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

Peter Cock p.j.a.cock at googlemail.com
Mon Dec 5 10:45:29 UTC 2011

2011/12/2 Hongbo Zhu 朱宏博 <macrozhu at gmail.com>:
> Hi, Joao,
> thanks for the response. When I spoke of slicing Bio.PDB.Chain, I meant to
> slice it using residue id, not list index. And these two ways are
> fundamentally different.
> For instance :
> not only slicing like this:
> or
> chain.child_list[2:12]  # slice using list index
> but also slicing like this:
> chain[2:12]   # slice using residue sequence id, not feasible at the moment
>                   # NOTE: this is fundamentally different from
> chain.child_list[2:12]
> or even:
> chain[(' ', 2, ' ') : (' ', 12, ' ')] # slice using residue full id, even
> better
> Of course one can play with child_list and obtain the same outcome. But I
> think it would be very convenient to implement it in the __getitem__()
> function.
> cheers,hongbo

Hi Hongbo,

I agree defining integer based slicing of Chain objects sounds like a good idea.

Could you write a couple of unit tests for the new slicing please (in
file Tests/test_PDB.py)? You can just give code snippets, a patch, or
create a branch on github it you would prefer.

Does it make sense to consider __add__ for the Chain as well?


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