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. > > 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. > And could i do this with pubchem in the same way? you can, but it's also going to take a long time. -greg ------------------------------------------------------------------------------ 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
