[Bioperl-l] First commit of Bio::Structure objects

[Kris Boulez]

Quoting Elia Stupka (elia@fugu-sg.org):
> > We (my collegues and I) still think that having methods like
> > 
> > $atom->residue
> > $residue->chain
> > $chain->residue
> 
> Ok, if you are talking hacks, then you can also have methods as above
> which are only get/sets of the actual ids, and then if the user needs it
> he can fetch it again by id?
> 
> i.e. $atom->residue_id,etc.
> 
I still haven't found a decent way to look at an 'id' in this case. A
residue for example only makes sense in the whole context. I.e. "it is
Val-42 from chain B from the third model from PDB entry 1XYZ". This
would leave us with something like "1XYZ.3.B.VAL-42".

I'm not sure the Ensembl (database ?)-centric way of looking at this is
the right thing. My first plan was to use references as unique ID's.

Can you elaborate a bit more on your proposal as I can't quite grasp it
(most probably my brains fault).

Kris,
-- 
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