Hi, On ven., 2011-11-11 at 10:36 +0100, David García Aristegui wrote: > "store it alongside the database records as mychem does it" mmmmmmm, > where? for me is unclear the MyChem database schema (obserialized field).
The Mychem project proposes a simple database schema for compound management. The database is managed with a Python tool, mychemdb-manager.py. However, the main goal of the project is to provide a complete set of cheminformatics functions to MySQL. Other projects, like Chemaztech, are using Mychem to provide a fully functional chemical cartridge. The obserialized field is a BLOB storing a binary OBMol object. It permits to perform fast query. If you need help about Mychem, or if you want to suggest some improvement, do not hesitate to contact me. The Mychem is alway maintained and under development (I'm currently working on the support of the last Open Babel release). > A good example of chemical structures database is MolDB, by the way!!! > http://merian.pch.univie.ac.at/~nhaider/cheminf/moldb5.html > > Best regards. Best regards, Jerome > > Hello, > > > >>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). > > > > you could: > > > > - store it outside the database in a file with pointers to the records in > > the database as Craig A. James suggested > > - store it outside the database in memory with pointers to the records as > > the Infochem cartridge for Oracle does it > > - store it alongside the database records as mychem does it > > - store it in a true database index structure as pgchem and Bingo do it > > (because PostgreSQL allows to do this through an official API as Oracle > > does too) > > > > I agree that the worst idea is to store the file as a huge BLOB in the > > database as MDL/Symyx/Accelrys apparently does. It is fast for searching, > > but a nightmare in all cases the index has to be altered (i.e. > > INSERT/UPDATE/DELETE) since you have to go through the DBMSes BLOB > > handling routines then. > > > > best regards, > > > > Ernst-Georg > > > > > > ------------------------------------------------------------------------------ > 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
