In making the .fs index you meant to write obabel 1.7_24.sdf -ofs
In using it to look for three connected aliphatic carbons you can use obabel 1.7_24.fs -sCCC -Oresults.smi or obabel 1.7_24.sdf -ifs -sCCC -Oresults.smi and it is necessary for the data .sdf and the index files to be in the same directory (I think). The .fs file contains, for every molecule that is indexed, only a fingerprint and the byte position of the corresponding molecule in the data file. So both are needed to do a substructure search, although you need to specify only one. The fs file can have a different name and can be made smaller by not indexing every molecule, e.g. by adding -f, -l, -s, -v, or --filter options to the first command above. Chris On 01/02/2012 15:45, Noel O'Boyle wrote: > The .fs file is just an index - it doesn't contain any chemical > structure. So you need the sdf file. > > Can they be in different directories? I don't know...Chris? > > - Noe > > On 1 February 2012 15:40, David García Aristegui<ariste...@cbm.uam.es> wrote: >> Hello, i'm testing the substructure search with .fs files... >> >> obabel 1.7_24.fs -ofs >> >> i move the .fs file to a new directory, and i execute: >> >> obabel 1.7_24.fs -ifs -sCCC -Oresults.smi >> ============================== >> *** Open Babel Error in ReadChemObject >> Difficulty opening 1.7_24.sdf >> >> 0 molecules converted >> >> "The datafile plus the -ifs option can be used instead of the index file" >> http://openbabel.org/docs/dev/FileFormats/Fastsearch_format.html >> >> Is mandatory to have the .sdf and the .fs files in the same directory? is >> not possible to do the search only with the .fs files? >> >> Best regards. >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
