I'm more comfortable using MySQL, so i prefer to use projects with this RDBMS.
In MyMolDB "(...)the Open Babel binary fingerprints and fingerprint bits of the molecules were precalculated and divided into 32 segments, these segments were converted to decimal numbers and stored in a mol_fp table, on which, all the substructure and similarity-related querying are based". http://onlinelibrary.wiley.com/doi/10.1002/jcc.21874/full Is this strategy best for performance reasons? Best regards. > 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
