[Biopython] Atom inheritance from Entity

[Spencer Bliven]

This exercise is really reinforcing the benefits of type annotations for
me. I'm turning up lots of API issues that I wasn't expecting.

The latest twist is that DisorderedAtom *does* inherit from
DisorderedEntityWrapper. So it expects atoms to be indexable like other
entities. And we mix disordered and ordered entities everywhere, and they
have different APIs, so there need to be type checks lots of places.
Obviously this works now, but I think having the type checks is going to
make writing correct parsers easier in the future.

-Spencer

On Thu, Sep 5, 2019 at 2:56 PM Lenna Peterson <lenna.peterson at gmail.com>
wrote:

> That's my vote - more in keeping with LSP.
>
> Lenna
>
> On Thu, Sep 5, 2019, 06:41 Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> Maybe there should be an additional top level base class (for all
>> entities including Atoms), and define Entity a subclass of this (for
>> entities with children)?
>>
>> Would this help with defining the interface (even if Atom has its own
>> implementations of those methods)?
>>
>> Peter
>>
>> On Thu, Sep 5, 2019 at 12:07 AM João Rodrigues
>> <j.p.g.l.m.rodrigues at gmail.com> wrote:
>> >
>> > Wouldn't it be weird for an Atom to have a get_children method? I'm
>> somewhat more fine with a None attribute than a useless method.
>> >
>> > A quarta, 4/09/2019, 09:08, Spencer Bliven <spencer.bliven at gmail.com>
>> escreveu:
>> >>
>> >> Entity also provides methods for managing ids, transforming atoms,
>> etc. My preference would be for everything to inherit from Entity and just
>> have 0 children. This is also consistent with Structure, which is an Entity
>> with 'None' parent.
>> >>
>> >> -Spencer
>> >>
>> >>
>> >> On 4 September 2019 at 08:02:19, João Rodrigues (
>> j.p.g.l.m.rodrigues at gmail.com) wrote:
>> >>
>> >> Hi Spencer,
>> >>
>> >> Something that bugged me in the past as well. It would be nicer to
>> have everyone inherit from a single point, but since Atoms don't have
>> children, it would be confusing to have these methods there. My
>> understanding is that Entity only exists to provide methods to handle
>> iteration over children objects. It's a compromise?
>> >>
>> >> Thanks for the efforts in typing the module!
>> >>
>> >> João
>> >>
>> >> Spencer Bliven <spencer.bliven at gmail.com> escreveu no dia terça,
>> 3/09/2019 à(s) 22:53:
>> >>>
>> >>> I was wondering why Atom doesn't inherit from Entity. It doesn't have
>> children, but it seems like it would be more consistent to have the whole
>> Structure stack inherit from a single point. Is anyone aware of the history
>> there?
>> >>>
>> >>> I ask because I'm trying to add type annotations to Bio.PDB, and mypy
>> flagged a number of places where my initial 'Entity' type conflicted with
>> Atoms. We can certainly get around this by accepting either Entity or Atom,
>> but I'm not sure that was intended.
>> >>>
>> >>> -Spencer
>> >>>
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