[Biopython-dev] slicing in Bio.PDB.Chain.__getitem__() ?

[João Rodrigues]

Hey Hongbo,

Interesting idea, but couldn't it be done already with child_list in a more
or less straightforward manner?

Best,

João
No dia 2 de Dez de 2011 10:43, "Hongbo Zhu 朱宏博" <macrozhu at gmail.com>
escreveu:

> Hi,
>
> I propose to add slicing to class Bio.PDB.Chain by changing function
> Bio.PDB.Chain.__getitem__().
>
> * Why is slicing necessary for Bio.PDB.Chain?
> Protein domain definitions are usually presented as the starting and ending
> positions of the domain in protein primary structures, e.g. in SCOP, or
> CATH. Slicing comes in handy when extracting domains from PDB files.
>
> * Why is slicing not available at the moment?
> I understand that the majority of Bio.PDB.Entity objects are not lists. And
> there is not internal *sequential order* for the child entities in these
> objects. For example, In Bio.PDB.Model, its child Chain entities do not
> really have a sequential order within Model. Slicing seems not make sense.
> But Bio.PDB.Chain is exceptional: Residue entities in Bio.PDB.Chain have a
> sequence order as presented in the primary structure and slicing becomes a
> reasonable operation.
>
> * How to slice a Chain entity?
> I think it can be realized by revising the
> function Bio.PDB.Chain.__getitem__(). For example:
>
>    def __getitem__(self, id):
>        """Return the residue with given id.
>
>        The id of a residue is (hetero flag, sequence identifier, insertion
> code).
>        If id is an int, it is translated to (" ", id, " ") by the
> _translate_id
>        method.
>
>        Arguments:
>        o id - (string, int, string) or int
>        """
>        if isinstance(id, slice):
>            res_id_list = [r.id for r in self.get_iterator()]
>            if id.start is not None:
>                start_index =
> res_id_list.index(self._translate_id(id.start))
>            else:
>                start_index = 0
>            stop_index = res_id_list.index(self._translate_id(id.stop))
>            return self.get_list()[start_index:stop_index:id.step]
>        else:
>            id=self._translate_id(id)
>            return Entity.__getitem__(self, id)
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