Hi, Check out chemfp. It can do efficient all-by-all similarity calculations. http://chemfp.com/
You can read about NxN searches here: https://chemfp.readthedocs.org/en/latest/using-tools.html#nxn-self-similar-searches On 10/21/2015 09:05 AM, seanph16 wrote: > I've been playing around with the open babel python command line now and have > been able to generate the Tanimoto coefficient for one molecule compared > against all molecules in my set, however can't figure out how to generate > the all-by-all comparison. > > This is what I am inputting: > > obabel MyMols1.smi MyMoles2.smi -ofpt > > Where the .smi files are copies of each other containing the same molecules. > > How can I generate the all by all comparison? I have seen in other forum > posts that others have done this (and it is a very slow process which is > fine) however can't find the commands that they used. > > Sean > > > > > > -- > View this message in context: > http://forums.openbabel.org/Generating-all-by-all-Tanimoto-similarity-scores-in-Microsoft-GUI-tp4658991p4658995.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
