On 13/04/2012 13:02, Jochen Schreiber wrote: > Hello everybody, > > i have a dataset where i know (form a clustering) which compounds are in > which cluster. > > For example Cluster 55: With 16 Compounds. > > Now i want to start a similarity search on each compound in this cluster with > babel. I will do this with tanimoto 0.7, 0.8 and 0.85 to look for which > tanimoto i get the best results. > > The best result would be that i find with one compound all other 15 compound > from this cluster. > > After i have done this i see that my results are very bad.
The command obabel Cluster55.sdf -oftp will show the Tanimotos from the first molecule in Cluster55.sdf to all the others using FP2 fingerprints So i want to change the fingerprint. In my first round i use the standard FP2 fingerprint. > > The results for FP3, FP4 oder MACCS are the same. Why is this so? Need i to > specify something in the txt-files? > > My cooperation partner in this projekt uses pipeline pilot with ECFP4. Is > there a way to use this fingerprint with babel? OpenBabel does not support this fingerprint. A paper which compares the effectiveness of 37 different descriptors in molecular similarity is Bender et al J. Chem. Inf. Model., 2009, 49 (1), pp 108–119 DOI: 10.1021/ci800249s. But since it is published by ACS I am not able to read the full text. Chris ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
