[Biopython] Atom inheritance from Entity

[John Berrisford]

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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
>>>
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at mailman.open-bio.org <mailto:Biopython at mailman.open-bio.org> 
>>> https://mailman.open-bio.org/mailman/listinfo/biopython
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org <mailto:Biopython at mailman.open-bio.org> 
> https://mailman.open-bio.org/mailman/listinfo/biopython

_______________________________________________
Biopython mailing list  -  Biopython at mailman.open-bio.org <mailto:Biopython at mailman.open-bio.org> 
https://mailman.open-bio.org/mailman/listinfo/biopython

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20190905/08cd4a8f/attachment-0001.htm>