Hi Dan, Regarding (1) the relevant section in the docs is at http://openbabel.org/docs/2.3.0/Fingerprints/fingerprints.html. I think that the section on Similiarity Searching answers this question.
Question (2) is about searching for exact matches. Currently the only way to do this is matching by canonical SMILES or by InChI, e.g. see the section on the InChI descriptor at http://openbabel.org/docs/2.3.0/Command-line_tools/babel.html#inchi-descriptor. If you are doing multiple searches, I would use the substructure search described at http://openbabel.org/docs/2.3.0/Fingerprints/fingerprints.html to extract a small set of potential exact matches and then search those using the InChI descriptor. I hope this answers your questions. I'm ccing to the openbabel-discuss list where someone else might have a better idea. Regards, Noel On 23 January 2011 14:50, Daniel Zaharevitz <zahar...@mail.nih.gov> wrote: > Hi Noel, > > I've been playing with Open Babel some more. I had no trouble getting it > working on my Mac using fink or downloading and compiling from scratch on my > Linux box. Things work generally as I expect but there are a few things that > I'm not sure about. There are two things I'm most interested in doing: 1) > using it to get a similarity score for a given structure w/r to a > (300K-500K) set of structures and 2) for a given structure check to see if > there are exact structure matches in a (300K-500K) set of structures. If you > have any pointers to documentation, suggestions or experience to pass on, > I'd appreciate it. Right now I'm not sure I understand the parameters > associated with similarity scores and I can't seem to find anything in the > docs beyond the tutorial examples. It seems the query is taken as a > substructure and thus if the entire substructure is present in the test > molecule you can get a score of 1.0 even if the test molecule contains more > than the query. If possible, I'm looking for 1.0 to be returned only if the > entire test molecule matches the query. > > Thanks, > DanZ > > > /******************************************** > * Daniel Zaharevitz > * Chief, Information Technology Branch > * Developmental Therapeutics Program > * National Cancer Institute > * zahar...@mail.nih.gov > * > ********************************************/ > > > > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
