Hi Jörg, as Noel already mentioned that is currently not possible with obabel, but chemfp will help you. I also would take the opportunity and point you to the ChemicalToolBox [1]. You can think of it as several abstraction layers and a nice GUI (in a webbrowser) to run several cheminformatic tools (including chemfp, Open Babel, RDKit) on your workstation, but also on a cluster, grid or cloud. We were able to cluster/search and filter >70 million of compounds.
Maybe it helps for your "large-scale" use case. Cheers, Bjoern [1] https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox > Hi all, a colleague is using OpenBabels similarity search and is > struggling with the "-s" input option, which allows only one query > molecule at a time. > > Is there already any command line tool snippet to allow the input of a > > > 1. fingerprint file with a multi SDFile as query, or > > > 2. two fingerprint files, one as db, the other as query > > > to get all similarities? > > > With an option to write to more compressed binary objects or > compressed text files? > > Cheers > > /.Joerg > > > > -- > Google+, LinkedIn, Twitter, FaceBook > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
