Hello Bjoern, My usechase is to do a similarity search on local sdf files with babel and cdk.
My problem now is that babel only one file expected and i have the complete pubchem compound sdf files with over 2000 sdf files. If i concat all sdf files to one file it has over 187 GB and the index will be over 2GB. What can i do? If i split i need to call my search but i want one output for the search and not several. With best Jochen Schreiber Am 02.03.2012 um 18:52 schrieb Björn Grüning: > Hi Jochen, > > we are running such setup in our lab with postgresql and pgchem. Maybe > you can explain your usecase a little bit better. I don't think the > fs-index from openbabel is the way to go for such huge datasets. > > As Chris mentioned the index should be smaller than 2GB. You will exceed > these. You can split your SDF files in chucks so that the resulting > indices are <2GB ... > > Ciao, > Bjoern > >> Must it be smaller then 2 GB? >> >> If i do a concat on all i gain a file which is about 187 GB. >> >> Any idea? >> >> With best >> >> Jochen Schreiber >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- > Björn Grüning > Albert-Ludwigs-Universität Freiburg > Institute of Pharmaceutical Sciences > Pharmaceutical Bioinformatics > Hermann-Herder-Strasse 9 > D-79104 Freiburg i. Br. > > Tel.: +49 761 203-4872 > Fax.: +49 761 203-97769 > E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de > Web: http://www.pharmaceutical-bioinformatics.org/ > ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
