Thank you all for your help, much appreciated. On Tue, Jan 14, 2014 at 9:10 PM, John May <john.wilkinson...@gmail.com> wrote: > 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 <igor.v.filip...@gmail.com> 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 <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 >> > > ------------------------------------------------------------------------------ > 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 >
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