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I have a large collection of structures (>10,000) that I've gathered from literature searches and I would like to find out which of those can be obtained from vendors. I know that eMolecules and ChemSpider provide such information, but getting that information for 10,000 structures in daunting.

On eMolecules, I can load a list of SMILES, search the databases, and download the results. The download process is not very robust, though, and I have to reconstitute a lot of pieces of information.

ChemSpider provides additional information regarding vendors, and I've tried using the ChemSpiPy API, but I consistently get an error from the ChemSpider server. Obviously something has changed with respect to the server that the API doesn't account for.

Are there other suggestions for where/how I might gather such vendor details for a very large collection of structures?

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You can try molport, they are an intermediate. Just ask them directly, it will be done in a jiffy. Or if you like you can do it in knime and use any API (like molport's API), which is much more fun, but for just a one-time thing a bit complicating.

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  • $\begingroup$ This is really more of a comment than an answer. $\endgroup$ – bon Jun 2 '16 at 7:37

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