Dear Greg, Am 25.03.2012 um 15:02 schrieb Greg Landrum:
> Dear Jochen, > > On Sat, Mar 24, 2012 at 3:42 PM, Jochen Schreiber <[email protected]> > wrote: >> >> i want to search against PubChem and Chembl with the RDKit to find similar >> compound for example with an tanimoto over 85%. >> >> I have seen that the DbCLI is the right way for me because i want to search >> against the sdfiles and not in the database. > > If you really want to search the SD files instead of the database (and > I don't understand why you would want to do this since searching using > DbCLI is much slower than searching using the database), then DbCLI is > probably the best way. It is one of my deliveries that my method which will be do the similarity search is working on sd files. This is a specification from the company. > >> >> At the moment i "create the db" for chembl with this command: python >> $RDBASE/Projects/DbCLI/CreateDb.py --dbDir=chembl --molFormat=sdf >> chembl_13.sdf >> >> It this the right way because it takes a long time and it isnt finished >> after 4 hours. > > Yes, that is the right way. It will take a very long time to process > with the default options. You may want to do try running CreateDb.py > with the --help option to see if there are things you can turn off. Ok it has finished this night. How can i set an parameter for the similarity? Like tanimoto or something else? I want to get all compounds that have an tanimoto over 85% to the query compound. > >> And could i do this with pubchem in the same way? > > you can, but it's also going to take a long time. > > -greg jochen ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
