Hi TJ, It would really help if you could file the infinite molecules as a bug. That way it won't slip through the cracks.
- Noel On 26 August 2010 17:10, TJ O'Donnell <t...@acm.org> wrote: > I just finished building an openCHORD database with 27M compounds - most > of those from Pubchem. The good news is that openBabel stumbled on only > 7 of them! Aside from earlier-reported (and cured?) cansmiles issues, > the remaining problems are 3 molfiles that do not produce canonical smiles > after 60 seconds of processing, and 4 smiles that hang on input. > > I've attached a tar file with the 3 sd files (1*.sdf), a smi file with > 4 smiles (infinite.smi) and a shell script I used to test this problem > using babel. This error occurs with 2.2.3 and 2.2.99 (my build as of > about a week ago). I've only tested this under linux. > > Essentially, these commands do not finish after 60 seconds: > babel -ismi <infinite.smi -osmi (or for any of the four in the .smi file) > babel -isdf <1*.sdf -ocan (although -osmi works fine) > > By the way, the 1* and the name in the smiles file is the > PUBCHEM_COMPOUND_CID > if that is of interest. > > TJ O'Donnell > > ------------------------------------------------------------------------------ > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program > Be part of this innovative community and reach millions of netbook users > worldwide. Take advantage of special opportunities to increase revenue and > speed time-to-market. Join now, and jumpstart your future. > http://p.sf.net/sfu/intel-atom-d2d > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
