On 11/16/11 3:55 AM, Ernst-Georg Schmid wrote: >> InChI-Key are exactly done for exact searching. > > exactly, unlike different SMILES canonicalization implementations > the InChI algorithm is standardized.
In my opinion, this is a common but incorrect criticism of SMILES. Variations in canonical implementations don't matter for cheminformatics, because each database uses just one implementation. The idea of a "universal" canonical form is an impossible goal. We constantly learn about chemistry and add that knowledge to our software, which changes the canonical form. Bugs are also inevitable, and bug fixes also change the canonical form. This is true whether you're using InChI, SMILES or some other canonical identifier. For example, I believe aromatic selenium was confirmed after the original SMILES papers were published. If SMILES had been an immutable standard, that new knowledge would have been ignored. In real life, bugs in a canonicalizer are a HUGE problem compared to whether the canonical form might change five years from now. Adapting to new version of canonicalization is a trivial problem - you just run through your database once and update your records. But bugs in the canonicalizer cause actual errors: duplicate structures, missing structures, and incorrect search results. If you choose InChI over SMILES because you think InChI is more stable, then you're overlooking the realities of managing a cheminformatics system. Choose the one that gives correct answers and is actively maintained by an open-source community. Craig ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
