Hi, I can just say that the pgchem::tigress performs pretty well: http://theplateisbad.blogspot.com/2010/11/pgchemtigress-sets-new-world-record.html
We had a rough time initially, because SEGV in OpenBabel crashed the whole database during the import, but now we have the whole PubChem in there. We have had two or more crashes with compounds from kanaya.naist.jp/knapsack_jsp/top.html and I'll look into that later. Yours, Steffen On Fri, 2011-11-11 at 09:29 +0100, David García Aristegui wrote: > 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 -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ------------------------------------------------------------------------------ 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
