Just an idea workaround: try reading the original SDF file in your substructure query instead of using an index.
It should be slower for sure, but maybe it will process all molecules, at least. On 05/16/2014 11:28 AM, Jacob Durrant wrote: > I've been trying to get substructure searches working with Open Babel for > some time. I always run into the same frustration. > > I have a SDF file with ~27,000 compounds. I first convert it to an fs file: > > -bash-4.1$ babel compounds.sdf -ofs > This will prepare an index of compounds.sdf and may take some time... > It contains 27036 molecules Estimated completion time 0 seconds > > It took 59 seconds > 27036 molecules converted > 37 audit log messages > > Now I try performing a substructure search: > > -bash-4.1$ babel compounds.fs -ifs -s"C(=O)O" results.smi > *** Open Babel Warning in Find > Stopped looking after 9778 molecules. > > 4000 candidates from fingerprint search phase > 3895 molecules converted > 1 warnings 134948 audit log messages > > I don't want it to stop looking after 9778 molecules. I want it to search > through the entire file. The -l option seemed promising. From the help file: > > Read Options (when searching) e.g. -at0.7 > t# Do similarity search:#mols or # as min Tanimoto > a Add Tanimoto coeff to title in similarity search > l# Maximum number of candidates. Default<4000> > e Exact match > Alternative to using exact in ``-s`` parameter, see above > n No further SMARTS filtering after fingerprint phase > > However, using this option doesn't resolve the problem. > > -bash-4.1$ babel compounds.fs -ifs -s"C(=O)O" results.smi -l 1000000 > *** Open Babel Warning in Find > Stopped looking after 9778 molecules. > > 4000 candidates from fingerprint search phase > 3895 molecules converted > 1 warnings 134948 audit log messages > > Can anyone tell me how to instruct Open Babel to keep searching beyond the > initial 9778 molecules? I'm using version 2.3.1 -- Oct 13 2011. Thanks. > > Thanks. > > ~Jacob > > > > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Best regards, Francois Berenger. ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
