Hi, I don’t know if it will solve the problem, but your use of the l option is not entirely correct. Since you want the read option, you should specify it as -al1000000
Kind regards, Fredrik 16 maj 2014 kl. 04:28 skrev Jacob Durrant <jacobdurr...@gmail.com>: > 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 > > > > -- > ============================== > Jacob D. Durrant, PhD > Rommie E. Amaro Research Group > University of California, San Diego > > Connect with me on LinkedIn > jacobdurr...@gmail.com > jdurr...@ucsd.edu > ------------------------------------------------------------------------------ > "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
signature.asc
Description: Message signed with OpenPGP using GPGMail
------------------------------------------------------------------------------ "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
