On 11/01/2012 14:23, David García Aristegui wrote: > "First of all, you need to create a fastsearch index (see above). The > index is created with the following command: > > babel mymols.sdf -ofs" > > http://openbabel.org/docs/dev/Fingerprints/fingerprints.html > > Could you please tell me the differences between the use of a 2D or a 3D > sdf file regarding the .fs generation?
The 2D or 3D coordinates will affect only the stereochemistry but should give the same result, if they have been constructed correctly. A 0D sdf file might not have any stereochemical information. Fastsearching has two phases. The first uses fingerprints (which are in the .fs file made by the command above). The default FP2 fingerprint is not sensitive to the stereochemistry, and so neither are .fs files. The results from the first phase are further filtered by SMARTS, which is sensitive to the stereochemistry. Chris ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
