(This discussion should really be on the dev list.) I just want to note in passing that I would consider 4096 as a bare minimum for use of RDKit's fingerprint and then only if there is a diskspace or memory constraint. For my own work, I use 16384.
Also, if the API needs changing to enable reasonable functionality now's the time to discuss it. The best place to propose and discuss such a change is over at https://github.com/openbabel/enhancement-proposals. - Noel On 30 March 2017 at 12:28, Andrew Dalke <da...@dalkescientific.com> wrote: > On Mar 29, 2017, at 12:47, Andrew Dalke <da...@dalkescientific.com> wrote: >> But I have no data sets which I could use in that evaluation. > ... >> A different option is that I can put the sparse->dense code into chemfp, >> where I can more easily control the parameters, label it "experimental" >> (which, I've found out, doesn't prevent people from using it), and get some >> feedback from that, which might inform future Open Babel development. > > Yet another option is that I can develop a stand-alone program to generate > the ECFP<n> fingerprints as an FPS file, and hope that someone here is > interested enough in doing an evaluation and/or interested in providing > feedback on my algorithm. > > (The only unusual thing about the algorithm is that I decided to use > xorshift128+ as the PRNG. RDKit uses a Mersenne Twister, but that has a large > initialization overhead, and the sparse->dense algorithm does a *lot* of PRNG > initialization. Using a MT adds 30% overhead.) > > I've placed a copy of said stand-alone program at > > http://dalkescientific.com/obecfp2fps.py > > It requires Python 2.7 and Open Babel >=3.4. > > > > Andrew > da...@dalkescientific.com > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
