But if i need to design a chemical structures database... the way to do it is just to store the SMILES or structure "id" in a table, and for the searches just work with the .fs binary file?
Is a good option to store in a table the id, SMILES, fp2 fingerprint and .fs for each structure, regarding the database performance? What do you think about MyChem? http://mychem.sourceforge.net/ Best regards. > On 11/10/11 7:44 AM, David García Aristegui wrote: >> Hello, i'm reading about substructure and similarity searches... >> http://openbabel.org/docs/dev/Fingerprints/fingerprints.html >> >> "On larger datasets it is necessary to first build a fastsearch index. >> This is a new file that stores a database of fingerprints for the files >> indexed. You will still need to keep both the new .fs fastsearch index >> and >> the original files. However, the new index will allow significantly >> faster >> searching and similarity comparisons" >> >> Does anyone know what is the best way to store the fastsearch index (to >> reuse it) in a chemical structures database? best field type to store >> it? >> (i'm using MySQL). > > Don't store it in the database. Just keep it in a file. It's a huge > binary file, and there's no point at all storing it in the database; > that's not what relational databases are good at. We use our own > fingerprint algorithms, but the idea is the same: fingerprints are stored > in an external file, along with the primary key to our SMILES table in the > database. > > Craig > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
