effectively do the inheritance on the Protein class?
from Bio.PDB.Structure import Structure
class Protein(Structure):
def __init__(self, protein):
self = protein
This is what I last tried and doesn't work.. I've tried Structure.__init__,
and several other things but to no avail. I'm sure this is simple OOP but I
really can't understand that well how to do it ...
Care to give a hand to a friend in need? :)
Thanks in advance! By the way, I assume that if I got no comments on
anything else on the GSOC thread that I'm doing a perfect job :P Thanks for
that too :D
Best!
João [...] Rodrigues
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