I’ve hinted at this before, but Pierluigi’s note gives me cause to be specific: Let’s not forget PubChem as a source of data other than 3d coordinates!
Over the years, Jmol has become research and teaching powerful - no VERY powerful. Resolver was a logical partner for Jmol because it is also powerful. But let’s not forget PubChem. This is particularly true if your teaching interests are like mine: Basic general and organic chemistry small molecules. In this small molecule situation, many, if not most, molecules of interest are going to be in PubChem. So what? Well for one thing, important look-up information is curated in PubChem. This is really what Marcus was striving for with his name look-up index help request, and this is what resulted in the ill fated Volhardt project conducted by two hacks with copies of Volhardt in their hands. Getting PubChem data (e.g. curated calculated IUPAC names) is fast and easy: http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?callback=corsPubChempcdM&smiles=CCOCCC Parsing is a bit of a hassle, but PubChem was exceedingly helpful in this regard. Using the above URL, I had to use a server proxy in order to use AJAX. I know that’s not true for sdf direct, but in this case with AJAX it is true. Fortunately, PubChem supports JSONP, and the above URL becomes: http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSONP?callback=corsPubChempcdM&smiles=CCOCCC No big deal, it’s sill AJAX. Notice that this is all between Jmol and PubChem only via Jmol SMILES. Points: 1) PubChem IUPAC is db stored, but the data is OpenEye Scientific calculated IUPAC. 2) While Resolver does not calculate IUPAC, its does use PubChem lookup, BUT, BUT, BUT, Resolver is subject to PubChem usage constraints. These constrains are not trivial. No way PubChem (OpenEye) was the source of the query data from Resolver below (all upper case IUPAC). This is from Markus’ aforementioned index - not PubChem: https://cactus.nci.nih.gov/chemical/structure/CCCCCCC/iupac_name 3) The PubChem proxy route was unacceptable because PubChem black lists. With JSONP, each user is querying PubChem independent of your app and server. Bottom Line: In my opinion, there is no question that PubChem IUPAC (and some other identifiers) SMILES —> Data queries could be more useful than Resolver to some Jmol users. There, I said it! The data extraction from the JSONP above is tricky because these PubChem data files are not consistent from compound to compound. You must, therefore, iterate through the data in a loop to cherry pick what you want. If anyone wants this extraction code, I’d be happy to post it. It’s not lengthy code. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org ------------------------------------------------------------------------------ Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
