6. CIR.... what's wrong with CIR? Igor
On Tue, 2011-04-05 at 11:36 -0400, qiancheng shen wrote: > Dear Geoffrey, > I appreciate your help very much ! Thank you for your time. > At first I thought it is a very simple problem, so I am > confident to find such a tool when a chemist friend asked me for help. > But maybe you are right, there is no such opensource tool exists. > I have tried many tools, and maybe I should give a list and > share my experience on this problem. > > 1. OPSIN , an open parser for IPUAC name. It can convert > IUPAC name to structure but not vice versa. > (P.S. You can also use OPSIN with CDK to generate > molecule images from IUPAC name.) > 2. ChemDraw. It can generate IUPAC name from structure, but > batch mode seems to be inavailable.(not opensource) > 3. Openbabel. It can convert structure to InChI name, but > not IUPAC name. > 4. OpenEye. Yes, it has a great tool to do this task, but not > opensource. > 5. Marvin Sketch. You can insert such IUPAC Name while > drawing a molecule, but not opensource. > > Thank you for all your help!! > > > Shen > > 2011/4/5 Geoffrey Hutchison <ge...@geoffhutchison.net> > > On Apr 4, 2011, at 4:31 AM, qiancheng shen wrote: > > > Thank you very much!! But all these tools are not suitable > for me......Any other ideas? > > > You also asked on CCL.net and several people also pointed you > to the NIH Chemical Resolver. Noel's link pointed out that > Cinfony and Webel can provide you with a Python solution to > query the Resolver and get a name. It won't work for all > molecules, only the 16 million or so in PubChem. > > Put frankly, I dont expect this be solved in the open source > space in the near term, unless the NIH or other government > organization sponsors it. It's tedious, difficult work to code > an IUPAC naming system. It has lots of tricky corner cases > (even the commercial ones have problems). People are willing > to pay money for such a solution, so there's a clear > capitalist incentive to write something like Lexichem, sell > it, and be financially rewarded for the work. > > Name to structure has a clear benefit for OPSIN and is > technically an easier problem: parse the chemical name into > determining structure. There may be many names for one > structure, but that's not a big deal. OPSIN was also used to > solve an obvious problem -- machine parsing journal articles > for data mining. > > Structure to name has been requested for Open Babel, basically > forever, but IMHO it's out of the scope of the project. > > Cheers, > -Geoff > ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
