As I understand, in the context of fastsearching, -s requires a SMILES string. For searching the .sdf directly you can use SMARTS (it may take a while of course). This should be better documented of course.
The reason is that a fastsearch is just an index of path-based fingerprints. You cannot use a SMARTS to search these (well, in theory maybe you could - that would be an interesting research topic). - Noel On 6 January 2014 08:59, Mark Forster <markf.opensou...@gmail.com> wrote: > Dear Openbabel Users > > I am seeking some assistance in understanding and using SMARTS based > substructure searching with Openbabel. > The overall goal would be to search large molecular data sets using > sophisticated substructure patterns. > What I need to help do that are pointers to documentation or examples of > such searches. > > The documentation page on Fingerprints was quite useful. > http://openbabel.org/docs/dev/Features/Fingerprints.html > > With this I was able to take a set of (say) 10 thousand molecules and > generate a fast search index with the command > obabel -ican 10k.can -ofs > which creates the fast index search file 10k.fs. > > > Then search for a specific substructure as SMARTS and seeking output as > SMILEs seems to work well. > obabel -ifs 10k.fs -osmi -s"C1CCNCC1C#N" > => One result > > However if I try a simple SMARTS patter [CX4] for an alkyl carbon, I get an > error. > obabel -ifs 10k.fs -osmi -s"[CX4]" > => ============================== > *** Open Babel Error in ObtainTarget > Cannot read the SMILES string > 0 molecules converted > > Ideally I want to use the syntax [C;R] for an aliphatic carbon in a ring or > perhaps > [C;r5,r6] to specify an aliphatic carbon in a five or six membered ring. > > Any examples or advice appreciated. > > Mark > > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
