I really think ChemicalEntity is just as bad a AtomContainer.
As for the 'nearly there' - ChemicalStructure is too long before you know it -
AnAtomAndBondPossiblyAStructureSubstractChemicalEntityContainer
Look how beautiful this could be:
for (Molecule m : Smiles.fromFile("/db/chembl.smi")) {
...
}
On 7 Oct 2013, at 09:09, Egon Willighagen <[email protected]> wrote:
> John,
>
> On Mon, Oct 7, 2013 at 9:59 AM, Nina Jeliazkova
> <[email protected]> wrote:
>> On 7 October 2013 10:28, Egon Willighagen <[email protected]>
>> wrote:
>>>
>>> On Fri, Oct 4, 2013 at 4:32 PM, John May <[email protected]> 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
>
> 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
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
>
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