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

[Kris Boulez]

Quoting Ewan Birney (birney@ebi.ac.uk):
> 
> Re: objct cycles - the DESTORY route is really hard to get right so I
> would encourage you Kris to go for the "parent object knows about the
> relationships" or (my solution) - punt on making children know about the
> parents, and force any script that wants to know about this to do its own
> bookeeping ...
> 
After a weekend of thinking about it, I think I understand the problem
and I agree that the only solution there is now (client needs to call
DESTROY method on object), will not work.
> 
> Most scripts probably wont need to go child--> parent as to get to the
> child they must have gone through the parent...
> 
Unfortunately I think they do. A typical use case would be "Give me all
the atoms which are less then 5 A away from this atom". Starting from
this list of atoms you would then want to know to which resideu/chain
they belong.

   $atom->residue->id

I see two possible solutions for this:

- store the residue/chain info as textual attributes when
  creating/modifying the Atom (if we do this why do we need objects and
  references)
- use an extra layer on top (as suggested by Chris Mungall), which is
  called 'Factory' in Design Patterns-speak (I think).


I'll implement the second one, unless someone starts shouting.

Kris,  
-- 
Kris Boulez 				Tel: +32-9-241.11.00
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