[Biopython] Atom inheritance from Entity

[Lenna Peterson]

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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