[Biopython] Atom inheritance from Entity

[João Rodrigues]

Hi John,

The relationship is linear: Structure-Model-Chain-Residue-Atom. Structure
has no parent (parent is None) and Atom is not of the same subclass (the
issue of this thread), so it has no children.

Then we have DisorderedEntities, Residue and Atom that represent
insertions/multiple occs.

Does this help?

Cheers,

João



A terça, 10/09/2019, 08:17, John Berrisford <jmb at ebi.ac.uk> escreveu:

> Hi
>
>
>
> Can you explain the parent child relationship in Bio.PDB.
>
> I’m asking as what I’m reading here seems to be the opposite way round to
> how it is defined in the mmCIF dictionary.
>
>
>
> Thanks
>
>
>
> John
>
> PDBe
>
>
>
> *From:* Biopython <biopython-bounces+jmb=ebi.ac.uk at mailman.open-bio.org> *On
> Behalf Of *Lenna Peterson
> *Sent:* 05 September 2019 13:51
> *To:* Peter Cock <p.j.a.cock at googlemail.com>
> *Cc:* Biopython Mailing List <biopython at mailman.open-bio.org>
> *Subject:* Re: [Biopython] Atom inheritance from Entity
>
>
>
> 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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