HI,
I guess these are well known but here is some relevant literature. I believe
there is also a section on AutoNom in the Handbook of Cheminformatics.
AutoNom : paper1 and paper2
Automated systematic nomenclature generation for organic compounds:
http://onlinelibrary.wiley.com/doi/10.1002/wcms.1118/abstract;jsessionid=E69A4C8E17812E34609142DBB3EA4B6D.f02t02?deniedAccessCustomisedMessage=&userIsAuthenticated=false
IIRC AutoNom has one of those “the implementation is xx thousands lines of
code” - now I would normally read that as a challenge but I think as David
points out it really is quite complex and would be very difficult to write one
from first principles.
Here’s something fun on to try in MarvinSketch -
‘edit > import name’, ‘myo-inositol’, ‘calculations > naming’,
'(1R,2S,3r,4R,5S,6s)-cyclohexane-1,2,3,4,5,6-hexol’, 'edit > import name’, error
J
On 14 Jan 2014, at 18:41, Igor Filippov <[email protected]> wrote:
> OPSIN is doing the reverse - converts name to structure, perhaps it's
> possible to re-use the algorithm?
>
> Igor
>
>
> On Tue, Jan 14, 2014 at 1:29 PM, David Hall <[email protected]> wrote:
> 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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