Hi Greg- No objection here. I've been using 1024 with 2 bits here. Are you still using 2048 for the default size?
TJ O'Donnell On Tue, Dec 28, 2010 at 11:33 PM, Greg Landrum <[email protected]> wrote: > Dear all, > > As I mentioned in an earlier message > (http://www.mail-archive.com/[email protected]/msg01430.html), > the default parameters for the RDKit fingerprint end up setting far > too many bits for drug-like molecules. The result of this is > similarity values that are in general too high and more frequent > occurrences of molecules that are similar to each other only due to > bit collisions. > > The easy solution to this problem is to decrease the number of bits > set per path found (the nBitsPerHash parameter) from 4 to 2. I propose > doing this for the Q4 2010 release of the RDKit. The downside is that > the fingerprints generated with that release will not be compatible > with fingerprints from earlier releases unless you specify > nBitsPerHash=4 on your own. The upside is a much more useful > similarity fingerprint. > > Any objections to me making this change? > > -greg > > ------------------------------------------------------------------------------ > Learn how Oracle Real Application Clusters (RAC) One Node allows customers > to consolidate database storage, standardize their database environment, and, > should the need arise, upgrade to a full multi-node Oracle RAC database > without downtime or disruption > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
