Thursday, February 17, 2011

OPSIN used for a Bioclipse wizard

Somewhere in January I added a new New Wizard to Bioclipse for OPSIN, but forgot to blog about that earlier, which will be available in Bioclipse 2.6 later this year (or just the hudson build service).

Posted via email from Egon's posterous


  1. Great stuff - looks useful.

    What would be truly fantastic (er, literally at the moment) would be a "New Molecule Set from Formula" wizard, that would generate the chemical space...

    Anyone with know-how in canonical checking or structure generation is welcome to help make this a reality :)

  2. I like that too.

    @gilleain: Maybe you could do an InChI search on the Chemical Structure Identifier Resolver with the truncated InChI. Not quite what you are talking about, but maybe close...

  3. @baoilleach : Well, my suggestion was only half-serious. I think it would be a bad idea to allow users to type in "C1000H2000" and lock the process forever :)

    Your suggestion has more merit, I think. Other 'small' spaces might be tautomers, as with Mark's recent CDK patch. Or Kekulé structures if I could work out how to adapt Edmond's Path/Tree/Flower algorithm (or some other method).

  4. Kekule structures are just resonance structures. Those you can already do with Miguel's code, though I would need to figure out first how the API works... (would make an interesting section for my CDK book perhaps...)

  5. @Noel. Yeah, 'searching' in online databases is currently a bit of a miss right now. You can search on 'name' in PubChem and ChemSpider, but something like substructure search is indeed needed.

    BTW, I very much like the idea of searching on truncated InChIs...

  6. Oh, and please file your ideas as feature requests at:

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