To keep it 'simple' let's set some assumptions: - I would like to cover 'only' organic compounds - I won't something that works in 95% of compounds, producing some clear warning for remaining 5%
Now, how can I classify compound as alkane, acid, ester etc. using RDkit? On Tue, Jan 14, 2014 at 7:29 PM, David Hall <li...@cowsandmilk.net> 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 <mmm...@gmail.com> 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 <dmaz...@bmrb.wisc.edu> >> 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 >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > CenturyLink Cloud: The Leader in Enterprise Cloud Services. >> > Learn Why More Businesses Are Choosing CenturyLink Cloud For >> > Critical Workloads, Development Environments & Everything In Between. >> > Get a Quote or Start a Free Trial Today. >> > >> > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk >> > _______________________________________________ >> > Rdkit-discuss mailing list >> > Rdkit-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> ------------------------------------------------------------------------------ >> CenturyLink Cloud: The Leader in Enterprise Cloud Services. >> Learn Why More Businesses Are Choosing CenturyLink Cloud For >> Critical Workloads, Development Environments & Everything In Between. >> Get a Quote or Start a Free Trial Today. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
