Conversion of IUPAC Names to Chemical Structures

Dear All,





Are there any programs or API converting IUPAC names to chemical structures? When some IUPAC names are extracted from some paper, say JMC, a program is needed to convert these IUPAC names to chemical structures.





Best regards,





Tiqing Liu

SciFinder Scholar can find a structure by its name, if it's in the Chemical Abstracts Database.

We are developing a name to structure tool, but it's not released yet.

It will be nice to know when ChemAxon is expecting to have a release on the tool.





I happen to be interested in the topic and did some Google Search.





Here are what I found:





http://sourceforge.net/projects/oscar3-chem/





A java library to parse IUPAC name.





Although the following are JRuby code, I assume it will be pretty straightforward to convert them into Java code.





http://depth-first.com/articles/2007/10/12/jruby-for-cheminformatics-parsing-iupac-nomenclature-with-opsin





and





http://depth-first.com/articles/2007/10/19/easily-convert-iupac-nomenclature-to-smiles-inchi-or-molfile-with-rubidium





It requires:


http://sourceforge.net/project/downloading.php?groupname=cdk&filename=cdk-1.0.1.jar&use_mirror=superb-east

We are planning to include our new name importer in Marvin and JChem 5.1, which are scheduled for May/June.





Have you experimented with Oscar's name importer? In my evaluation it recognized only slightly less than half of the names in my set, although the rate of incorrect errors among those was not bad. Our importer in development is now much better than that, but I should check if they have improved (the separate OSPIN package is not updated, but it seems the code in oscar itself is, although not not very frequently).

We just tried Oscar3 yesterday and seem at least we can get it to work (use Oscar to convert IUPAC to CML, then use Jchem to convert CML to smiles). We have not tested it on more examples. We have a thousand IUPAC names to convert in a few days. Maybe you can send me your beta version of the library and we can compare the two tools and see how they perform.