Certainly, RDKit can help, any cheminformatics toolkit with
SMARTS/substructures to quickly classify something as a ketone, ester,
ether, bond orders, ring finding, path finding, etc. can help.
As for how hard it is, I think for drug discovery, most would start with
the Nomenclature of Organic Chemistry:
http://www.iupac.org/home/publications/provisional-recommendations/under-review-by-the-authors/under-review-by-the-authors-container/nomenclature-of-organic-chemistry.html
That's only 1306 pages to go through.
After that, there's inorganic chemistry, although sections of that may not
be handled well by RDKit? I'm not sure about how RDKit handles crystals and
coordination compounds, etc.
http://www.iupac.org/nc/home/publications/iupac-books/books-db/book-details.html?tx_wfqbe_pi1[bookid]=5
Since RDKit recently added PDB support, people may be interested in naming
for peptides and amino acids
http://www.iupac.org/publications/pac/56/5/0595/
And cyclic peptides
http://www.iupac.org/home/publications/provisional-recommendations/under-review-by-the-authors/under-review-by-the-authors-container/nomenclature-of-cyclic-peptides.html
So there's a decent amount of work. I think it is possible, but not a
single weekend project.
I should mention that many commercial vendors have products for this, off
the top of my head:
http://www.acdlabs.com/products/draw_nom/nom/name/
http://www.chemaxon.com/library/iupac-name/
https://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/
http://www.eyesopen.com/docs/lexichem/current/html/mol2nam.html#chapter-mol2nam
So, at least 4 companies have some sort of algorithm. The only one I've
used is ChemDraw's, and then, I only have done maybe 5 molecules, so I
cannot claim that any of these products work.
-David
On Tue, Jan 14, 2014 at 11:04 AM, Michał Nowotka <[email protected]> wrote:
> Yes, I know there is no algorithm for that. This is why I'm wondering
> how hard it to write one and how RDkit can help here.
>
> On Tue, Jan 14, 2014 at 4:01 PM, Dimitri Maziuk <[email protected]>
> wrote:
> > On 1/14/2014 6:09 AM, Michał Nowotka wrote:
> >> Hi,
> >>
> >> Since there is no open source software converting structure to IUPAC
> >> name (I'm not talking about web services) I was wandering if one can
> >> be implemented using RDkit? Which parts of RDKit would help in doing
> >> that? Any pointers, suggestions?
> >
> > I've suspicion there's no algorithm for it -- cactus is the only one I
> > found that does it and my impression is they're doing a database
> > search... I'd like to be able to generate systematic names without web
> > searches, too.
> >
> > Dima
> >
> >
> >
> >
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