On Sat, Nov 27, 2010 at 6:49 AM, Greg Landrum <[email protected]> wrote: > At the moment there isn't a particularly satisfying way of doing an > equality search aside from adding a smiles column to the database and > just doing a straight equality search on that.
Ok. > To that end it's probably useful to know that the smiles generated by > the cartridge when you convert a molecule to text is canonical. If I'm not getting fooled, it seems the structure is also stored in canonical format; e.g if I store: 'COc(cc1)ccc1C#N' then I "select * from molecules;" I get back 'COc1ccc(C#N)cc1' If this is correct I should be able to search with the "=" operator directly, provided I prepare the query smilles with Chem.CanonSmiles, isn't it? That would avoid adding a specific smiles column. > > Without adding the smiles column, another option that should be > correct, though it's somewhat ugly, is: > select * from mols where m<@'CC(=O)c1ccc2c(c1)C(=O)C(=O)N2C' and > m@>'CC(=O)c1ccc2c(c1)C(=O)C(=O)N2' and > m::text='CC(=O)c1ccc2c(c1)C(=O)C(=O)N2C'::mol::text; > > If the molecule column is indexed, this will use the index so it's > actually reasonably efficient. If you don't care about stereochemistry > you can leave the last bit (SMILES comparison) out. > Yeah, ugly but I just tried and it actually works. > Having a less ugly way of doing equality querying would be useful; > that would be a good feature request. Ok, so where should I report it ? ;-) -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
