Re: [Cdk-devel] Important: Your vote needed on some API re-naming

[Nina J. <jel...@gm...>]

On 7 October 2013 11:09, Egon Willighagen <ego...@gm...>wrote:

> John,
>
> On Mon, Oct 7, 2013 at 9:59 AM, Nina Jeliazkova
> <jel...@gm...> wrote:
> > On 7 October 2013 10:28, Egon Willighagen <ego...@gm...>
> > wrote:
> >>
> >> On Fri, Oct 4, 2013 at 4:32 PM, John May <jo...@eb...> wrote:
> >> > There is no more Molecule in new CDK versions only AtomContainer, this
> >> > could be confusing - vote here: http://strawpoll.me/501772
> >>
> >> Nico Adams suggested on Google+ the obvious thing that I should have
> >> thought of last Friday too... why not go semantic all the way, and use
> >> ChemicalEntity as root container...
> >
> > +1
>
> the funny thing is, you were so close in the question title :)
>
> "Name for the primary *Chemical Structure* representation in CDK?"
>
> :)
>
> Importantly, the entity bit allows for mixtures, substances,
> nanomaterials, with ill-defined structure...
>
> OK. updated poll: http://strawpoll.me/514829



Actually I would vote for a Molecule representing a chemical structure
(where the structure is well defined) and a separate entity for substances,
etc., which could include structures as class members. Both could descend
from the same ChemicalEntity class, but not necessary.

And yes, I agree with John the simpler the model the better, too deep class
hierarchy doesn't help with efficiency.

Best regards,
Nina


>
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
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> ORCID: 0000-0001-7542-0286
>
>
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