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Thursday, August 06, 2009

ChemSpider fail #1: SMILES

Cheminformatics is difficult, I know. But I thought I used a simple SMILES when I typed C1CNCC1, but ChemSpider got it wrong :) The correct structure should be pyrrolidine, not pyrrole. I always mix up those names, so defaulted to ChemSpider to give me the correct name, which ChemSpider knows and where it also has the SMILES correct... there just seems something wrong with there search dialog:

There has been some talk about a ChemSpider Bugzilla, but I don't think this has materialized yet, and I'll have the default to info-at-chemspider-dot-com ...

8 comments:

  1. Thanks for the bug report. We will review and work on a fix for our next update if we have time pre-ACS Washington.

    We have been using BugZilla for over 2 years and like it. We have no intention of making it public access in the foreseeable future as we also manage a lot of internal and therefore confidential projects and have higher priorities right now than setting up a public access Bugzilla. I judge that the majority of our users will not use it and get value from it. Will you be in Washington? Would be good to say hi.

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  2. I'm afraid the "bug" goes beyond pyrrole. For some reason when entering a smiles string alternating double bonds are being added. For example CCCCC produces C-C=C-C=C. C-C-C-C-C produces the correct structure. This seems to be a very recent issue.

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  3. We believe that this bug is resolved on our development servers and will likely go live by the weekend.

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  4. the fix is now running on ChemSpider Live. Enjoy

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  5. Tony, what do you mean with ChemSpider Live? I just tested chemspider.com and I cannot reproduce the problem to be fixed there... :(

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  6. We are not longer working on three servers in a garage so we have development, staging and live systems...sorry, ChemSpider Live means what you see at www.chemspider.com. I just tried it and it works. Maybe cached?

    Please try it again. Also, check the new Patents and PubMed articles tabs we just released this morning.

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  7. Oh wow! It now shows the right structure... I *did* make sure to freshen my browser cache *before* I commented... so, ChemSpider is caching too? How do you refresh that cache?

    Thanx for getting it fixed, and I like the new design. Simpler, cleaner, nicer, IMHO.

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  8. Nothing special done on my side...just looked at the record, repeated the search. Reran the conversion through the services page here: http://www.chemspider.com/Services.aspx. That's where I convert names to structures...or SMILES to structures. Paste them in and Convert

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